Genomics

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Archive for Genomics

The Missing Piece in Genomic Selection: Why the Best Herds Still Walk the Pens

Sunday, January 11th, 2026

In 2025, you’re spending 2,000–5,000 dollars per heifer. Are those cows really staying long enough to pay you back?

Executive Summary: Right now, genomics has doubled Net Merit genetic gain in U.S. Holsteins—from about 40 to 85 dollars per cow per year—but many herds are still watching cows leave at roughly 2.7 lactations, just as they finally start to repay 2,000–5,000 dollar heifer‑raising costs. NAHMS culling data and Penn State’s longevity work show combined cull‑plus‑death rates near 37 percent and confirm that, with today’s higher rearing costs, real profit often doesn’t begin until third lactation or later. At the same time, UW–Extension, Lactanet, and CoBank document rising heifer‑raising costs, a roughly 15–18 percent drop in U.S. replacement inventories, and 2025 replacement heifer prices that commonly top 3,000 dollars, with top animals over 4,000 dollars in some regions. The article argues that if you keep raising every heifer in that environment, the real problem isn’t your proofs—it’s your replacement strategy—and the missing piece is using genomics as a hard filter on which heifers deserve a stall, backed by a simple breeding‑age structural check on feet, heels, capacity, and calving structure. It then lays out a concrete playbook: genotype and set a clear cutoff tied to your true replacement needs, walk breeding‑age heifers once with structure in mind, use corrective mating only where it removes real structural risk, and pull by‑sire reports on lameness, fresh cow problems, and early culls so you’re not blindly trusting early genomic proofs. Finally, it looks ahead to tools like 3D BCS/weight and AI lameness detection and makes the case that, in 2025’s tight heifer and margin environment, the herds that win will be the ones that combine genomics, barn data, and one strong “cow person” to keep more cows walking the pens into their fourth and fifth lactations.

You know, when you look back over the last 15–20 years, it’s pretty wild what we’ve all lived through on the genetics side of dairy. Genomic testing has changed which bulls you pick, which heifers you raise, and how fast your herd moves genetically. Geneticist George Wiggans, PhD, with USDA’s Animal Genomics and Improvement Laboratory, and his co‑authors laid this out in a 2022 Frontiers in Genetics review: once genomic evaluations came in, the average annual increase in Net Merit in U.S. Holsteins essentially doubled—from about 40 dollars per cow per year in the five years before genomics to about 85 dollars per cow per year in the genomic era—and they clearly state that this “doubled the rate of genetic gain” in U.S. dairy cattle based on CDCB trend data across millions of animals.

What’s interesting here is that it wasn’t just more milk. A landmark analysis by Ana García‑Ruiz, PhD, and colleagues in Proceedings of the National Academy of Sciences dug into the U.S. national dairy database. It showed that once genomic selection was implemented, generation intervals for sires shrank from roughly 6.8 years to under 3 years in key sire pathways. The annual genetic gains for low‑heritability traits such as somatic cell score, daughter pregnancy rate, and productive life increased by four‑ to fifteen‑fold compared to the pre‑genomic era. They based that on decades of Holstein pedigree, genomic, and performance data across the national system.

***Genomic Selection Doubled Genetic Progress—From $40 to $85 Per Cow Per Year***

So the data suggest genomics hasn’t just helped you chase production; it’s sped up progress in those “hard‑to‑move” traits many of us thought would take a whole career to shift. The problem is that a lot of that progress is still walking out the cull gate before it’s actually paid you back.

Looking at This Trend: What’s Actually in Net Merit Now?

Looking at this trend a bit closer, it helps to ask a simple question: what exactly are you selecting on today?

USDA’s most recent “Net merit as a measure of lifetime profit” revision, along with the Wiggans genomic selection review, makes it clear that U.S. dairy evaluations are now calculated for over 50 traits across production, fertility, health, calving, conformation, and efficiency. Net Merit pulls a large group of these into a single lifetime profit index using economic weights based on U.S. milk prices, feed costs, and culling patterns. That index includes milk, fat, and protein yields; several fertility traits such as heifer and cow conception rates and daughter pregnancy rate; cow and heifer livability; mastitis and other health traits; calving performance and stillbirth; age at first calving; a body‑weight composite; and feed efficiency via the Feed Saved trait, which uses body‑weight and residual feed intake data.

Over the last decade, USDA and the Council on Dairy Cattle Breeding (CDCB) have deliberately shifted the emphasis in Net Merit. When new health traits and Feed Saved were added, the economic weight on disease resistance and feed efficiency went up, while the weight on large body size was reduced because research showed that heavier cows require more maintenance feed and don’t necessarily return that cost in profit. Net Merit is now driven less by raw milk yield and more by health, fertility, and feed efficiency than it was in the early 2000s.

On the reliability side, invited reviews on genomic prediction in Holsteins report that genomic reliabilities for milk, fat, and protein in young bulls often sit in the 60–80 percent range when backed by a strong reference population, while fertility and health traits have lower reliabilities but are still significantly higher than the 20–30 percent levels typical of parent‑average evaluations. Those figures come from comparisons of genomic vs traditional proofs using large U.S. and Canadian datasets.

So, on paper, genomics and Net Merit give you a more complete, profit‑focused toolbox than we’ve ever had. And the genetic gains are real. The catch is that not everything you care about shows up on that proof sheet—and 2025 economics are unforgiving if cows don’t stay long enough to pay you back.

What Farmers Are Finding: Culling, Payback, and Short Careers

What farmers are finding, when they move from the proof sheet to the cull list, is that the picture gets uncomfortable pretty fast.

USDA’s National Animal Health Monitoring System (NAHMS) 2024 data reports that the typical overall cull rate for U.S. dairies—counting death losses—is about 37 percent per year. That’s in line with the 2018 NAHMS survey in the Northeastern U.S., which documented an annual cull rate of 31.4 percent plus a 6.2 percent death rate, for a combined 37.6 percent removal rate. Penn State Extension’s “Cull Rates: How is Your Farm Doing?” uses those exact numbers as the benchmark.

When you look at why cows leave, the NAHMS data show that only 26.8 percent of removals in the Northeast were voluntary—cows sold for dairy or lower producers. The other 73.2 percent were involuntary, driven mainly by infertility (23.3 percent of removals), mastitis (18.6 percent), lameness (9.1 percent), and on‑farm deaths (6.2 percent). Penn State highlights these figures to emphasize that reproductive problems, udder health, and lameness remain the big three behind most culls.

Removal Category	Share of Total Removals (%)	What This Means
Combined Annual Removal Rate	37.0%	Cows + deaths leaving your herd every year (NAHMS, Northeast U.S.)
Voluntary Culls	26.8%	Low production, dairy sales—you decided
Involuntary Culls	73.2%	Forced exits—health, fertility, injury
└ Infertility	23.3%	Cows that won’t rebreed on your timeline
└ Mastitis	18.6%	Chronic udder health failures
└ Lameness	9.1%	Foot/leg problems that won’t resolve
└ On-Farm Deaths	6.2%	Metabolic disease, injury, sudden death

So most cows aren’t leaving because they’re old, paid for, and you’re trading up. They’re leaving because something went wrong—often in the transition period or early in their productive life.

Now put that right next to the cost of raising replacements. A multi‑herd study from the University of Wisconsin–Extension calculated that the total cost to raise a replacement from birth to freshening averaged 2,227 dollars in 2013, not counting the calf’s initial value. That was up from 1,648 dollars in 2007 and 1,260 dollars in 1999, with feed as the largest single expense. The UW fact sheet “Heifer raising costs continue climbing upward” breaks down those costs and shows that feed alone accounted for over half the total.

More recent U.S. work hasn’t shown those costs going down. A 2025 article, drawing on Iowa State University Extension, reported that 2024 heifer‑raising costs in the Midwest were “just over 2,600 dollars” for a 24‑month heifer in many systems once you include feed, labor, housing, bedding, and overhead.

On the Canadian side, Lactanet’s “Analysis of the cost and value of dairy rearing programs” found that average rearing costs per heifer in Quebec were approximately 4,859 dollars for conventional herds and 5,070 dollars for organic herds, with a range from roughly 3,500 to over 7,000 dollars depending on housing, feeding, and management. Their 2023 follow‑up on the cost and profitability of rearing programs reinforces that rearing is a major capital commitment under supply management.

***Raising Replacements Now Costs $2,600–$5,000—Up 106% Since 1999***

So generally speaking, you’re tying somewhere between 2,000 and 5,000 dollars into each heifer before she ever steps into the parlor, depending on where you are and how you raise them.

Penn State Extension took those rearing costs and asked a blunt question in their 2025 article “Have Your Cows Repaid Their Debts?” Their analysis, based on NAHMS data and economic modeling, shows that with current heifer‑raising costs, it often takes until at least the third lactation for a cow to repay her development cost. They also point out—citing NAHMS‑based summaries and regional data—that the average U.S. cow only stays in the herd for about 2.7 lactations and that many cows are culled by the end of their third lactation. Morning Ag Clips picked up similar points in a 2024 piece titled “How Long Do Your Cows Stay in the Herd?”, quoting extension specialists who warn that a large share of cows leave before they’ve yielded a strong return.

***Most Cows Leave Right As They Start Making Money—The 2.7 Lactation Squeeze***

So the data suggest a tight squeeze: more expensive heifers, a payback point around three lactations, and an average cow productive life just shy of that. In a 2025 margin environment—where feed costs are still elevated, and component pricing is volatile—that’s a rough place to be.

If you run some simple numbers on a 200‑cow herd, the economic impact comes into focus. At a 37 percent cull‑plus‑death rate, you’re replacing roughly 74 cows per year. If you can move that combined rate down to 30 percent, you’re replacing about 60 cows. That’s 14 fewer heifers to raise. Using the documented U.S. cost range of 2,000–2,600 dollars per heifer, that’s 28,000–36,400 dollars per year in avoided heifer‑raising costs, before you even count the extra milk and butterfat performance from a higher proportion of mature cows. In Canadian quota herds, where Lactanet shows average rearing costs near 4,800–5,000 dollars, the same reduction in replacement needs could be worth 67,000–70,000 dollars annually.

Metric	Baseline (37% Removal)	Improved (30% Removal)	Annual Impact
Heifers Raised per Year	74	60	14 fewer
U.S. Cost per Heifer	$2,600	$2,600	—
U.S. Total Rearing Cost	$192,400	$156,000	Saves $36,400
Canadian Cost per Heifer	$5,000	$5,000	—
Canadian Total Rearing Cost	$370,000	$300,000	Saves $70,000

Here’s the thing I’ve noticed: once producers see that math with their own cull rates and rearing costs plugged in, continuing to raise every heifer “just in case” starts to look less like being conservative and more like one of the most expensive habits on the farm.

The Replacement Squeeze: Fewer Heifers, Higher Prices

As if the economics of raising replacements weren’t enough, the broader replacement market has been tightening the screws, too.

CoBank analysis of USDA cattle inventory reports shows that the number of dairy heifers weighing 500 pounds or more in the U.S. has fallen to its lowest levels in decades. CoBank’s 2025 analysis estimates about a 15 percent decline in dairy replacement heifer numbers over the past six years and notes that current inventories are at their lowest since the late 1970s. Their forecast suggests that heifer numbers will shrink further before beginning to rebound around 2027.

***U.S. Dairy Replacement Inventories Down 15%—Lowest Since the Late 1970s***

On the price side, market reporting describes multiple 2024–2025 sales where good Holstein replacement heifers routinely brought more than 3,000 dollars, with some top groups selling for over 4,000 dollars per head in California, Minnesota, and the Pacific Northwest. Market analysts have characterized current replacement heifer prices as “vaulting into record territory,” and these numbers align with both rearing costs and the tight national inventories reported.

So the data suggest that both raising and buying heifers are expensive right now, and that the industry as a whole doesn’t have a big surplus of replacements to fall back on. In a year when many herds are still feeling the aftershocks of 2025’s margin squeeze and processor pressure on components and quality, that makes your replacement strategy a high‑stakes business decision, not just a habit.

Structure, Environment, and Why Some Cows Don’t Make It to Third Lactation

Looking at this trend from the barn floor, the piece that doesn’t fully show up in Net Merit or genomic reliabilities is structured cow health in your specific environment.

On the hoof‑health side, multiple studies published in the Journal of Dairy Science and other veterinary journals have shown that cows with shallow heel depth and low foot angle are at greater risk for claw horn lesions and lameness on concrete, especially in freestall systems with higher cow traffic. Those studies link shallow heels, weak rear feet, and poor claw conformation with increased incidence of sole ulcers, white line disease, and chronic lameness—conditions strongly tied to reduced milk production, poorer fertility, and higher culling risk.

On the metabolic side, transition‑cow reviews and field studies emphasize that low body condition score and insufficient dry matter intake around calving increase the risk of negative energy balance, ketosis, and displaced abomasum. That’s particularly true in high‑producing cows fed energy‑dense diets to maximize early‑lactation yield and butterfat performance. Research on late‑gestation heat stress has documented “programming” effects: dry cows exposed to heat during the close‑up period produce less milk and experience more health issues in the subsequent lactation; some studies have even found effects on daughters’ performance. This is especially relevant in dry-lot systems and Southern herds, where late‑gestation cows and heifers are walking longer distances in the heat.

In Wisconsin freestall herds, hoof trimmers and UW–Extension educators have commented—both in extension meetings and in trade articles—that daughters from certain sire lines with flatter feet and thinner heels show up more often in trimming lists and lameness treatments, even when those bulls look acceptable for feet‑and‑legs composites on paper. While those observations are anecdotal, they align closely with the published links between heel depth, foot angle, and the risk of claw lesions on concrete.

In Western dry lot systems in California and parts of the High Plains, producers often report that very tall, angular cows with lighter bone and less body capacity don’t handle long walks between lots and parlors in summer heat as well as medium‑sized, deeper‑bodied cows that hold condition better through the transition period. When you overlay those barn‑floor stories with the heat‑stress and transition‑cow research, the pattern makes sense: cows whose structure and metabolism aren’t well suited to that environment are more likely to end up as early culls, no matter what their genomic index says.

If you swing your attention to pasture‑based seasonal systems, you see a different set of pressures. Ireland’s Economic Breeding Index (EBI) and New Zealand’s national breeding goals have been built around cows that can walk, graze, maintain body condition, and rebreed on a tight seasonal schedule. Research from Teagasc and New Zealand spring‑calving herds shows that higher fertility, genetic merit, and better body condition scores are associated with improved reproductive performance, survival, and profitability in those grazing systems, while very large, high‑output Holsteins bred for North American TMR feeding often struggle to hold condition and pregnancy on grass.

All of that suggests that Net Merit and similar indexes capture part of the story indirectly—through traits like productive life, fertility, health, and body‑weight composite—but they can’t fully see how structure and environment interact in your particular freestall, tie‑stall, parlor, robotic setup, or grazing platform.

And this is where I’d say we run into a quiet myth: that as long as the genomic index is high, the cow will “work” anywhere. The data and the barns both say that’s not always true.

What Farmers Are Finding: How High‑Performing Herds Actually Use Genomics

What farmers are finding, especially those who’ve been in the genomic game for a while, is that the herds quietly pulling ahead tend to follow a three‑part pattern. They use genomics as a strong filter, they add a simple structural check at the right time, and they let their own herd data tell them when a bull isn’t working in their environment—even if his proof still looks good.

1. Let Genomics Decide Who Deserves a Stall

First, they use genomics to decide which heifers even get to compete for a stall.

In many progressive Midwest and Northeast operations, every heifer is genotyped between three and six months of age. CDCB reports that hundreds of thousands of female dairy cattle are genotyped every year, and case studies profile farms that use whole‑herd genotyping to drive their replacement and beef‑on‑dairy strategies.

The pattern in those herds often looks like this:

Genotype the heifer group. All heifers—or at least all heifers from core cow families—get tested.
Rank on a profit index. Heifers are ranked on Net Merit in the U.S. or Pro$/LPI in Canada, and key functional traits—daughter fertility, productive life, mastitis resistance, calving traits, body size—are checked against herd goals.
Set a clear cutoff. An internal threshold is set based on how many replacements the herd truly needs annually, not “everything that hits the ground.”
Sort replacements vs beef. Heifers clearly below that line are designated for beef‑on‑dairy matings or other marketing paths instead of being automatically raised as core replacements.

Economic analyses from Iowa State, UW–Extension, and Lactanet all support this kind of triage. If genotyping costs around 40–50 dollars per heifer and the information lets you avoid raising 10–15 low‑merit animals that would each cost 2,000–2,600 dollars in the U.S. or 4,800–5,000 dollars in Canada, you’re avoiding 20,000–75,000 dollars of future rearing costs for a testing investment of maybe 4,000–7,500 dollars. Iowa State’s heifer‑inventory work and Lactanet’s rearing‑cost modeling both illustrate this scale of impact.

A lot of herds then pair this with beef‑on‑dairy. Extension surveys and industry reports from Iowa State, Kansas State, and High Plains fieldwork confirm that using beef semen on lower‑merit dairy cows and heifers has become a common way to add value to non‑replacement pregnancies and concentrate dairy replacements among the top genomic group. ROI analyses show improved calf value and better alignment between replacement supply and milk‑herd needs when this is done with clear genomic cutoffs.

Under the Canadian quota, Lactanet’s rearing‑program analysis and their work on cost and profitability emphasize that cows must stay in the herd long enough to repay higher rearing costs and generate a return on quota. Their numbers show average rearing costs around 4,800–5,000 dollars per heifer and a wide variation in cost per litre associated with heifer inventory, age at first calving, and productive life. Many Canadian advisors use those figures to support the rule of thumb that cows generally need three or more lactations to generate strong returns under quota.

So the first big step that successful herds have taken is to let genomics decide who deserves the chance to become a cow, instead of raising every heifer and hoping it works out. If you’re still raising every heifer in 2025, this development suggests you’re tying a lot of capital up in animals that will never pay you back.

2. Walk the Pens Before First Breeding

Second, the herds that are combining genomics with longevity add a simple structural check at breeding age.

Usually, that’s around 12–14 months for Holstein heifers in freestalls or tie‑stalls, and a bit later for seasonal grazing herds that breed heifers to fit a calving block. Someone—often the breeder, herd manager, or an experienced employee—walks through the breeding‑age pens with a few key questions in mind:

Compared to the older cows that come through the transition period well in this herd, does this heifer have enough body depth and chest width to eat what she’ll need on the diets and in the facilities you actually have?
Do her feet and heels look comparable to the heifers and cows that stay sound on your floors and paths, or are they noticeably flatter and weaker?
Does her rump and hip structure look like it will help or hinder calving and day‑to‑day movement in your barns or on your laneways?

Lameness research has tied shallow heels and low foot angle directly to higher odds of claw lesions and lameness on concrete, and transition‑cow research has linked limited intake and low body condition around calving to higher metabolic disease risk and weaker early‑lactation performance. Those are exactly the kinds of problems that drive early culling and drag down fresh cow management.

In a 70‑cow tie‑stall in Quebec, this might mean flagging just a few heifers as “structural concerns” and thinking about different mating or marketing plans for them. In a 400‑cow freestall in Wisconsin or an 800‑cow dry lot system on the High Plains, some producers have built simple 1‑to‑3 scoring systems and trained staff to mark heifers with clear structural issues during routine handling, then revisit that list when making breeding decisions.

Chasing tall, show‑style cows in freestalls or dry lots can be a costly luxury if they don’t walk and last. The herds that are winning on both banners and bank accounts are the ones that match their type to their environment rather than copying someone else’s ideal.

3. Use Corrective Mating Where It Really Pays

Third, these herds use corrective mating selectively, focusing on the animals where it’s most likely to pay off.

For the majority of cows and heifers—the ones that clear both the genomic filter and the structural walk—they keep breeding plans straightforward. They choose high‑index sires based on Net Merit, Pro$, or LPI that are solid for daughter fertility, livability, mastitis resistance, calving ease, and feet and legs, and they avoid bulls that are extreme for body size, or that carry trait weaknesses that clearly don’t fit their barns. USDA’s Net Merit documentation and our own Bullvine articles on genetic tools both suggest that letting multi‑trait economic indexes handle most of the weighting is a sound base strategy, as long as you pay attention to a few critical traits for your system.

For the smaller group of structurally marginal heifers, they still use good bulls—just more carefully. On narrower, shallow‑bodied heifers, they’ll lean toward bulls that are known to add strength and capacity without giving up too much on profit. On heifers with flat, thin‑heeled feet in concrete or dry lot systems, they’ll favor bulls with strong feet‑and‑legs evaluations and, where available, better claw‑health and locomotion scores. On heifers with awkward rumps, they reach for sires with more functional rumps and better daughter calving ease.

Herd‑level evaluations and extension case studies suggest that trading 50–100 dollars of index on these specific matings can be worthwhile if it reduces early structural culls and improves fresh cow management, especially when you look at lifetime milk and component yield instead of just first‑lactation performance.

Raising every heifer and then breeding them all to the same top‑index bull might feel simple. In 2025, it’s also a good way to waste both semen and stall space.

Step	Action	Financial Impact
1. The Filter	Genotype and set a hard cutoff.	Avoids $2,600+ in costs for “low-merit” calves.
2. The Walk	Visual check for feet, capacity, and rump.	Reduces involuntary culls in 1st/2nd lactation.
3. The Match	Corrective mating for structural outliers.	Ensures the best genetics actually survive to pay back debt.

Looking at This Trend from Your Own Records

There’s one more piece that high‑performing herds have learned to lean on, and that’s their own herd data.

Geneticists working on the U.S. genomic system have been clear that even with high average reliabilities, individual genomic bulls—especially the young, high‑ranking ones—can move once daughters calve across a range of environments. That point appears in Wiggans’ work as well as in invited reviews on breeding goals and selection strategies.

What farmers are finding is that by‑sire reports from their own herd management software are one of the best early warning systems they have. The pattern usually looks like this:

Once or twice a year, they pull reports that show lameness events, hoof‑trimmer findings, fresh cow problems (ketosis, DA, metritis), calving difficulty, and early culls by sire.
They compare each sire’s daughters to herd baselines: if daughters from one bull show significantly higher rates of lameness, fresh cow treatments, calving issues, or early culls, that bull moves onto a “caution” list.
They dial back that sire’s usage, especially in heifers, and watch how his official proofs move in the next couple of evaluation runs.

Extension educators and consultants in the Northeast, Midwest, and West have highlighted farms that do this, and their experiences align with what geneticists recommend: use national proofs for the big picture and your own data for local calibration.

In Western dry lot and Southern herds, some producers are also starting to sort these problem lists by calving season and sire to see whether certain bulls’ daughters struggle more when they calve into heavy heat. Research on late‑gestation heat stress suggests that cows calving after hot, dry periods may be at higher risk of poor performance and health problems. A few herds are using that insight to adjust which bulls they use on cows expected to calve in the hottest windows.

So here’s a fair question: do you know, off the top of your head, which bulls sired your last 20 early culls or your worst fresh cows? If the answer is no, your herd software probably does—and it’s worth asking.

New Tools Coming: 3D Cameras, AI Gait, and Why People Still Matter

Looking out a few years, it’s pretty clear that technology is going to keep adding tools to this mix.

Several recent studies and technical articles have evaluated three‑dimensional camera systems that estimate body weight and body condition score automatically from overhead images. These systems use depth sensors and algorithms to reconstruct the cow’s shape and have shown good agreement with scale weights and experienced BCS scorers in research settings and early commercial trials.

At the same time, dairy tech companies and research groups have been developing automated lameness detection systems that use cameras, accelerometers, or pressure mats with AI‑based gait analysis. Peer‑reviewed studies and industry case reports document systems that can detect subtle gait changes before cows are obviously lame, with high sensitivity and specificity. That kind of early warning can help target hoof trimming and fresh-cow management, and reduce the severity and cost of lameness cases.

Some research teams are already experimenting with combining these high‑frequency phenotypes—weight, BCS, locomotion, rumination—with genomic information to improve predictions for traits like resilience, feed efficiency, and long‑term health that are hard to measure at scale today. A 2024 bibliometric review on genomic selection in animal breeding and recent overviews of bovine genomics highlight this as a major emerging direction.

This development suggests that, in the future, we may be able to quantify and select for “resilience” and “structural soundness” more objectively. That’s exciting, especially for larger herds that need help catching subtle changes in body condition, movement, and fresh cow behavior.

But even as these tools roll out, every one of them still needs a human in the loop. Someone has to review the alert, examine the cow, and decide whether the system’s flags match reality. Judging coaches, classifiers, and long‑time herd managers have been saying for years that as our industry has gotten better at reading proofs and genomic reports, fewer people have had deep training in reading cows—feet, legs, capacity, udders, and how cows handle the transition period in real barns. Workshops and classifier training materials echo that concern.

From what I’ve seen, the herds that are making the most of genomics and new tech are the ones that still have at least one strong “cow person” in the mix. That person can look at a genomic report, look at a heifer, look at the hoof‑trimmer’s notes, and connect those dots. In 2025, when capital is tight and processors are picky, that skill might be as valuable as any piece of hardware you can bolt into the barn.

What To Do This Year: A Short List

If you’re thinking, “Okay, what do I actually do with all this?”, here’s a short, practical list based on the data and what successful herds are doing:

Genotype the heifers you’re serious about and set a real cutoff.
Test all heifers or at least those from your best cow families. Rank on Net Merit or Pro$/LPI, check fertility, productive life, mastitis, calving traits, and size, then draw a line based on how many replacements you truly need. Heifers below the line become beef‑on‑dairy or are marketed differently, instead of automatically being raised.
Walk your breeding‑age heifers once with structure in mind.
Before first breeding, take one good look at body capacity, feet and heels, and rump structure, comparing heifers to the cows that last in your herd. Use what we know about lameness and transition‑cow risk to flag structural outliers that are more likely to become expensive early culls.
Use corrective mating where it matters most.
For structurally marginal heifers, pick high‑merit sires that also bring better feet, legs, capacity, or calving traits—even if it means giving up a bit of index on those matings. For the rest, let multi‑trait indexes do the heavy lifting and avoid extremes that don’t fit your facilities or fresh cow management reality.
Pull one by‑sire problem report this year.
Use your herd software, vet records, and hoof‑trimmer logs to see which sires’ daughters show up more often in lameness events, fresh cow treatments, calving problems, or early culls. If one bull looks worse than the herd average, dial back his usage and watch how his proof moves in coming runs. Doing nothing with this information is also a strategy—and in 2025, it’s one of the riskiest ones you can pick.
Start planning how you’ll use new tech, but keep people at the center.
If you’re considering 3D cameras or lameness‑detection systems, think about who on your team will own those alerts and how you’ll use that data alongside genomics and good old‑fashioned pen walking. The tech can sharpen your view, but it won’t replace judgment.

The Bottom Line

So, looking at this trend as a whole, the data and the barns are pointing in the same direction.

The herds that are quietly getting ahead aren’t “all genomics” or “no genomics.” They’re the ones that:

Use genomic tests and economic indexes to decide which heifers truly deserve a place in the replacement pipeline, instead of raising every calf and hoping it works out.
Bring a straightforward, honest look at structure into the picture at breeding age to make sure those heifers’ bodies fit their stalls, floors, and walking distances.
Use corrective mating where it actually pays—on the smaller group of structurally marginal animals—while letting Net Merit or Pro$/LPI guide most matings.
Listen to their own herd data on bulls and adjust usage when their cows tell a different story than early proofs suggest.
And keep at least one strong “cow person” in the mix to connect what the numbers say with what’s happening in the pens, especially through the transition period and fresh cow management.

You’re already paying for genomics. You’re already paying a lot to raise replacements. Either you use genomics, structure, and herd data together to keep more cows past three, four, or five lactations—or you keep pouring 2,000–5,000 dollars into replacements that walk out just as they reach breakeven.

What’s encouraging is that you don’t need to overhaul everything overnight. Testing a few more heifers, drawing a firmer line on who you raise, walking one heifer group with structure in mind, and pulling one by‑sire problem report this year can start nudging your herd in the direction the data—and the best herds—are already heading.

Key Takeaways

Genomics doubled genetic gain—but not cow longevity. Net Merit now climbs about 85 dollars per cow per year versus 40 dollars pre‑genomics, yet the average cow still exits around 2.7 lactations—often before paying back her 2,000–5,000 dollar raising cost.
Most culls aren’t planned—they’re forced. NAHMS data show a 37 percent combined cull‑plus‑death rate, driven by infertility, mastitis, and lameness. Penn State’s analysis confirms real profit typically doesn’t start until the third lactation or later.
Raising every heifer is now a high‑cost gamble. U.S. replacement inventories have dropped roughly 15 percent to multi‑decade lows, and 2025 heifer prices commonly exceed 3,000 dollars. “Just in case,” heifer programs may be your most expensive habit.
Top herds treat genomics as a filter, not a trophy. They genotype early, set a hard cutoff tied to true replacement needs, walk heifers at breeding age for structural fit, and use corrective mating only where it actually reduces cull risk.
Your own herd data can catch what the proofs miss. Pull by‑sire reports on lameness, fresh cow problems, and early culls at least once a year—bulls whose daughters don’t hold up in your barns will show up there before proofs fully adjust.

Complete references and supporting documentation are available upon request by contacting the editorial team at editor@thebullvine.com.

Learn More

The $4,000 Heifer: Seven Strategies to Navigate the New Dairy Economy – Reveals seven concrete tactics to survive the $4,000 heifer era, from leveraging precise genomic cutoffs to recalibrating beef-on-dairy percentages. It arms you with immediate management changes to stop the cash-flow bleed and protect your replacement pipeline.
438,000 Missing Heifers. $4,100 Price Tags. Beef-on-Dairy’s Reckoning Has Arrived. – Exposes the structural deficit of 438,000 missing heifers that will dictate dairy margins through 2028. It delivers a long-term positioning strategy for navigating record-high replacement prices and the narrowing window of processor leverage.
Digital Dairy Detective: How AI-Powered Health Monitoring is Preventing $2,000 Losses Per Cow – Breaks down how AI-powered health monitoring replaces reactive “firefighting” with proactive precision, identifying metabolic issues 120 hours before clinical signs. It gives you the technological advantage to keep high-genetic-merit cows productive into their fourth lactation.

Join the Revolution!

Join over 30,000 successful dairy professionals who rely on Bullvine Weekly for their competitive edge. Delivered directly to your inbox each week, our exclusive industry insights help you make smarter decisions while saving precious hours every week. Never miss critical updates on milk production trends, breakthrough technologies, and profit-boosting strategies that top producers are already implementing. Subscribe now to transform your dairy operation’s efficiency and profitability—your future success is just one click away.

Categories : Genomics

Tags : culling strategy, Dairy Herd Management, dairy profitability, Genomic Testing, Heifer rearing, replacement inventory

Lucky or Calculated? The Surprising Truth About Genomics and Luck in Dairy Breeding

Tuesday, March 11th, 2025

Can genomics eliminate luck in dairy breeding? Discover how chance shaped Holstein’s history and why unpredictability still impacts your herd today.

I’ve always been fascinated by that eternal question in dairy breeding: can science and technology eliminate the role of luck? With April 2025’s genetic evaluation updates just around the corner, it feels like the perfect time to dig into whether our fancy genomic tools have truly kicked chance to the curb—or if they’ve just given us better ways to dance with it. After talking with industry experts and diving into the research, I’ve discovered something surprising: some of Holstein’s most influential bloodlines emerged from happy accidents that no amount of genomic testing could have predicted.

The Genomics Revolution vs. Lady Luck

Let’s be honest—whenever we talk about breeding success these days, we can’t help but focus on genomic selection, advanced mating programs, and all those impressive reproductive technologies. I mean, how couldn’t we? These tools have transformed our industry.

The April 2025 genetic evaluation updates are coming fast, with revised lifetime merit indices that shift to the 2020 genetic base. Have you been keeping up with the Council on Dairy Cattle Breeding announcements? They’re projecting some major PTA decreases: -750 pounds of milk, -45 pounds of fat, and -30 pounds of protein for Holsteins.

Don’t panic! As Chuck Sattler from Select Sires explained recently, “The 2025 base change is bigger than previous adjustments, but this is good news! It means that our cows are improving faster than ever.”

But here’s what keeps me up at night: Have we eliminated Lady Luck from the breeding equation? Or have we just given her a shiny new genomic lab coat?

The 75% Solution: What Genomics Can (and Can’t) Tell Us

I was digging through some research recently and found something fascinating from the National Center for Biotechnology Information. Our most advanced genomic prediction tools show only about 75% reliability for production traits. That means a quarter of what makes a cow productive remains outside our ability to predict!

This 75% reliability has been consistent for years. A 2011 Journal of Dairy Science study noted that this level is “adequate for marketing semen of 2-yr-old bulls,” but it’s far from perfect. The primary benefit? A shortened generation interval that increases the rate of genetic improvement.

Think about that 25% gap next time you’re making breeding decisions. It’s not just a tiny margin of error—it’s a significant space where luck, chance, and unexplained genetic interactions still reign supreme.

Lucky Breaks That Shaped Holstein History

You know what’s crazy? Looking back through Holstein’s history, some of the breed’s most influential genetic lines happened because of tiny accidents, missed connections, or just plain dumb luck. I’ve collected four of my favorite examples in this table:

Lucky Break Event	What Actually Happened	What Could Have Happened	Resulting Influential Sire/Dam	Long-term Impact
Missing Telephone	Spring Brook Bess Burke sold to George Miller	Would have been purchased by Lashbrook	Led to Osborndale Ivanhoe, Elevation, Starbuck, Aerostar	Shaped modern Holstein genetics
Injured Leg	Montvic Chieftain injured, Pathfinder offered instead	Whitney would have taken Chieftain	Round Oak Rag Apple Elevation	Foundation of influential bloodlines
Change of Clothes	Visitors saw Temple Farm May while Dunton changed	Might never have noticed the cow	A.B.C. Reflection Sovereign	One of the breed’s most respected sires
Wrong Semen	Inseminator arrived without Pabst Walker semen	Tiny Supreme DeKol would have been bred differently	Almerson Sovereign Supreme	Highly respected Canadian bull line

No Phone, No Starbuck? The Wild Story of the Missing Call

I can’t get over this first story—it blows my mind whenever I think about it. In the early 1900s, A.J. Lashbrook and his brother sold some inherited shares for $250 (not exactly chump change) to invest in Holstein cattle.

Their father spotted three gorgeous heifer calves at Spring Brook Farm, priced at $75 each. I mean, imagine that kind of deal today!

But get this—they didn’t have a telephone to confirm the purchase! So Dad had to return the next day, only to find that the calves had already been sold to George Miller. It turns out that Schilling, the Spring Brook Farm manager, had mentioned the calves to a local feed mill owner, who told Miller. Talk about bad timing!

One of those calves? Spring Brook Bess Burke. Miller raised them, bred them to Sir Johanna Canary DeKol, and sold them to F.C. Schroeder of Moorhead, Minnesota.

“Years later, Mr. Schroeder visited our herd and, when I took him back to the depot, remarked that Spring Brook Bess Burke 2nd was born in a box car just as the train passed the depot after leaving the stockyards,” said Lashbrook.

She eventually found her way to E.C. Schroeder in Minnesota, where she and her daughter made incredible production records when bred to Sir Pietertje Ormsby Mercedes.

Lashbrook later reflected (and I love this quote): “As I look back now, it was indeed fortunate that we did not have a telephone and that those calves never came to our farm. We were only small breeders and… probably never would have developed those cows.”

Here’s the kicker—without that missing telephone, there would have been no Osborndale Ivanhoe, no Elevation, no Starbuck, and no Aerostar. Can you imagine modern Holstein genetics without those bulls? I sure can’t!

The Data Behind Modern Breeding: What Science Tells Us

While historical anecdotes are fascinating, let’s look at what the research says about genomic selection today. A 2020 study published by the National Center for Biotechnology Information found something that really caught my attention: inbreeding can significantly impact how well genomics works as a prediction tool.

The study examined high-producing primiparous dairy cows and found that individuals with an Inbreeding Index between ≥2.5 and ≤5.0 showed a two-fold increase in negative correlations between genomic predictions and actual performance. This affected critical traits, including Milk Production at 305 days, Protein Production, Fertility Index, and Daughter Pregnancy Rate.

What does this mean for your breeding program? Even with perfect genomic tools, factors like inbreeding can throw a massive wrench into the works. Your carefully selected mating might produce unexpected positive or negative results based on genetic interactions our current models can’t predict.

The Luckiest Injured Leg in Holstein History

I love this next story. F.C. Whitney had purchased Montvic Chieftain from T.B. Macaulay. But Chieftain slipped and injured his leg while loading the bull onto the truck. Bummer, right?

Macaulay called Whitney and told him they could have Montvic Pathfinder for the same price!

Now, Pathfinder wasn’t winning any beauty contests. Whitney’s description of him as “as homely a brute as a man ever saw” makes me laugh every time. But his pedigree? Absolutely stellar, with multiple All-American winners. As the text says, “Montvic Pathfinder, some claimed, possessed the best pedigree ever written,” including “four All-American wins to his credit, including aged cow in 1935 and 1936.”

Whitney decided to take a chance on the ugly duckling. At his farm in New York, Pathfinder sired Montvic Pathfinder Prizetaker, proven in the herd of Eugene and Clarence Harvey, Cincinnatus, N.Y. In making his switch from Jerseys to Holsteins, Charles Hope, Round Oak Farm, Purcellville, Va., over four years, purchased 17 Prizetaker daughters from the Harveys, as well as several Montvic Chieftain 6th calves and bought Montvic Pathfinder Prizetaker, himself. He used a son of his, Round Oak Montvic PF General, who sired Round Oak Millie Elizabeth, Elevation’s third dam.

So, luck again. Had Chieftain not banged up his leg, Pathfinder wouldn’t have gone to the United States, and there would have been no Round Oak Rag Apple Elevation.

The Preferential Treatment Problem

The latest research has revealed something that fascinates me: genomic predictions can be significantly biased by the preferential treatment of elite cows. A 2018 study published in the Journal of Dairy Science simulated what happens when elite bull dams receive special treatment.

The researchers found that it could significantly skew genomic predictions when just 5-20% of elite bull dams received preferential treatment (introducing an upward bias in their performance data). This is especially true for traits with low heritability, where the accuracy of genomic predictions is already challenging.

This research explains why sometimes the offspring of “sure thing” matings don’t perform as expected. The genomic values looked great on paper but may have been inflated by the special treatment of the cow families in the reference population. It’s another way chance enters our breeding programs—through human bias and the limitations of our measurement systems.

When Your AI Guy Says “Sorry, I’m Out”

How many times has this happened to you? You call your AI technician with the perfect mating all planned out, and they hit you with: “Sorry, I’m out of that bull’s semen today.”

One of those cows was Tiny Supreme DeKol! Aylmer Petherick had chosen Pabst Walker for Tiny’s next mating, but the inseminator, on the day he came to breed her, wasn’t carrying his semen. “What else have you got?” Aylmer asked. He settled on Hainescrest Sovereign Tycoon.

Almerson Sovereign Supreme, the result of the mating, was eventually classified as Excellent and received a Class Extra rating en route to becoming one of the most respected bulls in Canadian history. It was highly regarded by leading cattlemen of the day, including Pete Heffering and Dave Houck. What a great example of turning what is available into something great!

Who knows? Your backup choice today might create tomorrow’s game-changing bloodline. All those genomic tools might guide your primary selections, but chance still decides whether those straws are in your AI tank when needed.

The 25-35% Gap That Keeps Me Up at Night

Here’s what fascinates me about genomic selection: for all its revolutionary power, it still can’t predict everything. Not even close.

According to research published in the Journal of Dairy Science, current reliability percentages for genomically tested young animals typically hover between 65% and 75% for production traits and even lower for health and fertility traits.

That means that 25-35% of a cow’s genetic potential remains unpredictable through our current genomic models. That’s a huge gap!

Four main factors create this uncertainty:

Gene interactions: Genomic models struggle to capture how genes influence each other. The same marker might perform differently depending on the overall genetic background.
Environmental influences: How genes express themselves varies wildly in different environments. I’ve seen genetically identical cows perform completely differently on neighboring farms.
Genetic recombination: Even with identical parents, each calf gets a unique genetic package. It’s like shuffling a deck of cards—you never deal the same hand twice.
New mutations: Sometimes genetic changes appear absent in either parent, creating traits nobody predicted.

ROI on Genomic Testing: The Numbers Don’t Lie

Let’s talk dollars and cents for a minute. Despite the limitations, genomic testing has demonstrated impressive financial returns. Recent industry analyses suggest that genomic testing of heifers delivers approximately $75-$200 in additional lifetime profit per animal tested, primarily through improved selection decisions and optimized heifer inventory management.

The financial return varies based on several factors:

Current replacement costs in your area
Your herd’s genetic level relative to the breed
How aggressively do you cull based on genomic results
Whether you use sexed or beef semen strategically

Even with these impressive returns, the unpredictable 25-30% of genetic potential means some animals will significantly underperform or overperform their genomic predictions. This variability creates risk and opportunity—sometimes, your lowest-ranked genomic heifer produces your best cow. Ask any experienced breeder, and they’ll have at least one story like this!

The Change of Clothes That Changed Everything

This next story makes me smile every time. “Luck played a part, too, in the A.B.C. Reflection Sovereign story.” History might have taken a different course if he had waited for them on his front porch. Doug Dunton walked up from the stable in his barn clothes when they arrived. That September 1942, Jack Fraser, Elgin Armstrong, and Cliff Chant, his herdsman, had stopped at Dunton’s to scout up some cows for Armstrong’s A.B.C. Farm.”

“Wait a minute while I change my clothes,” said Dunton as he approached the house. His visitors sauntered down to the barn. As they walked, they passed a big, white Lonelm Texal Alcartra daughter named Temple Farm May, getting ready to calve. Before the day was out, Armstrong bought the cow for $400.00. Dunton agreed to keep her until she freshened. She was bred to Inka Supreme Reflection, and the calf was A.B.C. Inka May.

What a find! A.B.C. Inka May did everything right. She was a ferocious producer with an Honour List record of 24,141 lbs. milk, 4.67%, and 1,128 lbs. fat in 1947, the same year she was an All-Canadian four-year-old. But her supreme achievement was as dam of A.B.C. Reflection Sovereign (EX-Extra), who many claim was the best bull the breed has produced.

So yeah! Luck also influenced this bull’s genetics. Who knows what would have happened if Dunton had not changed then?

Hidden Gems Hiding in Plain Sight?

This makes me wonder—what excellent cows are we walking past daily, fixated on our genomic printouts?

With the April 2025 evaluation changes, we’re facing a significant recalibration of genetic values. According to the latest announcements I’ve seen, the Net Merit $ (NM$) index is getting a serious makeover: increased emphasis on butterfat (+13% weighting), greater focus on feed efficiency (41% higher combined impact), and doubled weighting for cow livability.

This reranking creates an opportunity to spot “hidden gems” that our current systems might be undervaluing. Are you only chasing the highest numbers, or are you developing that breeder’s eye to recognize special animals others might miss—just like Armstrong spotted value in Temple Farm May?

The best breeders I know combine data with that indefinable “cow sense” that no genomic test can replace.

Navigating the Balance: Genomics vs. Serendipity

Here’s how I think about the interplay between precision and chance in different aspects of breeding:

Aspect of Breeding	How Genomics Influences It	Role of Chance Still Present
Selection Decisions	Identifies animals with superior genetic potential earlier and more accurately	Which animals you choose to test and develop still involves human judgment
Mating Choices	Predicts outcomes of specific matings with greater precision	Availability of preferred sires, conception success, and embryo viability remain variable
Trait Predictions	Provides reliable estimates for well-studied traits with high heritability	Novel traits, gene interactions, and environmental influences remain less predictable
Health Outcomes	Identifies genetic predispositions to certain diseases	Many health events remain unpredictable despite genomic information
Fertility	Helps select for improved reproductive traits	Individual conception events remain highly variable
Longevity	Predicts genetic components of productive life	Many factors affecting actual lifespan remain outside genomic prediction
Elite Animal Identification	Accelerates discovery of superior genetics	The specific combinations that create truly exceptional animals still involve elements of chance

Gearing Up for April 2025: What You Need to Know

The latest genomic technology has improved prediction accuracy. I’ve been reading about these new machine-learning algorithms that better account for gene interactions and environmental factors. According to recent research in the Journal of Dairy Science, these models have boosted reliability percentages by about 5-7% for most traits.

That’s progress! But even with these improvements, we’re still looking at about 20-30% of genetic potential remaining unpredictable. And that unpredictable zone? That’s where luck—both good and bad—continues to play its role.

The April 2025 genetic evaluation updates will incorporate these improved models but won’t eliminate chance. According to The Bullvine’s recent report (which I highly recommend reading), we’ll need to recalibrate our sire selection thresholds—what used to be a +2000 NM$ will become approximately +1300 NM$. It’s going to take some mental adjustment for all of us.

4 Ways to Balance Science with Serendipity

As we get closer to the April 2025 genetic evaluations update, here are four strategies I’m recommending to my friends in the industry:

Get familiar with the changes: Take time to understand the revised lifetime merit indices and that base change shift to cows born in 2020. Chuck Sattler from Select Sires advises: “The adjustments coming in April will mean you will likely need to recalibrate the selection levels used for A.I. sires and which cows are bred to beef or sexed semen.”
Don’t put all your eggs in one genomic basket. The industry focuses on an increasingly narrow range of elite genetics. Consider incorporating some differently-bred Holstein cattle that offer unique genetic contributions. Genetic diversity provides more opportunities for unexpected combinations that sometimes create magic.
Build in flexibility: What’s your Plan B when your first-choice matings aren’t possible? Those backup plans sometimes produce better results than the original! Avoid getting trapped in the mindset that there’s only one “right” mating for each animal.
Trust your eyes, not just the numbers. While genomic testing provides incredibly valuable data, don’t lose that breeder’s instinct. The best operations I visited combined quantitative assessment with qualitative judgment—they used printouts and indefinable “cow sense.”

The Bottom Line

As we approach these April 2025 genetic evaluation updates, I keep returning to this fundamental truth: breeding success has always emerged from a blend of scientific precision and happy accidents.

Genomic selection gives us unprecedented insight into genetic potential. Still, the stories of Holstein’s most influential animals remind us that some of our greatest breeding successes came from unexpected turns of fate.

So, does genomic selection take the luck out of dairy breeding? Not a chance. Genomics has given us better tools to capitalize on luck when it strikes. The technology helps us identify promising animals earlier and more accurately. Still, it doesn’t eliminate the fundamental randomness involved in genetic recombination, gene expression, and the countless small decisions that shape breeding outcomes.

The lesson? Use every scientific tool, but keep your eyes open for those unexpected opportunities that genomics can’t predict. Use genomic testing to identify high-potential animals, study the upcoming changes to evaluation indices, and align your breeding program with your farm’s economic goals.

But never forget that sometimes, the most valuable genetic combination might emerge when your inseminator runs out of your first-choice semen, when visitors happen to notice a special cow while you’re changing clothes, or when a replacement bull offered due to an injury turns out to be a breed-defining sire.

Holstein history shows us that luck creates opportunities—but only those with the knowledge and vision to recognize potential can transform those opportunities into lasting genetic contributions. As you prepare for the changes in April 2025, keep one eye on the data and the other open to the possibilities that might lead to your herd’s next great success story.

Key Takeaways

Luck shapes breeding success: Historical examples like Spring Brook Bess Burke and Montvic Pathfinder show how chance created legendary Holstein sires.
Genomics isn’t perfect: Current tools offer up to 75% reliability for production traits, leaving room for unpredictability in genetic outcomes.
Prepare for April 2025 updates: Recalibrate sire selection thresholds as Net Merit $ indices shift focus toward butterfat, feed efficiency, and cow livability.
Flexibility matters: Backup mating plans and a keen breeder’s eye can uncover hidden gems that genomic data might overlook.
Balance science with serendipity: Use genomic tools strategically while staying open to unexpected opportunities that could transform your herd.

Executive Summary

Dairy breeding has come a long way with genomic selection, but luck remains an undeniable factor in shaping success. This article explores pivotal moments in Holstein history, like Spring Brook Bess Burke’s missed purchase, Montvic Pathfinder’s unexpected rise, and Temple Farm May’s discovery, to show how chance created breed-defining sires. Even today, genomic tools offer impressive reliability (up to 75%), yet factors like genetic recombination and environmental influences leave a 25-35% prediction gap. As the April 2025 genetic evaluation updates approach, breeders must balance precision with flexibility to capitalize on unexpected opportunities. From backup mating plans to spotting hidden gems, this article offers actionable strategies to navigate the intersection of science and serendipity in dairy breeding.

Learn more

Genomics Meets Artificial Intelligence: Transforming Dairy Cattle Breeding Strategies
Discover how genomics and AI revolutionize dairy cattle breeding, enabling precise trait selection and accelerating genetic progress.
Rethinking Balanced Breeding for 2028 and Beyond
Explore how strategic mating decisions and precision genetic advancements shape the future of dairy cattle breeding.
How Genomics and Sexed Semen Are Remaking the Dairy Cow
Learn how cutting-edge technologies like genomics and sexed semen are helping farmers breed cows optimized for butterfat, protein, and profitability.

Join the Revolution!

Join over 30,000 successful dairy professionals who rely on Bullvine Daily for their competitive edge. Delivered directly to your inbox each week, our exclusive industry insights help you make smarter decisions while saving precious hours every week. Never miss critical updates on milk production trends, breakthrough technologies, and profit-boosting strategies that top producers are already implementing. Subscribe now to transform your dairy operation’s efficiency and profitability—your future success is just one click away.

Categories : Genomics

Tags : 1., Dairy Breeding, genetic evaluation, genomic selection, Holstein genetics

New Genomic Option for Canadian Dairy Breeders to Bypass Herdbook Requirements

Friday, July 12th, 2024

Find out how Canadian dairy breeders can now avoid the U.S. herdbook restrictions for genomic evaluations. Could this new choice simplify your breeding efforts?

Canadian dairy breeders are on the verge of an exciting change. Soon, you’ll be able to get genomic evaluations for domestically bred cows without needing to register them in National Breed Association herdbooks. This breakthrough will make it easier for all Canadian-born dairy cattle to receive genomic evaluations based on Canadian standards. Announced at Lactanet’s Open Industry Session, this change will simplify the process for Canadian dairy farmers, reducing the hassle of herdbook registration. Additionally, there’s a proposed fee waiver if you register your cattle promptly.

Genomic Evaluations in Canadian Dairy Breeding: Overcoming Challenges

Genomic evaluations are essential in modern dairy breeding, predicting future performance based on genetic makeup. Lactanet provides these services in Canada but faces challenges, especially for cows not registered in the National Breed Association herdbooks.

All genomic testing relies on the U.S. Council on Dairy Cattle Breeding (CDCB), which handles genotype quality assurance and haplotype analysis. The process involves higher costs and longer times, as breeders must go through CDCB directly, particularly for non-registered animals, costing US$6 per animal.

This system adds bureaucratic layers and financial strain, potentially discouraging breeders from using genomic evaluations entirely. Despite these challenges, genomic testing remains invaluable, allowing precise predictions of an animal’s potential and aiding better breeding decisions. However, until changes are implemented, Canadian dairy farmers navigate an inefficient system, limiting their ability to expand their genetic base and achieve top-rated status for their dairy herds.

Evolution in Genomic Accessibility: Canadian Calculations for All Dairy Breeders

Brian Van Doormaal, chief services officer at Lactanet, has announced fundamental changes that will make it easier for Canadian breeders to obtain genomic evaluations for cows not registered in National Breed Association herdbooks. This shift allows these evaluations to be conducted within Canada using Canadian calculations. Previously, breeders had to work directly with the U.S. Council on Dairy Cattle Breeding (CDCB) for such evaluations.

Although genomic testing will still occur in the United States, integrating with Lactanet means these genotypes can be shared in Canada. This eliminates the need to navigate the U.S. system for your genomic predictions, saving time and resources.

This change aims to increase inclusivity in genetic evaluations within the Canadian dairy industry. It expands the genetic base accessible to breeders and leverages Canadian service providers’ expertise and infrastructure. An associated fee may apply, but if an animal is registered within two months of testing, the fee could be waived, offering a cost-effective solution for breeders.

Lactanet is working with the CDCB on a new record-keeping process to ensure accurate tracking of these evaluations. Non-registered cattle will receive an alphabetic country code, differentiating them from registered animals and streamlining the identification process. This change will also align with other advancements, such as Lactanet’s transition to monthly official evaluations for Canadian females, potentially allowing more dairy cows in Canada to achieve top-ranked status in genetic rankings.

Ensuring Accuracy and Trust Through The Genomic Testing Process

The genomic testing process is key to accurately evaluating dairy cattle, with the U.S. Council on Dairy Cattle Breeding (CDCB) playing a crucial role. When you send a sample, the CDCB ensures quality through genotype validations and haplotype analysis. While future evaluations will be based on Canadian standards, the core testing and quality assurance will still rely on the CDCB’s infrastructure. This ensures that Canadian dairy farmers get consistent and reliable genomic evaluations, with the added benefit of local calculations.

New Logistics and Fee Structure for Genomic Evaluations

With the proposed changes, dairy breeders will see new logistics for obtaining genomic evaluations. Currently, the cost is US$6 per animal through CDCB. However, the fee structure might change once done in Canada, though specifics are still pending.

An exciting part is the potential fee waiver. If you register an animal within two months of testing, the fee might be waived, saving you money and encouraging timely registration.

Lactanet is working with CDCB on a solid record-keeping system to manage this. Registered animals will still have numeric country codes, while non-registered cows will get unique alphabetic country codes. This ensures explicit tracking and accurate genomic identification, enhancing trust in the genomic data.

Understanding the Logistics of this New Process is Crucial for Dairy Breeders

Understanding the logistics of this new process is crucial for dairy breeders. While genomic testing will still be done by the U.S. Council on Dairy Cattle Breeding (CDCB), Canadian service providers like Lactanet will handle the submission process. This means breeders can send samples through these providers, easing the workflow.

Regarding costs, though the exact fee is undecided, sending samples via Canadian providers will incur a charge. However, if an animal is registered within two months of testing, this fee might be waived, promoting timely registration.

Lactanet collaborates with the CDCB on a robust tracking system to ensure accurate record-keeping. Registered cattle will have numeric country codes, while non-registered cows will get alphabetic codes. This differentiation helps maintain clear genomic identification.

These logistics aim to make genetic evaluations more accessible and integrated within Canadian dairy breeding, leading to higher genetic standards and better breeding outcomes.

The Bottom Line

This new genomic option is a game-changer for Canadian dairy breeders. It will make genomic evaluations based on Canadian calculations available to all domestically bred cows. Although testing will still happen in the U.S., the process will be more streamlined and affordable for non-registered cattle in Canada. With the rise of automated milking systems and more accessible genotyping, this change is set to roll out later this year, transforming genetic evaluation and breeding for Canadian dairy producers.

Key Takeaways:

Canadian genomic evaluations for non-herdbook dairy cows may be available later this year.
Testing will still be conducted in the United States by the U.S. Council on Dairy Cattle Breeding (CDCB).
Genomic evaluations will be based on Canadian calculations, making them more relevant and beneficial for Canadian dairy operations.
The potential change allows all Canadian-born dairy cattle to receive a genomic evaluation, regardless of their herdbook registration status.
Fees are yet to be determined but might be waived if the animal is registered within two months of testing.
A new record-keeping process is being developed to differentiate between registered and non-registered cows via Canadian service providers.

Summary:

Canadian dairy breeders can now receive genomic evaluations for domestically bred cows without needing to register them in National Breed Association herdbooks. This change simplifies the process for Canadian dairy farmers and offers a proposed fee waiver if cattle are registered promptly. Genomic evaluations are essential in modern dairy breeding, predicting future performance based on genetic makeup. Lactanet, a Canadian service provider, has announced fundamental changes that will make it easier for Canadian breeders to obtain genomic evaluations for cows not registered in National Breed Association herdbooks. The change aims to increase inclusivity in genetic evaluations within the Canadian dairy industry and leverages Canadian service providers’ expertise and infrastructure. An associated fee may apply, but if an animal is registered within two months of testing, the fee could be waived. The new record-keeping process will ensure accurate tracking of genomic evaluations.

Learn more:

Categories : Genomics

Genomic Testing Transforms Profit Potential for the UK’s Dairy Herd: Key Insights from AHDB Analysis

Friday, July 5th, 2024

Learn how genomic testing is improving the profitability of the UK’s dairy herds. Are you using genetic insights to enhance your farm’s profits? Find out more.

Imagine a future where the United Kingdom’s dairy farms keep pace with global competitors and lead in efficiency and profitability. This potential is swiftly becoming a reality thanks to advancements in genomic testing of dairy heifers.

The latest analysis from the Agriculture and Horticulture Development Board (AHDB) underscores the significant financial benefits of genomic testing. It reveals a substantial gap in the Profitable Lifetime Index (£PLI) between herds engaging in genomic testing and those not. This article delves into the financial impact of genomic testing for the UK’s dairy herd, highlighting its potential to boost profitability and sustainability significantly. Improving genetics through genomic testing is a cost-effective and sustainable way to make long-term improvements to any herd.

Genomic testing is revolutionizing dairy farming. It is a powerful tool for enhancing herd profitability and sustainability. We’ll examine the statistical evidence of PLI differences, theoretical and actual financial benefits, and the significant rise in genomic testing of dairy heifers. Additionally, we’ll address the issue of misidentified animals and the breeding implications.

Genomic testing has dramatically shaped the industry since its introduction to UK producers. This transformative approach boosts farm profitability and ensures long-term sustainability. By leveraging genomic testing, dairy producers can make informed decisions that profoundly impact their operations and the broader agricultural economy.

Genomic Testing Revolutionizes Genetic Merit of UK Dairy Herds: AHDB Reveals Significant PLI Disparity with Profound Implications for Productivity and Profitability

Genomic testing is revolutionizing the genetic merit of the UK’s dairy herd, significantly boosting productivity and profitability. The Agriculture and Horticulture Development Board (AHDB) reports a £193 gap in the average Profitable Lifetime Index (£PLI) between herds heavily engaged in genomic testing and those less involved.

Producers testing 75-100% of their heifers have an average £PLI of £430 for their 2023 calves, compared to £237 for those testing 0-25%. This stark difference underscores the critical role genomic testing plays in improving the genetic quality of dairy cattle. It enhances health, longevity, and productivity, making it a powerful tool for herd management and breeding strategies.

This £193 PLI difference translates to an estimated £19,300 profit potential for a 175-head herd. However, real-world accounts show the benefits can exceed £50,000. This underscores the significant financial rewards that genomic testing can bring, making it a vital tool for informed breeding decisions that drive long-term economic and genetic gains.

Potential Gains and Real-World Financial Impact of Comprehensive Genomic Testing in Dairy Herds

Genomic testing offers a compelling route to profitability for dairy producers. Herds genotyping 75-100% of their heifers achieve an average £430 PLI, while those testing only 0-25% lag at £237.

This gap translates into significant gains. A 175-head herd could theoretically gain £19,300. However, real-world data suggests that the financial advantage can exceed £50,000, highlighting the profound impact of genomic testing on profitability.

Marco Winters Advocates Genomic Testing: A Cost-Effective and Sustainable Path to Long-Term Herd Improvement

Marco Winters, head of animal genetics for AHDB, underscores the cost-effectiveness and sustainability of improving herd genetics through comprehensive genomic testing. “Genetics is probably the cheapest and most sustainable way of making long-term improvements to any herd,” Winters notes. “And when it’s aimed at boosting profitability, the benefits directly impact a farm’s bottom line.”

Winters highlights that significant returns outweigh the initial investment in genomic testing. A 175-head herd can see theoretical profit gains of £19,300, but actual accounts show this figure can exceed £50,000.

Additionally, Winters emphasizes the sustainable nature of genomic testing. Enhancing herd health and productivity helps farmers avoid recurring costs associated with other improvement strategies, ensuring long-term viability and a competitive edge for UK dairy farms.

Precision Breeding Through Genomic Insights: Revolutionizing Herd Management and Breeding Strategies

As genomic testing gains traction, its implications for herd management are profound. With 20% of the recorded herd currently undergoing tests, which is expected to rise, dairy farmers recognize the potential within their livestock’s DNA. This shift highlights the industry’s evolution towards data-driven decision-making in animal husbandry, with genomic insights becoming a cornerstone of successful herd management strategies.

Genotyping not only clarifies lineage but also opens avenues for targeted genetic improvements. By identifying the exact genetic makeup of heifers, farmers can make informed decisions, enhancing traits such as milk production, health, and fertility. This precision breeding minimizes the risk of inbreeding. It ensures that the most viable and productive animals are chosen as replacements.

The financial benefits of genomic testing are evident. Benchmarking herds using tools like the AHDB’s Herd Genetic Report allows farmers to understand the impact of their genetic strategies on profitability. The industry benefits from increased efficiency and productivity as the national herd shifts toward higher genetic merits.

Genomic testing extends beyond Holstein Friesians to Channel Island breeds and Ayrshires, showing its broad applicability. This comprehensive approach to herd improvement underscores the AHDB’s commitment to leveraging cutting-edge biotechnologies to drive progress in dairy farming.

In conclusion, genomic testing is reshaping dairy farming in the UK. By embracing these technologies, farmers enhance the genetic potential of their herds, securing a more profitable and sustainable future. Genomic insights will remain a cornerstone of successful herd management strategies as the industry evolves.

Harnessing the AHDB’s Herd Genetic Report: A Strategic Blueprint for Elevating Genetic Potential and Ensuring Herd Sustainability

Farmers aiming to optimize their herd’s genetic potential should take full advantage of the AHDB’s Herd Genetic Report. This invaluable resource allows producers to benchmark their herd’s Profitable Lifetime Index (£PLI) against industry standards and peers. Farmers can gain critical insights into their herd’s genetic strengths and weaknesses, enabling more informed and strategic decisions regarding breeding and herd management. Accurately tracking and measuring genetic progress is essential for maintaining competitiveness and ensuring dairy operations’ long-term sustainability and profitability.

The Bottom Line

The transformative impact of genomic testing on the UK’s dairy herds is evident. Producers leveraging genotyping for heifers see remarkable gains in their Profitable Lifetime Index (£PLI), leading to significant financial rewards. This underscores the crucial role of genetic advancement, widening the gap between engaged and less engaged herds and inspiring a new era of progress in the industry.

Accurate breeding records become essential with rising genomic testing across various breeds and corrections of misidentified animals. Integrating genomic insights into herd management allows producers with better genetic information to achieve superior outcomes. AHDB’s analysis reveals a shift from a sole focus on milk production to a balanced focus on health, management, and fertility, setting a new standard for future strategies and ensuring the reliability of genomic testing.

Every dairy producer should utilize tools like the AHDB’s Herd Genetic Report to benchmark and enhance their herd’s genetic potential. Embracing genomic testing is an investment in long-term success, revolutionizing herd management for profitability and sustainability in a competitive dairy market.

Key Takeaways:

Genomic testing significantly elevates the genetic merit of dairy herds, leading to more pronounced differences between the top-performing and bottom-performing herds.
Producers who genotyped 75-100% of their dairy heifers achieved an average Profitable Lifetime Index (£PLI) of £430, while those testing only 0-25% had a PLI of £237.
Improved genetics can translate to a theoretical value difference of approximately £19,300 for a typical 175-head herd, with actual margins showing an advantage exceeding £50,000.
The uptick in genomic testing is notable, with around 100,000 dairy heifer calves tested, representing 20% of the recorded herd, expected to rise to 35% by year’s end.
A significant number of animals have been misidentified, indicating potential inaccuracies in breeding strategies that could affect both quality and inbreeding rates.

Summary:

The UK’s Agriculture and Horticulture Development Board (AHDB) has identified a significant gap in the Profitable Lifetime Index (PLI) between herds engaged in genomic testing and those not. This highlights the financial benefits of genomic testing for the UK’s dairy herd, which can significantly boost profitability and sustainability. Improving genetics through genomic testing is a cost-effective and sustainable way to make long-term improvements to any herd. The £193 PLI difference translates to an estimated £19,300 profit potential for a 175-head herd, but real-world accounts show the benefits can exceed £50,000. Precision breeding through genomic insights is revolutionizing herd management and breeding strategies, with 20% of the recorded herd currently undergoing tests. Genotyping not only clarifies lineage but also opens avenues for targeted genetic improvements, enhancing traits such as milk production, health, and fertility.

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Categories : Genomics

Leveraging Genomic Selection and New Technologies for Livestock Improvement: Opportunities and Challenges

Wednesday, May 1st, 2024

Explore how genomic selection is revolutionizing livestock improvement. Uncover the opportunities and challenges of new technologies in animal performance measurement.

Get ready to embark on a riveting journey that seamlessly blends science and nature. For over a century, genetic selection has continued to revolutionize the world of livestock breeding. By helping to enhance the productivity and prosperity of livestock populations, genetic selection has not just made a difference but has been a game changer.

Even more impressive, the last decade has witnessed a whole new surge in progress. With the rapid adoption of genomic selection across the globe, the pace of genetic improvement in certain populations has literally doubled. It is truly heartening to see how advancements in science can have such a profound and beneficial impact on our everyday life, particularly, our food supply.

“The adoption of genomic selection within the last decade has doubled the rate of genetic progress in some populations.”

As you continue to read this article, you will delve deeper into the intriguing world of genetic selection. You’ll also see how modern technology is shaping this landscape, and the potential challenges posed in the path of progress.

From Traditional to Genomic: Doubling the Rate of Gain in Livestock

Genetic selection has proven to be a darling in the quest to improve livestock populations for a long time, given its effectiveness in achieving long-term improvement. But that’s not all. You might find it of interest to know that in the past decade, the advent of genomic selection has greatly accelerated this progress. Yes, you read it right. Genomic selection has effectively doubled the rate of gain in some populations, thereby greatly enhancing livestock productivity and health.

What does this mean for livestock breeders and the whole industry? Well, through a twist of improved accuracy in genetic prediction for younger animals, genomic selection has not only had an impact on the growth of the livestock population but also managed to drastically decrease the generation interval. This in turn quickly propels genetic progress in dairy cattle, a significant achievement for an industry that heavily relies on genetic improvement for productivity.

You’re probably wondering how this mirrors across different livestock industries. Interestingly, while the beef industry is expected to bag modest genetic gains from genomic selection, the structure of the dairy cattle breeding industry has been forecasted to align with those of the poultry and swine industries.

Genomic selection has also demonstrated massive potential on the maternal side, leading to significant genetic gains. With the advanced technique of genotyping elite bull dams and the screening of large numbers of bull calves with markers, the intensity of selection has noticeably increased. This innovation aids the realization of genetic gains, a milestone that traditional selection methods might not have clinched.

Yet, like all other processes, genomic selection in dairy cattle breeding programs also comes with its challenges. Among these is that the minimization of the generation interval may inadvertently increase the rate of inbreeding per year. Nevertheless, the advantages brought about by genomic selection prove to be worthy. In particular, by enhancing the precision of estimated genetic merit for young animals, reducing generation intervals, and increasing selection intensity, genomic selection has significantly bolstered genetic gains.

The Intricacies of Breeding Programs and Genomic Evaluations

In a nutshell, breeding programs are a scientific endeavor aimed at identifying and propagating genetically superior parents for the successive generations of livestock. This complex process is typically orchestrated through a multifaceted index. This index ingeniously amalgamates information on various economically significant traits, transforming abstract concepts into a single, comparable numeric value. Picture this index as a translator, unmasking the complex language of genetics into understandable, practical information.

In the United States, the beating heart that supplies life to this intricate system is data. This data is meticulously harvested through the National Dairy Herd Improvement Program, a historic initiative that boasts a legacy of over a century. This invaluable repository of animal performance stats, pedigree records, and genotype data serves as the foundation for calculating genomic evaluations. These evaluations play a pivotal role in the breeding game, allowing for the ranking and selection of animals, thereby propelling the cycle of genetic enhancement ever onward.

However, an important note to bear in mind is that genetics isn’t the whole story. “Consider the concept of genetic potential not as an isolated aspect but rather akin to a seed. A seed holds immense potential within its tiny confines but requires a supportive environment to fully express its capabilities. Similarly, it’s paramount that animals are placed in suitable surroundings capable of nurturing their genetic potential”, you could say. The full realization of this potential is an orchestration, a duet between nature and nurture.

The Shift in Selection Index: From Yield Traits to Fertility, Health, and Fitness

As you’re aware, a significant shift has occurred in the net merit dollars (NM$) selection index over the years. Initially, the primary basis for selection was yield traits such as milk and fat content, as these traits brought direct economic benefits. However, as our understanding of these traits has evolved, there has been an increasing emphasis on traits related to fertility, health, and fitness.

This evolution reflects the broader recognition that sustainable livestock improvement goes beyond the quantity of yield. Rather, it incorporates factors that contribute to the animal’s overall well-being and sustainable productivity, such as health status and reproductive efficiency. Can you imagine the value of investing in an animal that can produce high quantities only for a short period due to health limitations, versus one that can consistently deliver optimum output over an extensive period because of superior health and fertility? It becomes clear that these traits significantly influence the long-term productivity and profitability of livestock operations.

However, as we know, there are challenges associated with this shift. Many of the new traits under consideration are harder to measure, require more resources, or entail changes to longstanding farm practices. For instance, evaluating an animal’s fertility or health status may require sophisticated screening tools and procedures. It might also necessitate a change in farmers’ routines and the adoption of new technologies for data collection and analysis. It can be burdensome and costly, but rest assured, it’s an investment that pays off in the long run.

The stakes are high, but so are the rewards of adapting to this transition. By focusing on a broader array of traits for genetic selection, we can breed animals that not only contribute to the economic output of farms but also enhance sustainability, improve animal welfare, and pave the way for the future growth and development of our livestock industry.

Joining Forces for Advanced Genomic Evaluations

Imagine, if you will, the backbone of significant scientific advancements. Can you see it? Yes, it’s collaboration. In the world of livestock genomics, the tale is just as you’d expect. Two key players have taken center stage – The Agricultural Research Service of the US Department of Agriculture and the Council on Dairy Cattle Breeding. United in purpose, they’ve embarked on a mission to create and present state-of-the-art genomic evaluations to an industry that is as essential as it is diverse – our beloved dairy industry.

This strategic alliance, it turns out, has been instrumental in facilitating the smooth and steady progression of genetic selection methods. What does this mean for the dairy industry? Simply put, it has the potential to leverage advancements in genetics for achieving long-term improvements in livestock. This leap forward can not only revolutionalize the dairy industry but also have lasting impact on our economy and dietary habits. So, here’s to the power of partnerships driving the future of genomic selection!

The Evolution and Challenges of the Net Merit Dollars Index

Picture this: an expanding universe of genetic qualities in the dairy industry that undergoes constant refinement. This evolving landscape is the narrative of the Net Merit Dollars (NM$) selection index. Born in 1926 with only two foundational traits—milk and fat yield—this particular index has since multiplied, reaching a stunning cluster of 36 individual traits in its recent 2018 update. Isn’t it amazing how dramatically things can change?

The NM$ index positions itself as the industry’s leading star, selecting and marketing most of today’s breeding stock. Significantly, the past century has seen a perceptible shift within the index, as traits once launched into emphasis, such as yield traits, have transitioned towards fertile, healthy, and fit traits.

But hold on! While the power of the NM$ index is indeed fascinating, it’s also accompanied by considerable challenges. The biggest obstacle? Updating and managing this high-powered index. It involves diligently estimating diverse values and mindfully tweaking the index – a task that, sure enough, often results in extensive debates among stakeholders regarding which traits should stay, go, or receive a new weight. As you can imagine, achieving consensus is no easy feat.

As we advance, one thing’s for sure: the NM$ index will continue to evolve, adapting swiftly to the needs and priorities of the ever-changing dairy industry. But with each revolution around the sun, we can also expect to grapple with new challenges brought on by technological advancements and changes in industry standards.

Exploring Opportunities and Challenges of New Technologies

Like any forward-looking industry, dairy breeding is embarking on prospects beyond the traditional methods. A growing trend is the adoption of sensor-based systems that continually monitor elements such as the farm environment, individual animal performance, and intricate milk composition. You might be excited to know that our urge to understand the life of our livestock doesn’t just stop at genomics. We yearn to grasp every detail about the environment in which these animals thrive. This includes understanding their dietary habits, housing conditions, the milking systems we employ, and even the infectious and parasitic challenges they face every day.

However, you must be aware that emerging technologies inevitably come with a catch—a series of challenges. These range from a lack of standardization or validation to the necessity for high-speed internet connections, increased computational requirements, and interpretations that are too often not supported by direct observations of biological phenomena.

Each of these hurdles, though seemingly daunting, carries with it the potential for progress, growth, and a better understanding of the complex world of dairy breeding.

In our commitment to keeping you abreast, this article will outline how U.S. selection objectives are developed, along with the opportunities and challenges that new technologies introduce to recording and measuring animal performance. So, strap in and let’s navigate these seemingly complex paths of genetic improvement together.

Emerging Role of Sensor-Based Systems in Livestock Breeding

Imagine a farm where not a single aspect of an animal’s life goes unmonitored or unnoticed. From feeding patterns to milking cycles, every detail about the animal’s life and behavior is meticulously tracked. This can be the reality with sensor-based systems, which are gaining ground in the livestock industry. These systems collect continuous, real-time data on the farm environment, as well as individual animal performance and detailed milk composition, playing a pivotal role in the expression of an animal’s genetic potential.

Sensor-based systems essentially pave the way for a more detailed understanding of the environment in which livestock perform. Insight into feeding schedules, housing conditions, milking systems, and even infectious and parasitic load all become accessible with these advanced technologies. Such a wealth of data empowers breeders to make better informed decisions, optimizing animal well-being and productivity at the same time.

However, as with any emergent technology, these sensor-based systems come with their own set of hurdles. For one, there’s an urgent need for standardization and validation of the collected data. Without it, comparing data across different systems or farms can prove to be a veritable challenge. Furthermore, these advanced systems typically require high-speed internet and robust computational power for efficient operation.

There’s more. As the data collected by these systems can sometimes provide overwhelming and complex insights, interpretations often prove to be difficult without a direct observation or understanding of the underlying biological phenomena. In other words, having hands on the farm still plays a crucial role in making sense of this high-tech data.

Despite the issues, the potential benefits of incorporating sensor-based systems in livestock breeding are too significant to be ignored. Your next generation of animals could be healthier, more productive, and better adapted to their environments, thanks to this technology. Painstaking measurement and recording of traits, a process that was once costly and time-consuming, could become a thing of the past. The future of livestock performance measurement is digital, and it’s time to adapt or be left behind.

Contending with Challenges: Standardization and Validation of New Technologies

As you delve deeper into the use of modern technologies in livestock breeding, it’s worth noting the hurdles that are part and parcel of advancements. One recurrent issue is the lack of standardization among different technologies. Implementing newer technologies often means needing a standard protocol to ensure data comparability and corroboration. However, this is hindered by diverging sets of SNP used between and within countries, different prediction equations, and varying marker-environment interactions.

Moreover, validation becomes another piece of the puzzle. We might be inclined to take at face value the data yielded by these technologies, but consider this: it needs to be accurate and reliable for it to be of any real use. To confirm this, a cross-validation approach is beneficially. But what does that entail? It involves using validation bulls, and though this method is not novel, its use certainly enhances confidence in the interpretation of the data obtained.

Beyond that, we can’t overlook the additional challenges. These technologies often come with increased computational requirements and demand for high-speed internet connections. In locations where these requisites are not met, the application of such advancements could be severely resisted.

Still, your understanding of the challenge is not complete without acknowledging the most crucial aspect. Application of these modern technologies often relies on measurements that are not backed by direct biological observations. You may question the significance of such data, and rightfully so. The technologies might provide continuous and detailed information, but unless it’s supported by direct observation, the sustainability of such systems is debatable.

But, as the saying goes, ‘where there is a will, there’s a way’. Hence, the focus should be on adequate protocols to guide data sharing and user-friendly interfaces that facilitate easy understanding. According to Goddard, 2008, developed countries have been successful in routinely incorporating this genomic information into international comparisons among proven sires contributing to genetic progress. But the potential doesn’t end there. Key collaborations between developed and developing countries could further enhance the accuracy of data imputation.

As an illustration, let’s look at the success of the ADGG (Agriculture Dairy Genetic Gain) in East Africa. Here, information and communication technology (ICT) has been harnessed to improve breeding practices. In such models of successful implementation, we find the assurance that these challenges can be successfully managed and overcome.

Keeping in mind the aim of livestock breeding, which is the long-term improvement of livestock populations, it’s evident that new technologies play a crucial role. While challenges exist, the profession’s resilience in seeking solution-based advancements has led to systems like the net merit dollars (NM$) selection index, which utilizes these technologies to make strategic decisions.

The final question you need to answer is this – Are you ready to embrace the future and its possibilities in the exciting field of livestock breeding?

The Bottom Line

As you navigate the intricate landscape of livestock breeding, keep in mind the exciting possibilities genomic selection offers. With its ability to double the rate of gain and drastically evolve our selection indices, it can unlock numerous advantages. Not without its challenges, as standardization, validation, and technological requirements pose hurdles to overcome. Yet, with collaborative efforts from organizations such as the Agriculture Research Service or the Council on Dairy Cattle Breeding, and the broader adoption of sensor-based technologies, unprecedented progress can be made. Stay tuned to the latest developments, as this exciting field continually evolves and shapes the livestock industry’s bright future.

Summary: Genetic selection has been a significant advancement in the livestock breeding industry for over a century, enhancing productivity and prosperity. In the last decade, genomic selection has accelerated this progress, doubling the rate of genetic progress in certain populations, particularly in dairy cattle. This has led to significant improvements in livestock productivity and health, particularly in dairy cattle, which heavily relies on genetic improvement for productivity.Genomic selection has also demonstrated massive potential on the maternal side, leading to significant genetic gains. The advanced technique of genotyping elite bull dams and screening large numbers of bull calves with markers has increased the intensity of selection, aiding the realization of genetic gains that traditional selection methods might not have achieved. However, genomic selection in dairy cattle breeding programs also comes with challenges, such as the minimization of the generation interval potentially increasing the rate of inbreeding per year.Breeding programs are scientific endeavors aimed at identifying and propagating genetically superior parents for successive generations of livestock. This complex process is typically orchestrated through a multifaceted index, which ingeniously amalgamates information on various economically significant traits into a single, comparable numeric value. The National Dairy Herd Improvement Program provides vital data for this intricate system, which serves as the foundation for calculating genomic evaluations.The Agricultural Research Service of the US Department of Agriculture and the Council on Dairy Cattle Breeding have joined forces to create and present state-of-the-art genomic evaluations to the dairy industry, revolutionizing the dairy industry and having lasting impacts on the economy and dietary habits.

Categories : Genomics

Unlocking the Potential of Genomic Strategies in Alternative Dairy Production: An Insightful Guide

Sunday, April 28th, 2024

Discover how genomic strategies can revolutionize alternative dairy production. Dive into our insightful guide and unlock the potential of this cutting-edge technology.

Have you ever wondered about the future of dairy? The intricate science of genomics and its potential applications may be the game-changer that the dairy industry needs. As consumers grow more conscious of ethical animal treatment and environmental sustainability, it’s time to delve into a sustainable alternative: genomics for alternative dairy production.

The future may appear very different to the dairy landscape we see today, as the science of genomics holds exceptional promise. In this article, we’ll explore the genomic strategies that are paving the way for alternative dairy production systems, and how these scientific advancements can promote both productivity and welfare in the dairy sector.

Understanding genomics and its potential in alternative dairy production systems

Delving deeper into the realm of genomics, you’ll find that it stands as a game-changer for various agricultural sectors, including dairy farming. Notably, genomic strategies are rapidly gaining traction in the arena of alternative dairy production systems.

The reason is simple: Genomics, quite similar to a road map, empowers us with the ability to decode the genetic fabric of organisms – in this case, dairy cattle. By looking at animals at a molecular level, we can better understand and harness their specific traits to meet varying needs, be it increased milk yield or better resilience against diseases.

For example, the work of Hayes, B.J., Bowman, P.J., Chamberlain, A.J., and Goddard, M.E in 2009 highlighted how genomic selection in dairy cattle has led to significant progress and concurrently posed unique challenges. Their study spotlighted the potential of genomics to aid in dairy cattle breeding decisions, enabling more accurate selection of superior individuals at an early age than conventional methods.

Genomics doesn’t stop at dairy cattle. There is compelling evidence from multiple realms of agriculture that substantiates the potential of genomic selection. It ripples across crop improvement studies and even addresses climate change challenges. High-throughput genomic technology, for instance, has identified potential target genes for mitigating climate change impacts and provided insights into grain yield improvement.

Imagine if we could replicate this success with dairy farms. By using genomic strategies, we could potentially optimize milk production, improve cattle’s resilience against varying stress conditions, and even navigate the challenges posed by climate change. The scope is indeed comprehensive and holds immense untapped potential.

However, like any other advanced science, genomics in alternative dairy production systems isn’t devoid of challenges. These can range from data management and analysis, the dilemma of integrating new information into existing breeding programs, to the ethical considerations of genomic manipulation. But, with each challenge comes an opportunity for solutions that promise a sustainable, productive, and resilient future for dairy farming.

It’s time to foster a comprehensive understanding of genomics and its application in alternative dairy production systems. Together, we can navigate the evolving landscape of dairy farming, making it smarter, better, and more sustainable for generations to come.

The role of genomics in creating healthier, more productive dairy cows in alternative production systems

Let’s dive a little deeper into how genomics is reshaping the future of alternative dairy production systems. After all, who wouldn’t want healthier and more productive cows by leveraging the powers of genomics?

Genomics revolutionizes traditional breeding methods by capitalizing on genomic data to inform faster, more precisely targeted selection for desirable traits. This innovative approach, known as Genomic Selection (GS), has shown immense potential in the acceleration of livestock improvement, as argued by Meuwissen T., Hayes B., and Goddard M in their study.

Known as a revolutionary tool, genomic selection focuses on the entire genome rather than just individual genes. High-throughput genomic technology facilitates identifying promising breeding germplasms, hence achieving notable gains in dairy production quality and efficiency.

How exactly does it work? Let’s break it down. Genomic selection uses the agricultural economic traits of maize, cattle, and pig populations, among others, to predict the genomic merit of a given animal based on its DNA profile. Statistical models are developed based on the presence of specific gene markers, with these markers being traced to particular traits such as milk production, growth rates, resistance to disease, and others. Sounds exciting, right?

Thus, the accuracy of Genomic Selection depends on several factors including the size of the reference population, the effect of QTL, and the heritability of the trait. However, as Hayes B.J., Bowman P.J., Chamberlain A.J., and Goddard M.E. point out in their research, continuous improvement in statistical models leveraging genomic information are critical to the effectiveness of GS-enabled breeding programs.

Notably, apart from enhancing productivity, genomics can help in modeling crop yield for rapid selection under changing environmental conditions, consequently aiding responses to climate change. Techniques like GS are now used for crop improvement, demonstrating the broad potential of genomics in the agricultural sector.

Enhanced Breeding Programs: Genomic information allows for more precise selection of desirable traits such as milk yield, disease resistance, longevity, and fertility. This precision breeding helps in developing herds that are not only more productive but also better suited to the specific conditions of organic and low-input farming systems.
Improved Animal Health and Welfare: Genomics can identify genetic markers linked to health and robustness, enabling farmers to select animals with better natural disease resistance and adaptability to stress. This is particularly important in alternative systems where the use of antibiotics and other interventions is restricted.
Sustainability and Environmental Impact: By enabling the selection of cows with higher feed efficiency, genomics can reduce the carbon footprint of dairy farming. Efficient cows convert feed into milk more effectively, thereby requiring less feed and producing less waste.

To wrap it up, the big picture is this: genomics could redefine dairy production highlights the promise and potential for alternative systems. The sky is truly the limit when we combine science and agriculture in such transformative ways.

How genomics can support sustainable and ethical dairy production in alternative systems

You might be wondering how exactly genomics can contribute to sustainable and ethical dairy production in alternative systems. Well, believe it or not, your breakfast milk may very well be the product of cutting-edge genomic technology.

A key factor in this equation is Genomic Selection (GS). GS, a breakthrough methodology in the field of crop improvement, has now proven its worth within the realm of dairy production. It works by identifying promising breeding germplasm with desirable traits for selection, ultimately boosting genetic gain in breeding programs. In other words, it can improve the inherent qualities of our cattle, the way traditional breeding has done for our crops.

What’s more, GS can greatly enhance food and nutritional security, a cornerstone of any truly sustainable agriculturesystem. By facilitating rapid selection under changing environmental conditions, it bolsters the resilience and adaptability of our dairy production herds.

Can you imagine having climate change-ready cows due to genomic selection? Although that might sound fantastical, genomics is already unveiling its tremendous potential in climate-proofing our agricultural practices. As increasingly erratic weather patterns and fluctuating temperatures punctuate our seasons, livestock resilient to these changes are beyond desirable — they’re critical.

In fact, genomics approaches have led to the identification of target genes capable of mitigating climate change effects. These are to cattle what the mutant loci associated with crop yield under varying stress conditions are to our harvests. The ability to identify such key features could be an invaluable tool in the race against global warming.

Beyond the ecological advantages, ethical dairy production is another arena where genomics can lend a helping hand. By being capable of pinpointing genes associated with animal health and welfare, genomic technology can aid in creating healthier, more productive dairy cows. Consider the advantages of cows with improved health and disease resistance, and the associated decrease in antibiotic use and improved animal welfare. It’s a win for us, the dairy farmers, and – most importantly – the cows themselves.

Practical Applications of Genomic Strategies

Trait Selection: Farmers can use genomic testing to select for specific traits that are crucial for the success of their farming model. For example, in organic dairy farming, traits like hoof health and udder health are highly desirable due to the reliance on pasture-based systems and limited use of chemical treatments.
Preservation of Genetic Diversity: Genomic tools can help manage genetic diversity within a herd, ensuring a healthy gene pool. This is essential for the resilience of the farm ecosystem and helps maintain productivity and adaptability over generations.
Customized Nutrition Plans: By understanding the genetic makeup of their cattle, farmers can tailor nutritional regimens that maximize health and productivity while minimizing environmental impact.

The Bottom Line

Embracing the power of genomic strategies truly signifies a potential revolution within alternative dairy production systems. It enables these systems not only to augment their productivity but also to foster a sustainable environment for future generations. By strategically adopting genomic technologies, farmers are empowered to not only enhance the health and lifespans of their livestock but also increment their yield considerably, causing a decline in their ecological footprint. As we stand at the cusp of an era brimming with advancements in genomics, it is set to become an indispensable component for sustainable agriculture. It remains the beacon of hope, illuminating paths to innovative solutions for age-old conundrums and thus, anchors the continuity and growth of the dairy sector amidst shifting terrains.

Categories : Genetics, Genomics

Genomics and Reproductive Performance

Thursday, September 12th, 2019

For decades dairy production systems have faced the challenge of attaining adequate fertility levels. Insufficient reproductive performance will result on reductions on the proportion of cows at their peak production period, increments in insemination costs, and delayed genetic progress. Moreover, impaired fertility is one of the most frequent reasons for culling and increased days open are associated with a greater risk of death or culling in the subsequent lactation.

An historical trend for declining dairy fertility has likely resulted from high prevalence of anovulation, reduced fertilization, and embryonic survival. Contributing factors to this condition include changes in cow physiology associated with greater milk production, challenges for optimal nutritional management, housing, increased herd size, reduced estrus expression, and current genetic makeup. In addition, the level of inbreeding has increased in the Holstein population, with present average values greater than 5%.

An uneventful and timely calving is a desired trait for improved fertility of dairy cows.

Relevant to this problem, starting in the sixties, breeding programs selecting for milk production have been very successful and current trends indicate increments on milk yield per cow of 1 to 2% per year. However, some unfavorable genetic correlations between production and other traits may exist, resulting in undesirable side effects, such as a higher risk for behavioral, physiological, and immunological problems.

However, although these negative associations between production and fertility traits are probable, it is possible to select for improved milk yield and fitness traits, including fertility. This fact is evidenced by increments in reproductive performance occurring in Holsteins after the implementation of genetic evaluations for daughter pregnancy rate (DPR) in 2003. The trend for DPR indicate a partial recovery in dairy fertility, despite no apparent slowing down in the rate of increase of milk production per cow.

Genetic Selection and Improved Fertility: It’s Not That Simple

Fertility traits are multi-factorial in nature, which makes it difficult to determine the degree of involvement of genetics on reproductive outcomes. It has been established that reproductive traits are largely influenced by the environment and may be affected by multiple genes with small individual effects. Consequently, genetic progress for fertility, by way of conventional breeding strategies is hindered by low heritability, which represents the proportion of visible variation attributable to genetic differences among animals.

From the biological perspective, genetic variation affecting fertility may be directly involved in the physiology of reproductive processes. However, genetics may also determine, to some extent, the behavior of other related traits that have an impact on fertility. Among others, these comprise factors such as the ability to maintain adequate body condition and feed intake during the transition period, the potential for adequate immune responses resulting in adequate health, and the capacity to retain early pregnancy.

Some significant obstacles can be anticipated when the logistics of selection for fertility are planned. High costs of reliable data collection, the long time period required for validation, and biased phenotypes, such as non-return rates and DPR, are a few of these challenges. Adding to these limitations, the influence of factors unrelated to fertility, such as breeding policy and voluntary waiting period, is a constant difficulty for precise reproductive estimations.

A New Hope: Genomic Tools are Here to Stay

Although small heritabilities for reproductive performance traits have been reported, when more objective measures of fertility were evaluated (interval to first ovulation, anovulation, and pregnancy loss), heritabilities were moderate to high (0.15 to 0.40). For reproductive disorders, such as metritis and retained placenta, heritability estimates were close to 0.20. Notably, genetic variation is manifest when DPR is considered, as daughters of the highest and lowest sires for DPR differ by 29 days open per lactation.

With the arrival of low cost genotyping, which is the ability to read the DNA, the use of marker analysis (single nucleotide polymorphisms; SNP) in the evaluation of dairy cattle genetics has become a reality. The use of genomic analyses allows for estimation of breeding values at birth, which reduces the costs of proving bulls and increases the genetic gain because of shorter generation intervals. In addition, genotyping platforms commercially available from several companies have become widely used in research, as well as at the farm level, where genotyping of females is gaining momentum.

As with genetic evaluations, genomic selection has extended to multiple traits of economic interest, including more specific health problems. In the US, indirect health predictions are available from the Council on Dairy Cattle Breeding and recent data indicate that these traits result in genetic improvement for resistance to adverse health events. Producer-recorded health events have been successfully used to identify genetic differences between individuals regarding susceptibility to common health disorders including retained placenta, metritis, displaced abomasum, ketosis, lameness, and mastitis.

Matching Fertility and Genomics?

Specific reproductive traits that are currently evaluated by genomic analyses in the US include daughter pregnancy rate, sire calving ease, daughter calving ease, sire stillbirth rate, daughter stillbirth rate, heifer conception rate, and cow conception rate.

New research exploring genomic variation related to novel fertility traits is in progress. As a result, multiple genomic regions associated with variation in cattle reproductive traits have been mapped. More recently, genome-wide association studies (GWAS) performed with thousands of SNP markers have facilitated the resolution of associated regions and the discovery of candidate genes.

Interestingly, genomic markers have been identified for many reproductive traits including ovulation rate, pregnancy rate, DPR, non-return rate, and estrus intensity. Genetic variation has also been identified for gestation length, dystocia and stillbirth, and postpartum fertility. In addition, genomic analyses have offered the capability for locating lethal recessive genes affecting fertility outcomes. As an example, five recessive defects on fertility were recently identified by examining haplotypes that had a high population frequency but were never homozygous. These lethal effects may result in conception, gestation, and stillbirth losses.

As indicated previously, some physiological measures of fertility, such as resumption of ovarian cyclicity, have moderate heritabilities. What is interesting is that cows resuming estrous cyclicity soon after calving are more likely to show estrus and to become pregnant in a timely manner. Therefore, decomposing aggregate reproductive phenotypes into their detailed components could result into an effective tool for selection. For example, calving interval could be decomposed into several reproductive components such as the postpartum interval to commencement of estrus cyclicity, expression of estrus, conception, maintenance of pregnancy, and gestation length.

Presently, a major goal for advancing in genomic selection for fertility is the collection of high numbers of accurate fertility phenotypes associated with the corresponding genotypes, coupled to large scale evaluations of the association between direct measures of fertility. These fertility measures include uterine health, resumption of postpartum ovulation, detection of estrus, pregnancy per A.I., and maintenance of pregnancy. Collecting accurate data represents another challenge and potential strategies may include using DHI resources and data recorded within on-farm herd management software programs.

Finally, selection for traits with low heritabilities could be integrated into new reproductive technologies, such as in vitro fertilization (IVF) and embryo transplant, that allow for higher rates of genetic improvement by increasing the reproduction of superior females. It is reported this strategy could increase genetic gain by 10 to 20% compared with traditional breeding schemes.

Our Research Effort

Our team of researchers from multiple United States institutions was awarded a 5-year grant to explore genomic variation associated with reproductive traits in dairy cattle (Genomic Selection for Improved Fertility of Dairy Cows with Emphases on Cyclicity and Pregnancy; Grant no. 2013-68004-20361 from the USDA NIFA). The overall objective was to develop a fertility database with genotypes and phenotypes based on objective and direct measures of fertility in Holstein cows. The subsequent goal was to identify SNPs and haplotypes significantly associated with fertility traits by use of genome-wide analyses and to consider this information to obtain genomic-estimated breeding values that can be applied in selection of dairy cattle for improved fertility.

Consequently, our approach was to test a significant number of cows (approximately 12,000 individuals from 7 states in the USA) that were enrolled at calving and monitored weekly on farm until pregnancy confirmation. The evaluations included uterine health, metabolic status during transition, resumption of postpartum ovulation, estrus, pregnancy per AI, and pregnancy loss, under different management practices and environments.

Our initial analyses indicated that overall, 71% of the population resumed ovarian cyclicity by 50 DIM. Conception rates at first and second A.I. were 32.8% and 33.7%, respectively. Pregnancy loss between 32 and 60 days after A.I. were 10% and 8.7% for first and second A.I, respectively. Overall, 19.7% and 4% of the population was sold or died before 305 DIM.

Using this population, a reproductive index (RI) calculating the predicted probability of pregnancy at first A.I. was developed. The RI considered logistic regression models that included cow-level variables that were thought to have a genetic component (diseases, anovulation, BCS, milk yield, etc.). Interestingly, when the index from this population of cows was categorized as low, medium, and high, there was a consistent agreement between categories of the predicted RI and the measures of fertility collected from dairy cows.

By means of the developed RI, our population of cows was ranked as highly-fertile pregnant (850 cows) and a lowly-fertile non-pregnant (1,750 cows) for subsequent DNA analysis. At this point, preliminary genome-wide analyses with our high- and low-fertility subpopulations are confirming that there is potential for genomic selection in the traits of interest. We are evaluating genomic variation for dichotomous variables (uterine disease, anovulation, detection of estrus, pregnancy per AI, pregnancy loss) and for a continuous variable (predicted probability of pregnancy based on the RI, services per conception) to maximize opportunities for prediction accuracy.

Our initial analyses have estimated the heritability and the marker effects for lameness, metritis, mastitis, resumption of cyclicity, pregnancy after first A.I., and the RI. Significant markers have been associated with genes in chromosomal regions previously reported as contributing to variation in fertility and health traits in dairy cattle. In addition, causal associations among multiple traits, including retained fetal membranes, metritis, clinical endometritis, resumption of cyclicity by 50 days in milk, pregnancy after first A.I., and lameness early in lactation were investigated. Finally, selection models using significant markers are going through checking and further validation. This large scale evaluation will eventually be combined with current selection traits to further refine genomic selection of cattle by dairy producers.

Conclusions

Fertility is a key component of modern dairy production systems. However, a trend for declining dairy fertility has been evident in diverse production systems. Although fertility traits are strongly influenced by the environment, there is evidence for genotypic variation providing opportunity for selection, as suggested by a partial recovery in dairy fertility since the incorporation of daughter pregnancy rate into bull genetic evaluations. There are current efforts placed in collection of high numbers of accurate fertility phenotypes associated with the corresponding genotypes, coupled with large scale evaluations of the association between direct measures of fertility (uterine health, resumption of postpartum ovulation, detection of estrus, pregnancy per A.I., and maintenance of pregnancy) and genomic variation on dairy cows under different management practices and environments. As the cost of genotyping is decreasing, the number of animals subject to genomic evaluations is expected to continue increasing. If adequate markers and causal variants for fertility traits are identified, molecular breeding value could be estimated for each trait enabling selection to proceed population-wide.

Source: dairy-cattle.extension.org

Categories : Genomics

Genomic Selection Has Changed Dairy Sire Selection

Monday, September 9th, 2019

Dramatic changes have occurred in dairy sire selection practices in recent years. These changes have been facilitated by the sequencing of the bovine genome, which led to the discovery of thousands of DNA markers, known as single nucleotide polymorphisms or SNPs. The development of predicted breeding values based on marker data alone (Meuwissen et al., 2001), coupled with a reduction in the cost of genotyping, has allowed for accurate genomic selection of dairy sires by AI centers. As described by Hayes et al. (2009) genomic selection refers to selection decisions based on genomic breeding values (GEBV). Before continuing the discussion on genomic selection, however, it is important to understand traditional progeny testing. Historically, progeny testing was key to genetic improvement of dairy cattle (Sattler, 2013), via identification of the best bulls for widespread use and as sires of bulls for the next generation.

Progeny Testing

As described by Sattler (2013), progeny testing has a three-fold purpose to: 1) provide information for AI sire selection decisions, 2) provide a critical mass of data needed for effective genetic evaluations, and 3) develop AI bulls with accurate evaluations for wide scale AI use. Elite cows were identified, mated to the best sires, and sons were included in a progeny test program to identify, based on daughter performance records, which bulls inherited desirable genes. Progeny test data were the basis for a bull to graduate from a young sire to a proven sire, and have semen made available for widespread use by producers. Furthermore, proven sires (sires with progeny) have long been used as sires of bulls for the next generation. Although progeny testing has been a successful AI center management strategy, it takes more than 3 years, is very expensive, and limits the number of bulls evaluated (Sattler, 2013).

Genomic Selection

Currently, selecting dairy sires for use in AI has shifted from progeny testing to reliance on genomic predictions of daughter health, milk production, and fertility. With genomic selection, the sire and dam of a future sire (next generation) are selected on the basis of DNA marker profiles and mated soon after puberty, with the next generation sire being marker-analyzed for desirable (and undesirable) traits soon after birth, or as an in vitro fertilization (IVF) embryo (Dalton et al., 2017). According to Sattler (2013) this allows AI companies to “test tens of thousands” of bulls rather than a few thousand bulls through a traditional progeny testing program. In addition, rather than wait for progeny test results, today many bulls are used as sire fathers and are widely marketed based on genomic evaluations (Sattler, 2013).

Use of genomic markers has reduced the generation interval, defined as the average age of parents when their offspring are born. Both males and females are contributing to the reduced generation interval, as elite genomic heifers 6 to 8 months of age routinely undergo ultrasound-guided trans-vaginal follicular aspiration (commonly known as ovum pick-up or OPU), followed by in vitro fertilization (IVF) and embryo transfer (ET). According to Garcia-Ruiz et al. (2016) the generation interval of sires of bulls has decreased from approximately 7 to 2.5 years, while dams of bulls has decreased from 4 to 2.5 years. Furthermore, genomic selection has increased the rate of improvement in economically important traits such as daughter pregnancy rate (DPR), productive life (PL), and somatic cell score (SCS) (Garcia- Ruiz et al., 2016). Consequently, Amann and DeJarnette (2012) argue that producers should get more value from each pregnancy resulting from sperm produced by a young marker-selected sire than by a mature progeny-tested sire.

Genomic selection presents many hurdles for AI centers. Embryos or newborn calves with desirable genomic predictions have a much higher acquisition cost than a calf with a good pedigree only (Amann and DeJarnette, 2012). Many sires will be replaced by better bulls before their daughters complete their first lactation; however, young bulls produce 35 to 50% of the sperm of a mature sire (>5 years of age). Consequently, AI centers will require additional facilities (housing, isolation and quarantine, semen collection) to collect semen from nearly twice as many bulls to produce the same total number of marketable straws (Dalton et al., 2017).

An ongoing challenge for the dairy industry is maintenance of data collection infrastructure necessary to support genomic evaluations (Sattler, 2013). A common misconception is that genomics will replace DHIA milk testing. This is not true, as genomics is based on the relationship of the phenotype and genotype. Therefore, genomics requires accurate data collection to establish the reference population to calibrate genomic results and to continually update the reference population (National DHIA, 2011). The flow of data (including milk recording, type classification, and health traits) into the system is critical as the size of the reference population impacts the accuracy of genomic predictions. The Council on Dairy Cattle Breeding (CDCB) currently performs genetic evaluations, which were previously done by the USDA. In the event that progeny test programs were discontinued, the CDCB would be able to assure data continues to be acquired for use in genomic evaluations (Sattler, 2013).

Will progeny testing continue?

According to Sattler (2013) genomic evaluations provide more accurate genetic information on young bulls than what was previously available. Genomic evaluations have, in fact, replaced progeny testing in regard to information for key sire selection decisions. Consequently, AI companies have reduced progeny testing efforts by approximately 20%.

Although the percentage of semen sold from bulls without progeny data has risen from approximately 10% in 2008 to greater than 60% in 2018, progeny-tested sires remain in demand as they continue to compete favorably with young genomic bulls. This is likely a result of the critical mass of data generated via progeny test, which facilitates the accurate evaluation necessary for continued widespread use.

Genomic evaluations continue to be a work in progress, and increased accuracy of genomic evaluations will likely occur in the future (Sattler, 2013). Taken together with increased rates of genetic improvement, the competiveness of young genomic sires will likely improve. For the foreseeable future, though, progeny testing will likely continue to provide enough progeny-proven sires to satisfy market demand (Sattler, 2013).

Source: dairy-cattle.extension.org

Categories : Genomics

Can you really trust dairy genomics?

Thursday, September 27th, 2018

You’ve had the option to include dairy genomics in your genetic toolbelt for nearly ten years now. By now, fear of the unknown mystery surrounding genomics has faded. The progressive dairy industry accepts this as a new era in rapid genetic progress.

Yet, we don’t blame you if you wonder whether genomic-proven bulls are your best option, when many daughter-proven sires still offer a great genetic package. With that in mind, we look for answers in the real proof data on bulls across the entire AI industry.

What did we learn about genomics?

In graphs 1 and 2, our geneticist, Ashley Mikshowsky, analyzed proof figures on nearly 6,000 industry Holstein bulls released between January 2010 and April 2015, that currently have a daughter proof.

Graph 1 shows TPI trends. The blue line on top charts the average GTPI by initial genomic release date. The orange line shows the average August 2018 daughter proven TPI for those same bulls. The space between the two lines represents the average TPI change from initial genomic release to daughter proof.

A graph to show the average trend comparing the genomic proof versus daughter proof of industry Holstein bulls

As you can see on the left side of the graph, the bulls first released in January 2010 changed 177 TPI points from their genomic debut to their August 2018 daughter proof.

When you compare that to the newest daughter-proven bulls, including those released as genomic sires in April 2015, you see only a 105-point TPI difference from their initial genomic proof to their August 2018 daughter proof.

This means the stability in GTPI from genomic release until daughter proofs has improved by more than 70 TPI points! As a bonus, it’s clear to see that the genetic levels of bulls continue to rise!

The same goes for Net Merit $. Check out those results in Graph 2.

Industry bulls first released as genomic-proven sires in January 2010 dropped, on average, 150 NM$ from their first release until their August 2018 daughter proof. Whereas, the bulls first released as genomic sires in April 2015 only changed 89 NM$ from their initial release.

A graph to show the average trend comparing the genomic proof versus daughter proof for the Net Merit $ value of industry Holstein bulls

Looking at these results, your argument might be that dairy genomics are still inflated. Yes, and while that is true, the gap between genomic and daughter proofs has clearly improved since the start of genomics.

Let’s dig deeper into genomic proof stability

To understand from another angle, we took a look at the facts and figures in a different light.

Graph 3 and Graph 4 are based on proof data that our geneticist, Ashley, evaluated from 1,073 industry bulls released in 2014. She uses this age group because those bulls released in 2014 now have a daughter proof for production, health and conformation traits.

Graph 3 shows that the bulls released in 2014 changed an average of -110 TPI points from their initial release in 2014 to their daughter proof in August 2018.

Nearly 120 of these bulls have a daughter-proven TPI within just twenty points of their original genomic TPI. Only about 30 bulls from the entire group of 1,073 lost more than 300 TPI points – that’s less than 3%.

A histogram showing the skewed bell-shaped curve distribution of the amount of change in TPI points an average bull had from his genomic proof to daughter proof

We see the same trend for NM$. Graph 4 shows the average NM$ change and standard deviation of the same 1,073 industry bulls. The average sire released in 2014 changed -89 NM$ from their initial genomic proof in 2014 to their daughter proof in August 2018.

More than 160 of the 1073 bulls held steady within the small 20-point swing from genomic to daughter-proven NM$. Just 12 bulls changed more than 300 NM$.

A histogram showing the skewed bell-shaped curve distribution of the amount of change in Net Merit $ an average bull had from his genomics proof to daughter proof

What are your genetic options today?

Still debating whether your best bet is to use daughter-proven or genomic-proven sire groups? Take a look at the top 10 daughter-proven TPI sires available from Alta today.

AUGUST 2018 Top daughter-proven sires

Sire Code	Sire Name	Aug. 2018 TPI
11HO11478	AltaLEAF	2712
11HO11437	AltaSPRING	2663
11HO11531	AltaSABRE	2624
11HO11493	AltaHOTROD	2616
11HO11601	AltaHIFASHN	2588
11HO11523	AltaHOTSHOT	2576
11HO11499	AltaMEGLO	2572
11HO11508	AltaCONSUL	2547
11HO11440	AltaCORNELL	2528
11HO11537	AltaJANGO	2508
	Average	2594

AUGUST 2018 Top genomic-proven sires

Sire Code	Sire Name	Aug. 2018 TPI
11HO12115	AltaFORCE	2826
11HO12165	AltaBUGGY	2820
11HO12122	AltaSTARJACK	2818
11HO12169	AltaEMIRATES	2813
11HO12161	AltaAROLDIS	2793
11HO12124	AltaGOPRO	2791
11HO11778	AltaROBSON	2789
11HO12188	AltaCUCHILLO	2785
11HO12287	AltaEDIFY	2784
11HO12270	AltaMANOR	2783
	Average	2800

Currently, our top daughter-proven sires average a solid 2594 TPI. Yet, the top, readily-available genomic-proven group offers a much more enticing 2800 TPI average. That’s a 206-point advantage over the daughter-proven choices!

It’s inevitable that some bulls will gain points and some bulls will lose points between their genomic proof and daughter proof – the data show us that. Yet we can also see genomic proofs continue to improve. Keep in mind that your odds are essentially zero that every single bull atop the genomic-proven list would drop to rank lower than the current list of daughter-proven sires.

With your genetic choices, keep these points mind:

Genomic proofs are still slightly inflated. Yet, we see less change from genomic to daughter-proven TPI and NM$ over time because of model adjustments made along the way.
Despite an average drop for TPI and NM$ from a bull’s genomic to daughter proof, you will make much faster genetic progress using a group of genomic-proven sires than a group of daughter-proven sires.
Make sure the genetic progress you make is in the direction of your goals. Select a group of genomic-proven sires based on your farm’s customized genetic plan. Emphasize only on the production, health or conformation traits that matter most to you to boost your farm’s future progress and profitability.

Proof analysis and graphs provided by Ashley Mikshowsky, PEAK Geneticist

For a PDF of this article please Click HERE.

Categories : Genomics

Lessons learned from genomic breeding in New Zealand

Wednesday, December 27th, 2017

In the coming weeks, Irish dairy farmers will be sitting down to select sires to breed the next generation of cows on their farms.

AgriLand recently caught up with Mark Ryder, LIC Europe general manager, to find out why the New Zealand industry has moved away from genomic selection after initially embracing it.

Ryder began: “From a New Zealand perspective, we were the first to get into genomics and we saw a lot of excitement in the New Zealand industry about the benefits that can be gained by shortening the generation interval.

“We got into it on a large scale initially and up to 40% of our 4.5 million inseminations were actually genomic.

“But, what we actually found, as we monitored the performance of the daughters of those bulls as they started milking in New Zealand, we found that we were getting quite a large variation.

We were creating some very elite females, but we were also creating some quite poor ones.

Ryder admitted that a large team of bulls was used and the average BW (breeding worth) that was expected was achieved. But, there was quite a large variation in the performance of the cows produced.

“Farmers were very unhappy about young cows leaving the herd early and they were getting quite a bit of wastage.

“In Ireland, it costs €1,400-1,500 to get a heifer into milk. If only 25% of those heifers coming in are any good, it’s not economic so we’ve changed our approach.”

Given this, the New Zealand based co-operative is now using genomics to select young bulls before proving them for the future. The process of proving a bull, he said, costs in the region of NZ$40,000-50,000.

Given the co-op’s stance, wholesale genomic semen sales now only equate to about 5-6% of all of the inseminations made on New Zealand farms and 94-95% of farmers are choosing straws from bulls with high reliability.

“We are encouraging farmers here to use teams of genomic bulls. But, you’re still going to get the same result.

It will deliver the average, but you are going to create heifers that aren’t going to last in the herd.

Due to this, Ryder encouraged farmers to focus on the use of high-reliability sires when it comes to breeding the next generation of their cows for their herds.

“LIC’s New Zealand bred bull team is backed up by daughter proven data, which includes at least one full lactation in New Zealand.

“The reliability of this information gives LIC the confidence that LIC sires have outstanding genetic merit to meet the individual needs of pasture-based farmers.”

From speaking to Ryder, it’s clear that LIC is not totally against genomics. But, instead, the co-op is focused on supplying its dairy farmer customers with reliable genetics that will go one to deliver in the parlour.

Risks with genomics

Along with creating “a large variation” in the off-spring produced, the LIC representative also touched on the dangers of genomics-on-genomics breeding.

“There’s a huge risk there and we see it a lot in this country. We are seeing it start to play out now as some of those genomic proofs aren’t delivering.”

This, he said, is been proven by the daughters of some bulls actually passing through the parlour.

Some of the indexes of those genomic bulls are dropping significantly. And, the way that the industry has been using it here, there’s a lot of genomics-on-genomics.

“There’s a lot of AI companies that have got genomic sires – bull calves that they’ve paid good money for – and all of a sudden they are not worth a hell of a lot because their sire – who was genomic – has now dropped. Correspondingly, those bulls have dropped as well,” he said.

Source: AgriLand

Categories : Genomics

Can You Trust Genomic Evaluations? 7 Facts Exposed

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Tuesday, June 6th, 2017

Successful dairy cattle breeding is about using the facts available including the degree of trust that can be placed in the numbers. The facts used by breeders can vary all the way from in-herd observations, to show results, to including actual performance and genetic evaluation indexes. This article will deal with the genetic evaluation indexes that are based to a great extent on an animal’s DNA analysis. Often just referred to as ‘genomics.’ In this article, The Bullvine will cover details, from recently released studies and articles. We will look at how genomic evaluations are adding trustworthy information to the toolkit that breeders can use to advance their herds genetically.

1) Accuracy

Before there were genomic indexes, there were parent average genetic indexes (PA’s) for heifers that did not have their performance (production and type) records of for bulls that did not have daughters with a performance recorded. The prediction accuracy for PA’s was low, standing at 20-33%. Breeders knew that there would be a wide variation from the PA numbers, once performance data was added in.

In 2008, based on the study of the DNA profiles of daughters proven sires, genomic (genetic) indexes were published by genetic evaluation centers that used both pedigree performance information and an animal’s DNA profile. Immediately the accuracy of the genomic indexes doubled (60-65%) those for PA’s. Of course, this was lower than the accuracies for extensively daughter proven sires, but a significant step forward.

Alta Genetics has recently published an excellent article on the accuracy of genomic index predictions – “How genomic proofs hold up.” The study compares genomic indexes at the time of release as young sires and what their indexes are in April 2017.

The study reports:

Young sires released in 2010 2014 decreased by 171 vs. 52 in TPI and by 151 vs. 74 in NM$.
For the 1078 US A.I. Holstein bulls released in 2013, their April 2017 indexes decreased on average by 99 TPI and 103 NM$. The degrees of change for TPI were: 4% of bull lost more than 300 TPI points; 9% remain, in 2017, within 20 TPI points of their 2013 indexes; and 19% increased in TPI from their 2013 to 2017 indexes. For NM$: 2% on the bulls changes by more than 300 in NM$; 9% were within 20 NM$ in 2017 of their 2013 indexes, and 9% increased in their NM$ index.

Definitely, there was an increase in accuracy of prediction of genomic indexes from 2010 to 2017.

Take Home Message: With each passing year, breeders can place more and more trust in the accuracy of genomics indexes. As more animals have their DNA profile established and as more SNIP research is conducted breeders can expect to see further increases in accuracy of genomic indexes. Also, there will, in the future, be the publication for additional genomic indexes for specific fats and proteins, for lifetime performance and for health and fertility traits.

2) Improvement Rates

CDN has recently reported on a study “Analysis of Genetic Gains Realized Since Genomics.” This study compares two five-year time periods: (a) animals born (2004-2009) immediately prior to the existence of genomic evaluations; and (b) animals born (2011-2016) after genomic evaluations were available to breeders.

The rates vary by trait with the range in compared indexes being from a small improvement rate to over 500%. Note that in Holsteins the rate of genetic gain in protein %, lactation persistency (LP), daughter fertility (DF) and milking temperament (MTP) went from negative to positive. In Jerseys LP, MSP and daughter calving ability (DCA) went from negative to positive, yet metabolic disease resistance (MDR) went slightly negative. Similar rates of improved genetic gains were achieved by both Ayrshire and Brown Swiss breeds.

Take Home Message: Congratulations to the breeders for trusting and using the genomic index information to make faster rates of genetic improvement. A word of thanks goes out to the genetic evaluation centers all over the world for doing the research on and implementation of genomic indexes. The very significant increased rates of genetic gain may not be duplicated in the future for all traits as breeders are now selecting for many new economically important traits not previously evaluated and published.

3) Terminology

It is a known fact that the term ‘genomics’ has not always been interpreted correctly by everyone.

Over forty years ago, when genetic indexes were first published, frequently breeders thought of them as only being for production traits when they were available for both production and type traits. Today many people refer to genomic indexes as only being for production traits when they are available for production, type, fertility, health, other functional traits and total merit indexes (TPI, NM$, …).

Take Home Message: Interpret genomic indexes to be genetic indexes that include both pedigree and DNA profile information. Breeders can find genomically evaluated sires for all traits at all A.I. studs. Breeders can use one or all the genomic indexes as part of their herd’s breeding plan.

4) Inbreeding

Alta Genetics recently published an article, “Inbreeding: Manage it to Maximize Profit,” on sire options to limit the effects of inbreeding.

The article covers:

When selection is practiced in a population, it results in a concentration of good genes and thus inbreeding. So, inbreeding is a natural outcome of selecting the best and eliminating the rest.
Every 1% increase in inbreeding results in $22 – $24 less profit over a cow’s lifetime.
There is not a magic level of inbreeding to be avoided. The current average level of inbreeding in North American Holsteins is 7-8%.
A Midwest US study shows that superior inbred high genetic merit cows are more profitable than inferior genetic merit non-inbred cows.

The average inbreeding level of the top 25 NM$ (April ’17) daughter proven Holstein sires is 7.9% for genomic future inbreeding index (GFI). For the top 25 NM$ genomically evaluated sires the average GFI is 8.2%. Having genomic bulls with a higher level of inbreeding than proven sires is as expected when selection pressure is high, when generations are turned rapidly and when there is extensive focus placed on a single total merit indexes (NM$ or TPI or Pro$ or LPI or …).

Take Home Message: A.I. sire mating programs are designed to take into consideration the level of inbreeding of future progeny when a sire x dam is recommended. If a Holstein sire has a GFI of 9% or higher a breeder should require that that bull should have positive proof values for all of DPR, HCR, CCR, LIV, PL, SCC, immunity and calf wellness. Breeders should use and trust that inbreeding is being handled by sire mating programs.

5) Functional Traits

At the same time, as genomic evaluations became available, breeders started paying attention to a host of functional traits. These traits have economic significance and include milk quality, fertility, heifer, and cow health (immunity, wellness, disease resistance, livability, …), birthing, productive life and mobility. In the future, these functional traits will be expanded as on-farm data, and DNA profiling on animals are recorded and farm data is sent to data analysis centers. Noteworthy is the fact that animal wellness and welfare will be front and center for consumers of dairy products.

Take Home Message: Breeders can trust in the published genetic evaluations for functional traits as animal DNA profiles play a significant role in increasing the prediction accuracies from 15-25% to 60-70%. Functional trait improvement will require that breeders pay attention to both genetic and farm management.

6) Feed Efficiency

Feed accounts for 50-60% input costs for heifers and cows on dairy farms. Any gains that can be made by selecting genetically superior animals for their ability to convert feedstuffs to milk and meat have the potential for breeders to make more profit.

Research and data analysis are underway or nearing completion in many countries including US, Netherlands, and Canada on using DNA data combined with nutrition trial data to produce genomic indexes for feed efficiency. Other trials are underway to electronically capture on-farm data on feed intake, dry matter intake (DMI). It is a well-established fact that level of production is highly correlated to DMI.

CDAB has just published that “AGIL/USDA has demonstrated the feasibility of publishing national genomic evaluations for residual feed intake (RFI) based on the data generated by the 5-year national feed intake project funded by USDA National Institute of Food and Agriculture (NIFA), involving several research groups”. “The next step for CACB is to develop a proposal on how to collect data for use in genetic analysis for feed efficiency.”

Take Home Message: There will be genomic indexes for feed efficiency likely with 2-3 years. Once again breeders will have a tool they can trust into breed animals that return more profit.

7) Breeder Acceptance

A.I.’s are reporting that 60 to 90% of their semen sales are from genomically evaluated bulls. That fact on its own says that breeders purchasing larger volumes of semen are putting their trust in genomic evaluations. However, breeders wanting daughter proven sire proofs need to be given that option provided they are prepared to pay extra for their semen.

Take home message: Breeders check books tell the whole story – Genomic Evaluations are trusted.

The Bullvine Bottom Line

In less than a decade the use of DNA data in genetic evaluations has gone from unknown and not understood to a trusted source of very useful information. Having genomic indexes has given breeders the opportunity to advance their breeding programs, their herds, and their on-farm profits. Trust in information is important to dairy cattle breeders and they have and will continue, in the future, to place their trust in genomic indexes.

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Categories : Genetic Evaluation System, Genomics

How do genomic proofs hold up?

Thursday, May 11th, 2017

We’re well into the genomic era. If you’re like most producers, you’re now comfortable incorporating genomic-proven bulls as part of your balanced breeding program.

Yet, you might still have questions about the difference you can expect between a bull’s first genomic proof and his daughter proof. To answer your questions, we’ve done an in-depth proof analysis of all industry bulls. Our goal was to find out how genomic proofs hold up. Do they become more or less accurate with time?

What did we learn?

Graph 1 shows the average change in TPI from initial genomic proofs to April 2017 daughter proofs. The TPI change from genomic to daughter proof is the amount of space that separates the blue and orange lines.

Graph 1. Change in TPI from genomic release to April 2017 daughter proof

This graph includes all industry bulls released between January 2010 and April 2014. As you can see, the bulls released in January 2010 had an average change of 171 TPI points from their first genomic release to their April 2017 daughter proof.

Now, fast forward a few years. Bulls released as genomic sires in April 2014 saw only a 52 point TPI difference from their initial genomic proof to their April 2017 daughter proof.

This means the stability in GTPI from genomic release until daughter proofs has improved by more than 100 TPI points! As a bonus, it’s clear to see that the genetic levels of bulls continue to rise!

The same goes for Net Merit $. You can discover those results in Graph 2.

Industry bulls first released as genomic-proven sires in January 2010 dropped, on average, 151 NM$ from their first release until their April 2017 daughter proof. Whereas, the bulls first released as genomic sires in April 2014 only changed 77 NM$ from their initial release.

Graph 2. Change in Net Merit $ from genomic release to April 2017 daughter proof

So, even though genomic numbers are still slightly inflated, the gap between genomic and daughter proofs changes less with each passing proof round.

Want more details?

Let’s look at the facts and figures in a different light. We’ll focus in on all 1,078 industry bulls released in 2013. We use this group because all bulls released in 2013 should now have a daughter proof for production, health and conformation traits.

The bell-shaped curve of Graph 3 shows the mean and standard deviation change in TPI on the 1,078 industry bulls released as genomic-proven sires in 2013.

Graph 3, which shows the bell-shaped curve distribution of TPI change from the initial genomic figures of bulls released in 2013 to their April 2017 daughter proof Graph 3. Histogram of difference in TPI from genomic release in 2013 to April 2017 daughter proof

As you can see, on average, these bulls changed less than 100 points from their initial release in 2013 to their daughter proof in April 2017. One hundred of these bulls have a daughter-proven TPI within just twenty points of their original genomic TPI. Only about 40 bulls from the entire group of 1,078 lost more than 300 TPI points – that’s less than 4%.

We see the same trend for NM$. Graph 4 shows the average NM$ change and standard deviation of the same 1,078 industry bulls released in 2013. These sires changed about -103 NM$ from their initial genomic proof in 2013 to their daughter proof in April 2017.

Ninety-five bulls held steady within the small 20 point swing from genomic to daughter-proven NM$. Less than 20 bulls changed more than 300 NM$.

Graph 4, which shows the bell-shaped curve distribution of NM$ change from the initial genomic figures of bulls released in 2013 to their April 2017 daughter proof Graph 4. Histogram of difference in NM$ from genomic release in 2013 to April 2017 daughter proof

What are your options today?

Still debating whether daughter-proven or genomic-proven sire groups are your best option? Take a look at the top 10 TPI sires available from Alta today.

April 2017 Top Dtr-proven bulls	TPI
11HO11434 \| AltaCR	2531
11HO11379 \| AltaRABO	2476
11HO11348 \| AltaBGOOD	2474
11HO11143 \| AltaEMBASSY	2462
11HO11380 \| AltaROBLE	2461
11HO11283 \| AltaMERCI	2450
11HO11272 \| AltaGILCREST	2444
11HO11446 \| AltaPITA	2430
11HO11202 \| AltaOAK	2425
11HO11405 \| AltaKADO	2419
AVERAGE	2457

April 2017 Top Genomic-proven bulls	TPI
11HO11630 \| AltaMORENO	2742
11HO11778 \| AltaROBSON	2733
11HO11725 \| AltaAMULET	2712
11HO11724 \| AltaSTEEL	2684
11HO11826 \| AltaLOBELLO	2681
11HO11758 \| AltaNIXER	2676
11HO11672 \| AltaKERMIT	2667
11HO11736 \| AltaRECOIL	2656
11HO11734 \| AltaPOLISH	2651
11HO11720 \| AltaFLYWHEEL	2643
AVERAGE	2685

Currently, our top daughter-proven sires average a solid 2457 TPI. Yet, the top, available genomic-proven group provides a 228 point TPI advantage!

Some bulls gain points and some bulls lose points. But your odds are nearly zero that every single bull atop the genomic-proven list would drop to rank lower than the current list of daughter-proven sires.

As you make your genetic selection decisions, keep in mind:

Genomic proofs are slightly inflated. Yet, with each proof round, we see less change from genomic to daughter-proven TPI and NM$ because of model adjustments made along the way.
The average TPI and NM$ change from genomic proof to daughter proof for bulls released in 2013 is about -100. Despite that change, you still make much faster genetic progress using a group of genomic-proven sires than a group of daughter-proven sires.
Make sure the genetic progress you make is in the direction of your goals. Select a group of genomic-proven sires based on your customized genetic plan. Emphasize only on the production, health or conformation traits that matter most to you to boost your farm’s future profitability.

Source: AltaGenetics

Categories : Genomics

Genetic Gain Before and After Genomics

Wednesday, May 3rd, 2017

You’ve likely heard the statement: “Genomics has doubled the rate of genetic progress”. In this article, we find out if this claim is true by looking at genetic gain for indexes and individual traits before and after the implementation of genomic evaluations.

Female Genetic Trend for LPI and Pro$

Figure 1 shows the genetic trend for LPI and Pro$ for Canadian Holstein females based on year of birth. The trends for LPI and Pro$ are essentially identical but since the scales for the two indexes are different they are plotted on different lines.

Prior to genomics, which began in 2009 for Holsteins, the average LPI for females born during the 5-year period from 2004 to 2009 was increasing by 50 LPI points per year. Since the introduction of genomics (vertical line in Figure 1), this rate of genetic progress has increased substantially. For females born in the past five years, from 2011 to 2016, the average LPI has increased gains of 107 points per year – over twice the amount of annual gain prior to genomics.

During the same time periods, the annual genetic trend for Pro$ increased from $79 before genomics to $176 per year during the past five years. This has happened without selection for Pro$ as the index was only introduced in August 2015. However, since Pro$ is made up of many of the same traits as LPI and the two indexes are correlated by 96%, selection for LPI was leading to an associated progress for Pro$ before this national index existed.

Genetic Gain for Individual Traits

Like for overall indexes, genetic gain for individual traits can be assessed before and after genomics. Figure 2 shows the relative genetic gain by trait realized during the five years before genomics and during the most recent five years with genomics. Genetic gain is expressed in standardized units so that gain can be comparable across traits with different units of expression.

When comparing the gains achieved during the two 5-year periods, we can see that:

Gains achieved with genomics have been positive for all traits, including lower heritability functional traits. Prior to genomics, gains for most functional traits were slow and even negative for some traits, such as Daughter Fertility. The impressive gain for these low heritability traits is a direct result of the increase in the accuracy of genetic evaluations due to genomics. Overall, the largest gains relative to the five years before genomics are seen for functional traits.
Gains achieved with genomics were doubled for Fat and Protein Yields while also making considerably higher genetic gains for deviations.
Gains achieved with genomics were the highest for overall type traits, especially Conformation and Mammary System, but these traits were also achieving the highest rates of genetic progress prior to genomics. These past and continued gains are partially due to the high selection intensity for these traits.
Gains achieved with genomics were doubled for Feet and Legs, which is the least heritable among the five overall type traits. Since genomics significantly increases the accuracy of published evaluations, the genetic gain realized for this trait has been large.

Another way to compare the genetic gain achieved pre- and post-genomics is presented in Table 1. Here, gains are expressed in the same units as proofs for each given trait. For example, yields are expressed as EBV based on kilograms while most functional traits are expressed as Relative Breeding Value (RBV) points.

In Figure 2 we saw that with genomics, there has been twice the amount of genetic gain realized for Protein yield in terms of standard units. Referring to Table 1, we can see that the combined gain for Protein yield during the five years prior to genomics was 11.8 kg, or around 2.4 kg per year. In the past five years with genomics, the combined gain was 24 kg, or 4.8 kg per year. This means that females born in the last 5 years in a herd with average management are expected to have 305 day lactation yields that increase roughly 5 kg per year, on average. In this case, double the genetic gain translates into double the performance increase for protein yield.

Likewise, when looking at the functional traits, the combined gain for Herd Life during the five years prior to genomics was 1.12 RBV points, or 0.22 RBV per year. Over the past five years, however, with genomics, the combined genetic gain for this trait was tripled to 3.36, or two-thirds of an RBV point of gain per year. Significant gains with genomics have also been observed for other functional traits, meaning that Holsteins today can be expected to last longer in the herd due to improved calving and reproductive performance along with higher resistance to disease.

Genetic gains have increased substantially across the board since the implementation of genomics in Canada. While all traits have benefitted from the increased accuracy the technology provides, this is particularly true for lower heritability functional traits. The increased gain for individual traits translates into a rate of progress that has doubled for both of Canada’s national genetic indexes.

Authors:
Lynsay Beavers, Industry Liaison Coordinator, CDN
Brian Van Doormaal, General Manager, CDN

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Categories : Genomics

Dairy Cow Genomic Feed Efficiency Study Nearing Completion

Monday, March 27th, 2017

A University of Wisconsin research professor is nearly finished with a study on genomic selection for feed efficiency in dairy cows.

Dr. Kent Weigel is the chairman of Dairy Science department, specializing in breeding and genetics. He says, “We’re trying to do 8,000 cows, we’re over 6,000 so far, and form a genomic reference population that then we can use to make predictions for feed efficiency. You know, using those data (sets), we can predict the feed efficiency of any heifer calf or the feed efficiency daughters of any bull at any breeding company.”

Weigel tells Brownfield the study has required a lot of labor over the past five years, making detailed measurements of each cow. “Specifically, how efficiently does each cow utilize the energy that she consumes, and in order to do that you measure every individual cow’s feed intake for a couple of months in the middle of lactation.”

Weigel says the results of the research will be available to the industry soon, saying, “Within the next month or later this year.”

Weigel says measuring feed efficiency on this scale wouldn’t have been possible a few years ago, but genomics technology has reduced the expense and labor.

Source: Brownfield

Categories : Genomics

Genome Alberta Dairy Researchers Gain Scottish Support

Tuesday, February 7th, 2017

Scotland may be best known for bagpipes, but it’s the data derived from Scottish dairy cows that is music to the ears of genomic researchers.

As it seeks to enhance feed efficiency and reduce methane emissions with the power of genomics, a Genome Alberta project is part of a global initiative. The effort includes a dairy research herd at Scotland’s Rural College (SRUC) Dairy Research Centre on the outskirts of Dumfries, South West Scotland, supported primarily by funding from the Scottish government.

The project aims to use milk mid-infrared (MIR) spectral data to estimate feed efficiency and methane emissions as the data correlates well with both traits. Compared to the current method of collecting phenotypes to predict these traits, MIR data is easier and less expensive.

Best of all, this data is already being collected. In order to use it for their purposes, however, researchers must increase the amount of data they compile from cows for which they already have phenotype information on the targeted traits.

As it turns out, the SRUC research herd fits the bill.

Numbers game

“We’ve been running 200 cows for 45 years now,” said Eileen Wall, Team Leader of Integrative Animal Sciences at SRUC.

“We phenotype the heck out of our research herd animals and follow them from birth through three lactations of production data, gathering weekly information on key aspects like feeding behavior and feed intake, including regular milk MIR profiles.”

Having gathered hundreds of thousands of rows of research phenotypes, Ms Wall and her team tie into a national evaluation system and obtain data on every milk-producing cow in the country. In collaboration with National Milk Records, they have collected MIR data on 1.5 million cows over the last year in what she calls a “really stunning example of the research community working with industry,” assisted by funding from Innovate UK and BBSRC (British Biological Sciences Research Council).

One product of all this data is a powerful set of genetic prediction tools for traits of interest to dairy producers.

“Our dairy research herd serves as an excellent resource for reference phenotypes. The prediction tools developed to date were based on more than half a million records taken from over 900 Holstein Friesian cows from 2003 – 2014 on a range of phenotypes and dietary components. As we continue to collect records on farm and spectral data we can routinely update and improve tools as well as test and develop tools to predict new phenotypes.”

In turn, the Scottish results are helping the Efficient Dairy Genome Project develop a similar set of robust prediction equations using MIR data.

“Based on our experience, we can share information with the Canadian researchers and help them avoid any mistakes that we made along the way; so it’s a combination of pooled data and shared learning.”

Also, since North America and the UK have different production systems, pooling data should produce better genomic predictions for a wider range of cows and systems.

Feeding progress

Motivating research in both Canada and the United Kingdom is the potential benefit for producers.

“Feed is the highest intake cost for dairy farmers. If we can increase the efficiency of milk production, it will help farmers save money and stay competitive. Right now our government is stressing the need for research to have real-life applications so that results don’t stay on paper but are translated to the field.”

For the UK dairy industry, reducing feed waste has the potential to cumulatively increase profitability by 17 million GBP (British pounds) per year. The hope is that Canada can realize similar benefits by making active selection decisions for critical traits. Who knows, maybe Canadian farmers will even don kilts as a show of solidarity.

Source: The Cattle Site

Categories : Genomics

Bottom Line Top of Mind in Genome Research

Thursday, January 5th, 2017

In light of some recent election results, “giving the people what they want” isn’t always the way to go. When those people are the beneficiaries of research efforts, however, it’s not a bad idea.

That’s certainly the case with a Genome Alberta project to develop and apply more accurate genomically-enhanced breeding values for traits of importance to the commercial cattle industry. Researchers may have started with a theory, but practical results for industry are a top priority.

“One thing we talked about at a recent team meeting was user tools being generated by the project and how best to roll them out,” said John Crowley, a co-lead on the project and a research geneticist with Livestock Gentec at the University of Alberta.

“We need to pinpoint the most effective way for industry to use the information on breed composition. It can be a huge aid in guiding your decisions on what breeds you cross with or what animals within a breed will be of interest to you.”

Ultimately their goal is a decision tool to maximize hybrid vigor, what Dr Crowley calls “that extra bump in performance you get when crossing two unrelated breeds or animals.”

Begin with the end user in mind

In regard to breeding values, the team is looking at how to package and communicate the findings and encapsulate them in one or two easy-to-read figures.

“You can sum up genetic scores in different ways. It may be that a maternal and all around index would be best for the end user, where the economic value of each trait is given its own weighting.”

Since he also serves as Director of Scientific and Industry Advancement with the Canadian Beef Breeds Council (CBBC), Dr Crowley is sensitive to the needs of industry and is closely following their reaction.

“People seem pretty happy with our progress. Research participants are excited about the information they have received so far and glad they had a chance to dip their toes in genomics, so to speak.”

One of their main research partners is Cow Calf Health and Management Solutions (CCHMS). Genome Alberta researchers are working with 10 CCHMS clients and gathering valuable feedback to inform the project.

Breeding success

Another end user for the project is breeding associations for whom phenotypic data and genotypes can be quite valuable.

“It’s helpful for these associations to see how bulls are performing on a commercial farm instead of just being circulated around the seed stock sector. This gives them the opportunity to grab more of the data.”

As Dr Crowley explained, often what go into the genetic evaluation of an animal are its own physical measurements and those of immediate relatives, sire or dam.

“To get a proper evaluation you need to see a lot of progeny perform. Unless an animal becomes the sire for many seed stock progeny, he doesn’t get the chance to show what he can do as there is a disconnection between commercial farms and seed stock farms; this project is trying to close that gap a bit.”

How the end user perceives this project depends on their particular interests. For example, Cargill’s focus is more on immediate benefits and what is being done to improve certain traits.

“They’re looking at the most economically relevant traits such as carcass quality, feed efficiency and female traits. The Cargill representative who saw our findings was quite interested and planned to share them with his staff and colleagues. He liked that we are looking at this from a whole value chain perspective and also appreciated the chance to learn more about this field of study.”

Though there is still a long way to go on the project, Dr Crowley and his colleagues feel they’re on the right track. Given recent events, it’s reassuring to know that listening to the people isn’t always a bad thing; you just have to choose the right people.

Source: The Cattle Site

Categories : Genomics

Trend in Genomic Versus Proven Sire Usage

Thursday, August 11th, 2016

Click to enlarge

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Categories : Genomics

A Q&A on DWP$ and WT$

Friday, July 1st, 2016

The Dairy Wellness Profit $ and Wellness Trait $ indexes may have you wondering whether you should adjust your genetic plan to include this new information. Here we have answers to 14 questions to help you decide what’s best for your dairy to make the maximum genetic progress in the direction of your goals!

What is Dairy Wellness Profit $ (DWP$) and Wellness Trait $ (WT$?)

These are genetic indexes calculated by Zoetis from producer-recorded data, in herds that are genomic testing or have genomic tested in the past.

How is the WT$ index compiled?

WT$ is a combination of the Wellness Traits (Ketosis, Displaced Abomasum, Retained Placenta, Metritis, Mastitis and Lameness). This means it is an index analogous to a 0-100-0 index, with 100% weight on health traits. However, those weights are divided between the various Wellness traits that Zoetis calculates.

Do each of the Wellness Traits get their own evaluation?

Yes. They are then combined into a Wellness Trait $ index to combine the expected impact.

How is DWP$ compiled?

DWP$ is a genetic selection index that equates to a genetic plan of 34% Production – 56% Health – 10% conformation. This differs from TPI (46-28-26) and the overall NM$ index (43-41-16).

The breakdown of the weight on health is different as well. DWP$ puts 30% of the weight on WT$, leaving 26% for the CDCB evaluated health traits of PL, DPR, SCS, DSB, DCE, CCR, HCR.

Are the Wellness traits developed by Zoetis?

The WT$ calculation is not a new concept, as it was first published in 2004, however this is the first routine evaluation and first genomic prediction for those traits.

Did Alta test all bulls for DWP$ and WT$?

No, but we tested the sires that we predicted would do well on the respective indexes based on their health trait values and how they rank on a 34% Production-56% Health-10% Conformation index. We are listing the top ten DWP$ sires and top five WT$ bulls in each of three categories: G-Stars, FutureStars and daughter-proven sires.

What is Alta’s testing plan going forward?

This will be dependent on the feedback from the customers and the demand for this information. In the short-term we will continue to test those sires that rank well on a traditional 34-56-10 index.

How can we predict which sires will do well on these indexes?

Because the correlation between DWP$ and a traditional 34-56-10 index is very high, we can predict quite well which sires will rank well on the DWP$ index.

How do these Wellness traits compare to Productive life?

Productive life encompasses every reason an animal leaves the herd, and the length of time she is productive compared to herdmates.

The Wellness traits are some of the exact reasons cows may leave, but instead measure incidence of disease, not departure from the herd. Of course many cows are affected, but do not leave the herd. Therefore the Wellness traits measure different things than Productive Life, however there is obviously a strong relationship between PL and WT$, with a stated correlation of 0.41. The relationship gets stronger if the combination of PL, DPR, and SCS is used, reinforcing that all the health traits are related to each other.

How should you use this information?

It’s still as important as ever to create your own, customized genetic plan based on your goals and the situation on your dairy.

Our stance at Alta has always been that the most important part of setting a genetic plan is getting the correct amount of weight in each of the three ‘buckets’ for production, health, and conformation – based on the current situation and future goals for your dairy. Once your genetic plan is decided, changing which individual traits are emphasized within each bucket will have far less impact.

If you select sires based on TPI (46% Production-28% Health-26% Conformation) or NM$ (43-41-16), the current DWP$ weighting of 34-56-10 puts significantly more weight on health than those two indexes, at the cost of production and conformation.

If your current genetic plan is set at 70-30-0, changing to DWP$ as a selection goal would be analogous to changing from 70-30-0 to 34-56-0. That doesn’t mean the change is wrong – it is just a VERY significant change, which should only be made because your goals or situation have changed, not just because there are new traits available.

However, if your genetic plan is set at 50-50-0, moving some of the 50% weight on health, and putting it towards the wellness traits, is a much less drastic adjustment.

Changing the bucket weights in a genetic plan is always a strategic decision. Therefore, plans should change only when economics or the situation on your farm changes, not just because new traits become available.

Is there anywhere else to get information on these traits?

In Canada, CDN has been calculating an evaluation on clinical mastitis for some time now, and those evaluations are readily available. They are also collecting data on each of the other five traits, and expect to have evaluations available within the next year.

In the Netherlands, these traits are routinely collected and evaluated. In the US, the CDCB is currently evaluating the possibilities to do genetic evaluations for these traits.

What is the correlation between DWP$ and other indexes?

The correlation between TPI and DWP$ is 0.89. The correlation between NM and DWP$ is 0.92. The correlation between a 34-56-10 index calculated with Alta’s Bull Search or AltaGPS is 0.94.

Are the Wellness traits heritable, or driven more by management?

Many traits that are heavily influenced by environment still have a genetic component, and the Wellness traits are no different. While the heritability of these traits ranges from 6%-8%, they should not be eliminated from a selection plan simply because of low heritability. Daughter fertility, Productive Life, and other traits also have relatively low heritability, but many herds have made substantial genetic progress, and see real results for these traits through genetic selection.

What is the reliability of the Wellness Traits?

The reliability of the Wellness Traits is ~0.50. This is relatively low compared to other traits that are routinely selected for. This means more re-ranking can occur between animals as more data is gathered.

Comparatively, the reliability of other CDCB health traits such as PL, DPR, and SCS is around .70 on young AI bulls because there is more historical data available for these traits.

Reliability is a measure of the precision of an estimate, and the likelihood that estimate changes over time. It is NOT how likely traits are to pass from one generation to the next.

Source: Alta Genetics

To view a listing of Alta’s top 10 DWP$ and top 5 WT$ sires, please Click HERE.

Categories : Genetic Evaluation System, Genomics

Genomic Testing Goes Mainstream to Commercial Dairy Herds

Monday, March 28th, 2016

Animal Health National Sales Meeting Advances in genomic testing create new opportunities for commercial dairy producers to have more control over their herds’ profit potential. With an abundance of available replacement heifers, producers have the ability to replace less profitable cows with genetically superior heifers, shortening the generation interval and accelerating the genetic progress.

Genomic testing offers a powerful screening tool to predict what heifer will be a top performer and which will be below average. The payoff can be big, as investing money toward feeding and housing heifers that are not going to contribute to the bottom line only narrows profit margins.

Technology advancements make testing affordable
Once a tool only affordable for dairy producers owning elite dairy herds to identify the best bull mothers, genomic testing is now cost effective on a large-scale basis. Costs have fallen dramatically since genomic testing first hit the market in 2008, and it is now possible to test for as low as $28 per head or approximately 1 percent of the cost to raise a heifer.

Managing genomic information to find genetically inferior calves is quite simple. Dairy producers select a key indicator, such as the predicted transmitting ability (PTA) of net merit dollars (NM$) which estimates the expected lifetime profit of a cow compared to the breed base of an average cow born and raised in the same environment. NM$ include traits that capture an economic impact, such as milk yield, health, longevity, fertility and calving ease. If a heifer does not meet the minimum requirements for NM$, she could be sold prior to breeding.

Another option is to breed the bottom-end replacements to a beef sire and sell the resulting crossbred calves as higher-dollar beef animals. Depending on market conditions, it may be possible to pay for testing costs for all of the replacements just from the increased value of the crossbred calves.

Conversely, a heifer that ranks high in NM$ might be a candidate for sexed semen. Keeping the calves with the best genetics and applying sexed semen, while selling calves with the poorest genetics, can deliver substantial cost savings. Ultimately, producers realize value by collecting the NM$ information at an early age, allowing them to gain an understanding of how profitable the animal will be as a lactating cow.

How it works
Genomics got its start in 2004 with the sequencing of the bovine genome, which is made up of approximately 25,000 useful genes. Sequencing allowed basic information about genetic coding to be used to improve how genetic values of cattle are estimated.

Neogen-logo[1] For genomic selection, researchers look for markers or single nucleotide polymorphisms (SNPs). A SNP is a place in a chromosome where the DNA sequence can differ among individuals. SNPs are most useful when they occur close to a gene that contributes to an important trait. Most traits are controlled by many genes, making this a very complex process. Significant progress was made when a genotyping computer chip was developed that could identify more than 50,000 SNPs (50K test) on the genome.

Genomics has rapidly advanced in the past decade. Today most laboratories use custom chips that are able to use fewer SNPs through the use of imputation. Imputation is a method that uses knowledge of the parental genome in calculations to predict the genotype of the calf.

The Council on Dairy Cattle Breeding (CDCB) maintains the genomic database and produces a genomic evaluation report on a weekly basis containing data on every animal. Producers can take a tissue sample from a calf and submit it to a laboratory, which then sends the genotype to the CDCB. The CDCB then calculates PTAs that are equal to progeny tests on many daughters of sires.

While the reports contain extensive data, most dairy producers prefer to use simple rankings, such as Net Merit, Cheese Merit or Fluid Merit. For those who like more details, reports can be run to work with custom-made indexes.

Testing for commercial operations
Neogen Corp. recently introduced Igenity-Essential in response to requests by commercial dairymen for a more convenient and cost-effective genomic assessment of their animals that can be done during times of low milk prices.

An alternative to traditional USDA-CDCB evaluations, Igenity-Essential can be performed soon after a calf is born, and test results are received within two to three weeks after tissue submission. Ideal for simple heifer sorting, Igenity-Essential is powered by a low-density 7K chip with custom content to examine 15 traits essential for improved milk production and reproduction. For the commercial dairy producer looking for a simple but effective sorting tool, this is an excellent option. It is available for Holsteins and Jerseys and contains the key content needed for an accurate genomic evaluation to make management decisions.

Find out more information at www.neogen.com or contact your local Merck Animal Health representative.

Source: Merck Animal Health

Categories : Genomics

Do genomic proofs hold up?

Thursday, February 18th, 2016

Seven years into it, genomics has become nearly as common of a term as AI. We’re now used to the genetic technology and feel confident using genomic-proven bulls as part of a balanced breeding program.

However, you may still have questions about the difference to expect between a genomic proof and a daughter proof. Or maybe you’re looking for comparisons on the genetic merit between genomic-proven and daughter-proven sires.

Peace of mind from increasing proof stability

Closer analysis of proof stability shows the ever-increasing stability we see with each passing proof round.

Graph 1 below illustrates the change in TPI for all industry genomic-proven Holstein bulls first released between January 2010 and December 2012. As the graph shows, the bulls released in January 2010 had an average change of 164 TPI points from their first genomic release to their December 2015 daughter proof (the difference shown as the amount of space between the blue line and the orange line).

The decreasing change in TPI from first genomic release to Dec ’15 dtr proofs for industry bulls released between 2010 and 2012.

Fast forward to December 2012, and the bulls released at that time saw only a 67 point TPI difference from their initial genomic proof to their December 2015 daughter proof.

This means that the stability in GTPI from the time of genomic release until daughter proofs has improved by nearly 100 TPI points!

The same goes for Net Merit $, shown below in Graph 2. Industry bulls first released as genomic-proven sires in January 2010 experienced an average change of -135 NM$. That change from first genomic proof to December 2015 daughter proof decreased to just -63 NM$ for the group of bulls first released to genomic line-ups in December 2012.

The decreasing change in NM$ from first genomic proof to Dec ’15 dtr proof for industry bulls released between 2010 and 2012.

This shows that while genomic proofs are still slightly inflated, the gap between genomic and daughter proofs changes less with each passing proof round.

If we take a look at the facts and figures in a different light, and zoom in on just the bulls released in 2012, the stability remains. The bell curve below shows the average change in TPI for the 1,060 industry bulls released as genomic-proven sires throughout 2012 that now have milking daughter proofs.

As you can see, the average change in TPI was -89 points. Nearly 70 bulls have a daughter-proven TPI within ten points of their original genomic proof, and only 40 bulls of that entire group gained or lost more than 300 TPI points.

And for NM$, the same trend holds true. As you can see below, the average change in NM$ from the group of all industry bulls released throughout 2012 was at -92 NM$ from initial genomic proof to December 2015 daughter proof. Sixty-three bulls held steady within the small 10 point swing from genomic to daughter-proven NM$.

If you are still debating whether daughter-proven or genomic-proven sire groups are your best option, take a look at the top 10 TPI sires available for you from Alta today.

Compare your top daughter-proven sire choices with your top genomic-proven options.

Despite the solid 2364 TPI average from the top daughter-proven sire options, the genomic-proven group provides a 220 point TPI advantage! Your odds are nearly zero that every single sire on the genomic-proven list would drop in production, health and conformation traits after receiving a daughter proof to rank them lower than the current daughter-proven stars.

As you make your genetic selection decisions, keep in mind:

While genomic proofs are slightly inflated, they continue to become more accurate and see less change in TPI and NM$ with each passing proof round because of model adjustments made along the way.
Even though the average change in TPI and NM$ for bulls released in 2012 is about -90 from genomic proof to daughter proof, the currently available genomic sires will still make much faster genetic progress than the current daughter-proven bulls available.
Make sure the genetic progress you make is in the direction of your goals. Use a group of genomic-proven sires selected based on your customized genetic plan with emphasis only on the production, health or conformation traits that matter most to you.

Please Click HERE to download a PDF of this article.

Written by Gerbrand van Burgsteden, Global Product Development Analyst, Alta Genetics

Source: Alta Genetics

Categories : Genomics

Making progress on low heritability traits – Zoetis Webinar #7

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Friday, January 8th, 2016

Accelerating genetic improvement via genomic testing has been available to US dairy producers for more than five years. Until genomics became available, it was difficult to justify female selection of low heritability traits… the information was too low accuracy and slow from traditional methods. With the advent of genomic evaluations and the greatly improved accuracy it brings to genetic estimates, it’s important to re-evaluate long-held beliefs with the improved gains that can be made in low heritability traits.

The seventh installment of this video series covers “Making Genetic Progress on Low Heritability Traits”:

What does low heritability mean?
How do GPTA’s translate to real herd differences in low heritability traits?
Proof it works
Why some herds may see better results

Presenter

Dr. Weigel grew up in Iowa on the family farm (Weigeline Holsteins) and graduated from Iowa State University with a Degree in Dairy Science. He received both his M.S. and PhD from Virginia Tech, with his dissertation focusing on the prediction of genetic merit for lifetime profitability in Holsteins. Before joining the R&D group of Zoetis (formerly Pfizer Animal Health) in 1995, Dr. Weigel served as a post-doctoral fellow at the University of Guelph working on the implementation of Multiple Across Country Evaluations (MACE) for conformation traits of Holstein sires. Dr. Weigel’s current role with Zoetis is in Outcomes Research and he remains active as a breeder of Registered Holsteins.

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The webinars will be moderated by The Bullvine with presentations by Zoetis or Holstein Association personnel. The Bullvine is an online source for dairy genetic and other industry happenings around the world, through their coverage via articles, videos and podcasts. Viewers will attend the presentation live at a specified time and date, and archived presentations will be accessible through other websites after each presentation.

The following webinars will take place from Noon Eastern time (9:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

This webinar is proudly sponsored by:

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Categories : BullvineTV, Genomics

Putting Genomic Results to Work – ZOETIS Video #5

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Thursday, November 5th, 2015

To get the most from genomic testing the results have to be used to make decisions that have a positive impact on herd and genetic management. Matching herd data with animal identification and genomic data can be challenging without the right technology. Enlight is a program offered through the Holstein Association, USA to help CLARIFIDE users manage data for easier management decisions. In the fifth installment of this webinar series, Lindsey Worden, Holstein Association Director of Genetic Services, reviews ways to put your genomic results to work, including:

How the Enlight program offer solutions on how to benefit from the results of genomic testing.
Measuring the success of your genetic advancement program

Don’t miss this opportunity to learn more, and see how you can put genomics to work in your herd.

This webinar is proudly sponsored by:

Presenter

Lindsey Worden has worked as Holstein Association USA’s Executive Director of Holstein Genetic Services since October 2013. In her role, she oversees staff responsible for maintaining the Association’s genomic and genetic testing programs and software programs such as Red Book Plus/MultiMate, as well as other performance programs such as classification and production records products, providing guidance and direction for various Association initiatives. Worden was HAUSA’s project manager for the development of the Enlight™ genetic management tool, which was developed in collaboration with Zoetis, and now oversees the team responsible for supporting the product. Prior to her current responsibilities, she served as Holstein Association USA’s communications manager for more than 6 years. Worden is a graduate of the University of Wisconsin-Madison where she studied dairy science and life science communications and was an active member of the Association of Women in Agriculture, Badger Dairy Club and the dairy judging team. She has had a lifetime of involvement in the dairy industry and Registered Holsteins growing up on her family’s dairy operations in New York and New Mexico, and in her free time still enjoys helping out on her family’s Central New York dairy and working with her cattle. Worden works out of the Holstein Association USA headquarters in scenic Brattleboro, Vermont.

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The following webinars will take place from Noon to 1:00 pm Eastern time (9:00 a.m. – 10:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

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Categories : Genomics

The Economics of Genomics – Zoetis Webinar #4 Video

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Thursday, October 8th, 2015

You know genomic technology works better than other alternatives on your dairy. And you understand genetics are permanent, so decisions today impact results into multiple generations to come.

Many next ask, how do I know if it’s worth the investment? This topic will take a look at multiple ways genomic testing and selection can improve your profitability and efficiency, and in some scenarios, even your cash flow. Topics covered in this video are:

Improving profit and cash flow through strategic choices and selection
Improving profitability by using genomic test results versus using alternati
ves.
Other areas difficult to measure

Don’t miss this opportunity to learn more, and see real herd-modeled financials.

Presenter

Cheryl Marti is the U.S. Marketing Manager for Dairy Genetics and Reproductive Products for Zoetis. She received her B.S. from the University of Minnesota in Animal Sciences, her M.S. in Dairy Science (Genetics emphasis) at the University of Wisconsin – Madison, and her MBA from UW-Whitewater. Cheryl worked in the AI industry at ABS Global for over 11 years in many different capacities, including management, marketing, training and technical support of the Genetic Management System (a genetic mate assignment program), and also worked in the Sire Acquisition and Research areas. She joined Pfizer Animal Health, now Zoetis, in 2005, first as a Fresh Cow Reproduction Manager in the Great Lakes states and later as a Dairy Production Specialist in WI where she often worked with large dairies on genomics, reproduction, records analysis, and transition cows until mid-2014 when she moved into her current role. Her experiences include working with herds of all sizes across the U.S. and over a dozen countries on 6 continents. Cheryl’s passion for the dairy industry and genetics began at her family’s Registered Holstein farm in Sleepy Eye, MN, where she owns some cattle, and her sister and brother-in-law own and operate their family farm of 700 acres and a 160-cow dairy called “Olmar Farms.

This webinar is proudly sponsored by:

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The following webinars will take place from Noon to 1:00 pm Eastern time (9:00 a.m. – 10:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

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Categories : Genomics

Using Genomics as the Ticket to the Future

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Wednesday, June 24th, 2015

“Genomics has taken dairy cattle genetics to new heights.” Of course, there are breeders who agree and others who disagree with that statement. Regardless of our individual opinions, breeders definitely know more about the genetic make-up of the top animals than we did prior to 2008.

Let’s do an analysis on using and relying on genomics to achieve genetically improved dairy cattle in the future through increased accuracy, profitability, and genetic advancement.

Strengths

allows for reducing the effects of biases found in the phenotypic data used in genetic evaluations (accuracy)
can be used for both parentage verification and genetic indexing (accuracy)
increases the accuracy of genetic indexes for young bulls and genetically elite females (accuracy)
provides for enhanced accuracy when culling of heifers based on genetic indexes (accuracy)
allows for decreasing the generation intervals (rate of genetic advancement)
reduces the number of young bulls that need to be sampled. Each one costs $50,000. (profitability)
allows breeders to focus on replicating their best genetically indexed animals or families (genetic advancement)
can be used for decisions beyond genetics including in health and management (profitability)
fits a breeding model that uses genetic indexes and yields rapid genetic gain (genetic advancement)

Weaknesses

currently, not enough young females are being tested to know accurately the population average and ranges
adds to the cost for documenting animals
took some control out of the hands of breeders and breed associations
resulted in more friction amongst breeders
required that breeds incur the cost of education/awareness programs
does not fit a breeding model that uses show results or requires 90+% reliability for sires used

Opportunities

provides the opportunity for more on-farm profit including the need to raise fewer heifers (profitability)
reduces the loss that breeders incur when they get low-end heifers from low genetic merit unproven sires (profitability)
allows for breeders to implement new models for breeding and marketing (profitability)
results in a more rapid genetic improvement for both herds and breeds, at less cost (genetic advancement)
allows for the genetic evaluations for additional important traits (profitability and genetic advancement)
allows for the genetic evaluations for traits on which it is hard to capture field data (profitability and genetic improvement)
allows for the accuracy of comparison for animals originating from foreign sources (accuracy)
allows for re-structuring of or adding to services that breeders need (profitability)

Threats

The following threats are largely based on changes in the status quo.

devalues some animals previously considered elite and of some animals capable of winning at local shows
if not used wisely can result in increased levels of inbreeding
provides for breeders to discontinue participation in performance recording programs, yet they can make significant genetic improvement
could result in fewer A.I organizations and thereby potentially less choice for breeders
may require that a new genetic evaluation formula be developed

Where from here?

The position taken by breeders relative to genomic information very often depends on whether they see genomics as a threat or as an opportunity. It’s time to be positive. It’s impossible to turn back the clock. We need to stop the negativity on the topic of genomics or toward the people using that information. Breeders and industry stakeholders need to work nationally and internationally for collective benefit. With further research and development genomics will provide discerning breeders with information so they can achieve their breeding and profitability goals.

The Bullvine Bottom Line

The Bullvine strongly supports using genomic information. Although it is not the only tool, it is a very constructive one for improving the total genetic merit of dairy cattle. Progressive and pro-active breeds and breeders will use and further develop this tool.

The first webinar in the series to be held on Noon (EST) Wednesday July 8th 2015, and will focus on the basics of genomics to provide producers with a better understanding of the benefits of knowing more about their heifers. Click here to reserve your seat!

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Categories : Genomics

Smoking is good for you…and other facts dairy breeders should know

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Monday, June 1st, 2015

In the 1920’s and 30’s cigarette companies not only denied the health risks of smoking, they actually promoted them as a good thing, by putting up testimonials and stats about doctors who smoked. During the 1920s, Lucky Strike was the dominant cigarette brand. This brand, made by American Tobacco Company, was the first to use the image of a physician in its advertisements. “20,679 physicians say Luckies are less irritating,” its ads proclaimed. Of course many years later we are well aware of the health risks (480,000 people die prematurely each year in the US, due to smoking or being exposed to smoke). It’s flashbacks to this false advertising experience that dairy breeders are referencing when they distrust the use of genomics in dairy cattle breeding. They feel that it’s just the AI companies “forcing” genomics down their throats, in the same way that the tobacco companies “forced” smoking down the throats of millions, by using the weight of doctors’ credibility.

For a long time, physicians were the authority on health. Patients trusted their doctor’s education and expertise and, for the most part, followed their advice. When health concerns about cigarettes began to receive public attention in the 1930s, tobacco companies took preemptive action. They capitalised on people’s trust of physicians, to quell concerns about the dangers of smoking. Thus was born the use of doctors in cigarette advertisements. Executives at tobacco companies knew they had to take action to suppress the public’s fears about tobacco products.

When genomics was first introduced to the dairy cattle breeding world, it was controlled by the major artificial insemination companies. According to some breeders they “hammered” the benefits of genomics down their throats and left breeders almost no choice but to use high index genomic sires, as there were limited other options. The ironic thing is that high praise for the product is about where the similarities between the Tobacco industry and the dairy breeder world part ways.

Unlike cigarettes that were eventually exposed for their many alarming health risks despite the early endorsement, genomics had the opposite reaction – distrust. At the time, almost daily I was reading warnings in other “leading” dairy publications against using genomic sires. This pandered to the old school mentality that fosters breeder concern about using Genomics. Instead of basing their comments on facts, they used hearsay, conjecture and outright fear mongering to defend their negative comments. (Read more: The Genomic Bubble Has Burst?)

The facts are pretty clear. Genomics increases young sires’ reliability by 30% and 1st crop proven sires by 5%. In effect, that says that a young sire with a 50K genomic test and a proven sire will now have reliability comparable to an early 1st crop proven sire pre-genomics. This would indicate that, if you were willing to trust a 1st crop proof prior to the introduction of Genomics, you should now be ready to trust a genomic young sire from a proven sire as their reliabilities are very comparable. Furthermore, genetics marketing is also supporting this. Genomic young sires are set to outsell proven sires because most breeders are confident in the numbers and are making sound breeding decisions based on them. As we mentioned in our article Genomics – Lies, Miss-Truths and False Publications, genomically evaluated bulls with 65% reliable gLPIs, breeders can expect 95% of the time that their official proof will be within 400 LPI points (within about 10-15%). (Please note that this figure reflects the change in the CDN system). Yes, genomic young sires do, on average, drop below their original predicted values but, they are, on average, still higher than the current proven sires that they are competing with.

The interesting part is that, while promoting smoking was a “cash cow” for the Tobacco industry, the increased use of genomic young sires has actually caused problems for the AI companies, even though genomic sires now account for 50% of semen sales. This led me to propose that genomics will soon be used by 84% of dairy breeders in the world. (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!) This is actually scary news for most AI companies. That is because the average genomic young sire produces about 20,000 doses of semen a year. That is about 10 to 20% of the semen production of a healthy proven sire. This means that instead of housing 1 proven sire, these companies now have to house four to nine extra young sires, in order to produce the same amount of semen. So while genomics was first expected to help these companies save money on bull housing, it has actually resulted in them having to increase their housing expenses.

Here at the Bullvine we think the facts about genomics speak for themselves:

Genomics is a Tool
On a daily basis, it drives me nuts to see the number of breeders who refer to Genomics as a selection tool. Genomics increases the reliability of individual traits and indexes. That’s it. The term “Genomics” is misused by many. They should be referring to “High Index” sires, meaning list toppers on the gTPI, gLPI, and other lists. This may seem like a minor thing. I am even guilty of it myself, from time to time. However, it’s really an enormous error when you consider it from a breeder viewpoint. Over the past week, I looked at more than 100 comments about Genomics from naysayers. Every single one of them would have been more accurate if they had used the term “High Index” actually than Genomics. Most of the reservations against Genomics have more to do with reservations about the use of high index sires. The debate between selecting for “High Index” or “Proven” pedigrees will go on for years to come. The point that many miss is that Genomics is a tool that can help both strategies. Since Genomics helps increase the accuracy of the indexes, it will help both approaches excel into the future.
The Numbers Don’t Lie
It’s always easy to quote a case-by-case example and find a few cases that help support a point of view. However, it takes consideration of the full spectrum to get a truly accurate assessment of how any program or any tool is working. This means that we can be 95% sure that the current top gLPI sire, RH Superman (gLPI of +3473), will be higher than +3000 LPI, once he has his official progeny proven index. That prediction is over 90% reliable, and that would make him among the top 3 active proven sires in Canada. In the US, sires like Delta (gTPI of +2691) will end up over +2300 gTPI placing him in the top 20. (Editor’s note: Prior to the regression to bring high genomic young sires closer to proven sires, sires like Extreme and Alta1stclass would have actually been higher than the current top proven sire). Yes, genomic young sires do on average drop below their original predicted values, but, they are on average still higher than the proven sires of that time.
Falling Numbers are not an Indicator of System Failure
Whether it’s young sires’ indexes dropping or semen prices going down, neither of these two events accurately predict the value of Genomics. You see Genomics is new to the industry and, with anything that is new, there is a period of figuring out how the “new world” will work. During that period, aggressive breeders and semen companies have sought to maximize revenues for themselves and the breeders they represent. This has meant testing the market to see exactly what should be the maximum revenue price for each animal or dose of semen. Simple economics teaches us that we need to test to find the point that maximizes revenue. That is either by selling at high prices and reduced quantities or selling at a medium prices and increasing quantities. Both are sound strategies. At times, due to exclusivity and extremely unique genetics, young sire semen has sold for up to $10,000 a dose and, with the removal of the exclusivity and with other sires coming out after the fact, that semen is now available at a significantly reduced price. (Read more: $10,000 a dose Polled Semen). The breeder who purchased this semen, Ri-Val-Re Holsteins from Michigan, actually made out very well with his investment, as he had a clear plan with the use of IVF to maximize his return. (Read more: Breeding R-Val-Re: Where looking good in the stall is just as important as looking good on paper) It has also led to other attempts and premium pricing or pricing models. This is not a failure of the system. This is progressive individuals trying to discover how the new system is going to work. Does it always return maximum profits?….No. However, does it help those individuals understand the new market and how they can operate to maximize efficiency in the future? ….Yes. Just because you are not able to justify these prices for your breeding program goals, does not mean that it will not work for others. The important thing is for you to understand your personal dairy genetic plan and goals and make sure you are constantly evaluating and improving them. (Read more: What’s the plan?). It is interesting to note that since the introduction of Genomics, the rate of genetic advancement has more than doubled. Coincidence? I don’t think so. Today more breeders can make more sound decisions. The industry, as a whole, is benefiting.

The Bullvine Bottom Line

Unlike cigarettes, where there is certainly no question left about the health risks of smoking, genomics and cigarettes are not interchangeable. There is significant proof that genomics does, in fact, provide good “health” for your dairy breeding program. To genomic detractors, I ask you “Where is your smoking gun”? Where is your proof that genomics does not work?

Not sure what all this hype about genomics is all about?
Want to learn what it is and what it means to your breeding program?
Download this free guide.

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Categories : Genomics

The Bullvine proves Genomics does not work!

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Wednesday, April 1st, 2015

April Fools. There are just those breeders who will never accept Genomics as a tool in their breeding toolbox. For those of you who have or are still need convincing on why to use genomics in your breeding strategy we offer the following articles:

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.

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Categories : Genomics

Are You Making the Most of Genomic Information?

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Wednesday, March 25th, 2015

Much has been written about genomic indexes since they were introduced in 2008, yet one key ingredient has been ignored. That ingredient is how can a breeder use the genomic information to analyse and plan for the future breeding of their herd? To fill that need Holstein Association USA, and Zoetis joined forced to develop the Enlight service that any Holstein producer in the USA can benefit from using.

Let’s hear about Enlight from Lindsey Worden

Lindsey is the Executive Director of Genetics Services at Holstein USA and when listening to her speak about Enlight you can hear the enthusiasm in her voice. Enthusiasm for what a breeder using Enlight can do to advance their herd. As Lindsey says, the advancement can cover more than genetics. It extends to others areas including management, reproduction, health and in the future nutrition. That is a wide scope. For U.S. dairy people interested in learning the opportunities available, go to Holstein USA’s website to learn more.

Enlight Home Dashboard

One final matter that Lindsey emphasized to The Bullvine – “Enlight is a free tool for any dairy producer who is genomic testing their Holsteins through Holstein Association USA or Zoetis, using CLARIFIDE^®, a genomic testing product. Enlight is web-based, and has a direct connection to the Holstein Association USA herdbook database, so all animals in Enlight must also be in the Holstein herdbook”. It should be noted that a herd’s data contained in Enlight is proprietary to the herd owner and is not shared with others.

Worden Draws on Experience

Lindsey grew up on her family’s dairy farms in New York and New Mexico, and was active in 4-H and Holstein Junior programs, including dairy judging and showing. She followed that by studying Dairy Science and Life Science Communications at the University of Wisconsin-Madison. After college, she joined Holstein Association USA. That was over eight years ago, and she has filled a number of positions of increasing responsibility at Holstein USA. Lindsey is familiar with all facets of dairying from the small breeder’s herd, to the large commercial herd, to the show scene and to the international trade in genetics. She gives major credit to her parents for giving her and her brothers the opportunity to experience life, both on and off their farms. Lindsey attends many industry events and is always eager to speak with breeders to understand their positions, their concerns and their needs, and to explain Holstein USA services.

Enlight – Animal Snap shot

Working to Shared Benefit

In short, Enlight was developed in partnership by Zoetis and Holstein USA. They saw an opportunity to combine their collective strengths for the benefit of producers. It is novel in that a private company and a breeder not-for-profit association joined forces to provide a service, and refreshing to see that providing dairy people with a complete package is central to the service.

Excellent Uptake

Lindsey reported to The Bullvine that since July (2014) there have been over 600 herds enrolled in Enlight, and those users have genomic tested over 260,000 animals in total.

U.S. dairymen can expect to hear more about Enlight in 2015 as Holstein USA, in collaboration with Zoetis, will have this service as a focal point at meetings and in communications through out this year. It is interesting to hear the many different ways Enlight users are taking advantage of genomic information in their herds. Many begin with testing a few animals and eventually work up to testing most or all of the heifers born on their farm. Dairymen are using the information to make decisions about which animals will be parents to the next generation on the farm, making sure they are keeping and propagating the best genetics in their herds, and using the lower end genetics for recipients, or culling when they have excess animals to sell.

One important part of Enlight is that it is real-time. Enlight is refreshed every night, so whenever a dairyman registers a calf, or has new genomic or genetic information available, it can be viewed in Enlight. Since the service if free and web-based, users can run the analysis of their animal as often as they wish.

Enlight – Genetic Progress Graph

Expanded Service

For dairy farmers, linking all pieces of information on their animals together is important. Sandy-Valley Farms have been using Enlight for a few months now to capture their actual and genetic information in one place, to obtain genomic information instantaneously and to download information in Excel documents. And Danae Bauer of Sandy-Valley looks forward to using Enlight even more in the future as more options and screens are added to it. (Read more : PINE-TREE MONICA PLANETA IS THE NEW GENOMIC SUPER STAR MAKER, and DANAE BAUER: CAPTURING THE PASSION)

Holstein Association USA continues to see interest in genomic testing grow each year, and with the availability of Enlight to help producers make better use of their information, and a partnership with Zoetis, that trend is only expected to continue to increase. As more breeders are exposed to how using genomic information can improve their herds, more and more will adopt the technology and find benefit in keeping track of their genetics with Enlight.

The Bullvine Bottom Line

With many dairymen already using Enlight, there are many users that Holstein USA or Zoetis can direct interested producers to in order that they can hear a fellow dairy person describe the benefits as they see them. Enlight is definitely a win – win – win for producers – breed association – private service provider.

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.

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Categories : Genomics

Tags : CLARIFIDE, Enlight, Holstein USA, Zoetis

Dairy farms need ‘wake up’ call on genomics

Wednesday, March 18th, 2015

The dairy industry needs to “wake up” to the dangers of using genomic bulls on maiden heifers, according to a breeding specialist.

Munster AI’s Doreen Corridan claimed that more heifers are experiencing difficult calvings this year because both farmers and farm advisors ignored best practice by mating low reliability bulls with maiden heifers.

“I’m hearing about a lot of calving difficulties and Caesareans in heifers that were carrying calves by some genomic bulls that have since topped the latest spring AI list,” said Ms Corridan.

Among the farms that are facing culling first calvers due to problems this spring was the Greenfield demonstration farm in Kilkenny. Management there decided to use two genomic bulls on maiden heifers in an effort to accelerate EBI gain in their 2015 calf crop.

“It was our own mistake and we definitely won’t be doing it again,” said Teagasc specialist on the Greenfield project, Abigail Ryan.

She added that the risks associated with using genomic bulls on maiden heifers were considered worthwhile last year because of the sires’ very high EBIs and low calving difficulty scores. However, the plan has backfired, with two heifers subjected to Caesareans likely to be culled this year.

“We ended up with two Caesareans out of the 89 heifers that have calved down so far this spring. They’re barely milking now and I’d say they’ll be culled, even though they were smashing heifers. We jacked a good few of them too, but these animals are all doing fine now,” she said.

Teagasc research has shown that every Caesarean can end up costing the farmer over €700 in dead calves, higher culling rates, lower milk yields, labour, and veterinary costs.

“We cost Caesareans at six hours in labour for the farmer and a minimum of €160 for the vet,” said Teagasc geneticist, Donagh Berry.

“We also assume that the cow has a 5pc higher chance of dying, and 25pc more likely to be barren. There’s also the cost of the calf and the loss of 600kg of milk.”

Even calving interventions that don’t require a vet cost farmers dearly.

“What we class as severe assistance by the farmer will result in a 5pc increase in barreness, 50kg less milk and additional hours of labour. That’s going to be close to €150 per cow,” said Mr Berry.

Workload

Doreen Corridan believes that genomic proofs are not as accurate on calving difficulty as other production traits. This may be partly due to the subjective nature of scoring calving difficulty for farmers at a time when they are under severe workload stress.

“Gene Ireland is the only way that we can get accurate information on crucial issues such as calving difficulty and congenital defects,” said Mr Berry.

“It ensures that we have a minimum number of animals in commercial situations where the farmer has no vested interest in playing with the figures.”

Ms Corridan’s advice for farmers is never to use a bull on maiden heifers that has a calving difficulty index of more than 2pc, or a calving index reliability that is lower than 90pc.

“Yes, you are compromising your genetic gain, but at least you are guaranteeing that your heifers survive into cows.

“A lot of Teagasc advisors were mating genomic bulls with maiden heifers. Both they, and some farmers, need to cool the jets on the chase for elite EBI calves,” she said.

Source: Independent.ie

Categories : Genomics

Arm Chair Quarterbacks, Monday Night Football and Tuesday Morning Genomics

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Monday, March 9th, 2015

If you were the coach of an NFL football team, would you select your players based solely on looking at them or would you want to see their performance statistics, in order to decide how to assemble the best team possible? That is the question that Don Bennink (Read more: NORTH FLORIDA HOLSTEINS. Aggressive, Progressive and Profitable!!) asked at the recent genomics conference. (Read more. Genetics in the Age of Genomics – Seminar Recordings and Recap) While it’s a pretty simple question, it may forever change the way you make your mating decisions.

For generations, we have all been taught to look at a cow the same way, and that’s the way we continue to teach the next generation to look at dairy cows today. But just because that is the way it has always been done, does not mean that we have been doing it correctly. We all start out learning the parts of the dairy cow and have learned the same way as we always have on how to evaluate cows. In fact, one major publication did seven editions in a row about how to evaluate cows, and each one presented the same way it’s been done for generations. It doesn’t seem to matter that evaluating type or conformation has been proven not to be the most accurate way to determine longevity (Read more: She ain’t pretty she just milks that way).

For years, it has been assumed that, if a cow had “high type” and lots of production, she was the perfect cow. But we all know that perfect cows don’t always exist (Read more: The Perfect Holstein Cow). Nevertheless, we have bred for these two key areas: high type and lots of production. We totally disregarded that we did not make substantial gains in profitability. And, furthermore, herd life actually decreased, even though we all bought into to the theory that a high type cow is a long lasting cow. Unfortunately, actual performance data shows that, as we bred for this the cows were actually lasting less time than before. In fact mortality rates increased; conception decreased and the number of lactations that most cows lasted decreased.

Through the years, the use of high production and low fertility bulls has actually decreased overall herd conception rates. Don points out that when he “first started milking cows, and AI was in it’s infancy, farmers up and down the road, had a 60% conception rate. Today people brag if they have a 30% conception rate.” Don also points out that in 1996, 93.4% of the calves that were born in the US lived, (i.e. a 6.4% stillborn rate). In 2002, the stillborn rate increased to 11% (i.e. 89% lived) and by 2007, 14% of the dairy calves died at birth. It’s only in more recent years that the industry has acknowledged this trend and has started to put more emphasis on conception and the significant impact it has on profitability. The reason for this is we put so much emphasis on a two-year-old production that we were killing reproduction. That is because cows that get back in calf regularly drop in production because they have to use some of their energy to support the development of their calves. So the sires that gave the maximum amount of milk were also the sires who had the lowest conception rates. We all know that a cow that is milking hard is the hardest cow to get back in calf. No matter what their conformation.

The thing is that we have the systems and technology to make the changes we need to make for the future. As Don points out, we don’t need to go to the 125-year old technology of type evaluation to solve this problem. Instead of having to use theory to predict longevity, we can actually measure productive life through the actual length in months that cows last in herds compared to their herd mates. We don’t need type evaluation to guess who will last longer; we have the actual information. We have the ability to see just which cows will last longer, not from trying to figure out what type trait links best to longevity. We have actual longevity data, SCS, fertility, conception, still births, etc.

We are all armchair quarterbacks. We are all willing to second guess the mating decisions of others after the fact. The challenge is that, with the technology we have available today, we don’t have to do as much second guessing as in the past. Tools like genomics and new performance data such as DPR, Still Birth Rate, and Productive Life tell us everything we need to make an informed decision. Don asks, “Can you just pick the perfect team by just looking at your players? Or would it help to know which players have drug issues, which ones will end up in jail, which ones will last a full season, and which quarterbacks can actually complete a pass, or know how many sacks your linebackers have made in the past. As a coach, you want all this data to choose your team. Well we are not coaches we are dairy farmers, and we make our money milking cows. Don’t you want that data on your animals? Or are you just going to keep looking at them and think that you can guess which ones could perform?”

In today’s day and age, we not only have traits that are more directly connected to longevity than type evaluation, we also have genomic testing that can more accurately predict what sires and cows will last longer. Every Tuesday we now receive genomic predictions on animals. We don’t need to wait till for a quarterly classification visit, that may or may not catch a cow on her best day, to evaluate what we think from looking at her is the probability that she will last more lactations. We can actually get much more accurate data at a younger age on how long she will stay in the herd.

The Bullvine Bottom Line

Sometimes it can be hard to change the way we have always played the game. When something has been done for generations, there will always be those who are resistant to change. However, the industry has changed and the amount of information available today to make mating decisions is light years ahead of what it was just a few years ago. The game is changing, and you need to change what you base your breeding decisions on. . The best coaches and quarterbacks make their decisions based on performance data, not on hypothesis. Genomics has helped take away the guessing game. We can now know at a very young age, what the genetic potential of that calf is. We can make better decisions faster. In the past art and practical knowledge was what drove mating decisions. However, today’s breeding world calls for a different approach. It takes a level of focus and commitment, and it’s a business. It is just like football, where the coaches now use all the information possible to decide what players to put on the field and how to use those players for the big game on Monday nights. Tools like genomics have changed the game forever.

Not sure what all this hype about genomics is all about?

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Categories : Genomics, The Bullvine

Tags : Dairy Cattle Classificaiton, Don Bennink, Genetic Evaluations, Genomics, NORTH FLORIDA HOLSTEINS

Genomic Testing – Are You Missing Out?

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Thursday, August 21st, 2014

When The Bullvine mentions genomic testing to production oriented breeders, we frequently get the reaction “Oh, that’s just for herds that sell high priced animals. I focus on running a profitable milking operation. I don’t need to spend money on testing my animals.” Well, in fact, that is not an accurate assessment of the benefits available from using this tool at the present time. If you are among those not using genomics, Stop Procrastinating! It is a tool that everyone breeding their herd to improve it genetically should not be without.

Only Very Moderate Uptake – So Far

Currently, there is an 8% uptake of genomic testing of all Holstein heifer calves. The total is less in other breeds. We have barely scratched the surface. Half a century ago, official milk recording was at the same low level. Today it is recognized as a much-needed toll both on-farm and in the national herd. Obviously the question that breeders need answers to is ‘How will I benefit from genomic testing all my heifer calves?’

Known Benefits

Much has been written about benefits and opportunities available to breeders who are submitting samples for DNA testing. Those range from selecting the best mates for your females, … to parentage verification, … to how to manage your heifer herd, … to deciding which heifers to breed and which ones to cull or implant, … to polled or not polled, …to finding the genetic outlier of an individual mating, …to an aid in marketing heifers in sales.

Just recently Holstein USA and Zetas launched an exciting service called Enlight. Breeders that submit their samples to Zoetis can through Holstein USA’s website summarize and analyze their heifers for their genetic qualities. This is the first, and no doubt other breeds will establish similar services in the future. Breeding to get the genetics that work best for you and then managing them in the best way possible is definitely important.

At the industry level, genomic testing has also proven beneficial. Alta Genetics, a few years ago, working with large herds in the USA, parentage verified all young sire daughters. It was a significant step forward in accuracy of sire proofs so they could guarantee their product to their customers. Companies like Zoetis and Neogen initiated genomic testing services so they could help producers and also as complementary to their other products. A.I companies have been able to restrict their young sires sampled to only top genomically evaluated young sires, thereby saving millions for themselves by not sampling the bottom enders and millions for breeders that did not have to raise, calve in and milk the lower genetic merit daughters of the bottom end bulls. All of these benefits are leading to cost savings in the hundreds of millions of dollars.

However six years into using genomics we are only starting to reap the rewards.

Genomics Will Make the Future Brighter

Breeders often mention that they want sires to use and females in their herd that are superior to what is available today for traits that are difficult or impossible to measure. Here are some thoughts and facts that may help breeders to decide to use genomic testing so they can have animals that are even more profitable than their herd is today. It does however require that genomic testing becomes routine (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!).

Heifers:

Investigation, at the farm level, is being done in beef heifers on growth rates, diets tailored to genotype, immunity to common diseases and age at first estrus. The results of those studies will be able to be applied to dairy heifers since little similar research is being conducted for dairy heifers. Already breeders can test for the genetically inferior heifers, so they do not need to be raised. Up to $500 per heifer in rearing cost could be saved by having the retained heifers calving by 22 months of age. Remember that it is age at first estrus that is important, for which we have very limited farm data. First breeding depends on a breeding actually occurring. With heifers genotyped and selected for first estrus significant savings will be possible.

Feed Efficiency:

Two major research projects, one in USA and The Netherlands and one in Australia and New Zealand, will identify the cows that are genetically more efficient at converting their feed to milk. Within a couple of years, we can expect to see reports relating genomic information to feed efficiency. This type of research is costly and not currently practical at the farm level, but using research herds this investigation is well underway. Reducing feed costs by 5-10% through genetic selection would result in many millions in savings. That is likely to be crucial to the dairy cattle breeding industry as dairy competes to feed a hungry world. (Read more: Feed Efficiency: The Money Saver and 15 Strength Sires That Will Still Fit In Your Stalls)

Inbreeding:

CDCB already makes available the inbreeding level of genomically tested animals based on their genomic results. No doubt further research results will provide numbers associated with inbreeding. Think about it. In the past the inbreeding level for two full sisters, based on pedigree, has been considered the same. However, by using their genomic profiles the level of inbreeding can be much more accurately known for each sister. A recent report from CDN, for the time period 2010 to 2013, shows that inbreeding rates are increasing not decreasing. Even though breeders are aware that inbreeding is a negative to future profit, they continue using fewer sire lines. More in-depth study of presence or absence of genes that negatively affect the viability of our cattle take time. Why do we always expect someone else to take responsibility for the level and rates of inbreeding? (Read more: 6 Steps to Understanding & Managing Inbreeding in Your Herd and Stop Talking About Inbreeding…)

Disease Resistance:

The list is long on diseases that breeders want their animals to be resistant to. Many research projects are underway to relate the genotype to particular types of mastitis, respiratory diseases, wasting diseases and even production limiting diseases like milk fever. CDN and Canadian milk recording agencies have been capturing field data for a number of years now on eight production limiting diseases. In time, the relationships between genetic lines and these diseases will be better-known. So that selection can be carried out to avoid problem bloodlines. When more animals are genomically tested, and bloodlines prone to diseases are identified great steps forward will be able to be made. It takes considerably more than 8% of the population genomically tested to move breeding for disease resistance to reality. (Read more: Genomics – Opportunity is Knocking)

Reproduction:

Failure to get animals to show good heats, to produce good oocytes and conceive when bred is the leading frustration on most dairy farms. The role that genetics plays in that frustration is now receiving attention by many researchers and organizations. In the past, the capturing of useful data to do genetic analysis relative to reproduction has been a significant problem. The relating of genomic results to reproduction holds out considerable hope. Early embryonic death, haplotypes that negatively impact reproduction, genetic difference between animals for cystic ovaries and many more are all areas of concern for breeders. Once again both genomic and on-farm data are needed to move forward. (Read more: 10 things dairies with great reproduction do right and Are Your Genetics Wasting Feed and Labor?)

Misconception:

I hear breeders say “Genomic indexes are just like production indexes.” However, that is not so. There are genomic indexes for production traits, conformation traits and management traits. Genomics is a dynamic science. It is best if breeders know not only the genomic values for the animals currently in their herds but also their ancestors. To build the genomic history for a herd necessitates that testing start as soon as possible. Genomics is a tool every breeder will benefit from using no matter what their selection goals are. (Read more: Better Decision Making by Using Technology and FACT VS. FANTASY: A Realistic Approach to Sire Selection)

In Another World

Outside the world of dairy cattle but totally related to DNA analysis, there is a study just under way in the United Kingdom, where 100,000 people with cancer or rare diseases are being genotyped to better understand people’s ability to avoid or resist cancer and disease. One of the terms used in the news release was that before there was DNA profiling this work would not have been possible. Relating that back to dairy cattle, if we do not have the DNA information for animals we will be limited in our ability to eliminate deleterious genes from our cattle.

Will Genomic Testing Pay?

The question for breeders appears to have been one of cost – benefit. “What will I get for the fifty dollar cost of doing a low-density test?” The fact is that, to date, milk producers have not taken the opportunity for more rapid genetic advancement by testing all their heifers. However, the tide is about to change. With new information coming out almost weekly on how the genetic (aka genomic) make-up of an animal relates to profitability, breeders without genomic information on their herd will not be in a position to know which sires to use or how to manage or feed their animals. Genomic testing needs to be viewed as an investment rather than a cost. Invest $50 shortly after birth to save hundreds over the cow’s lifetime.

The Bullvine Bottom Line

Every journey requires that a first step be taken. The first step is that breeders submit samples for DNA analysis. Every breeder will benefit by knowing the genomics of their herd. No doubt the cost of testing will come down as more breeders participate. Future success in dairying will require genomic testing, just as current success depends on capturing and using performance information. Are you prepared for using genomic information to assist in creating your future success in dairying?

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

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Categories : Genomics

Tags : Canadian Dairy Network, Council for Dairy Cattle Breeding, Disease Resistance, Enlight, Feed Efficiency, Genomics, Holstein USA, Inbreeding, Neogen, Reproduction, Zoetis

Proper Use of Genomic Evaluations

Wednesday, August 6th, 2014

Over the past 5 years, genomic evaluations have been the hot topic for dairy cattle genetics. Yes, the technology is exciting. However, any new technology typically receives undue hype after its launch and unrealistic predictions of impact are promoted. The initial period of unwarranted hype about a new technology is usually followed by a time of reflection, which in turn is followed by periods of disillusionment and, eventually, proper implementation of the new technology.

Definitely, genomic evaluations of dairy cattle have been the topic of considerable hype and, perhaps, unrealistic expectations have been nurtured by some. Let’s face it – the potential positive impact of a new technology is likely to be emphasized and the potential downsides are likely to be glossed over. So, where are we on the hype/reflection/disillusionment/proper adoption path in regard to genomic evaluations? Probably, somewhere between reflection and disillusionment, but proper adoption will be the next step.

Reliability versus Accuracy

An overriding problem is interpretation of the “accuracy” of genomic evaluations. How is “accuracy” measured? Well, most would say by the reliability published alongside each genomic PTA (transmitting ability) for an individual trait or for an index that combines traits into a single value (such as Net Merit). However, are reliability and accuracy the same thing? No, they are not!

Accuracy has a specific statistical (scientific) meaning in addition to an intuitive meaning. Accuracy is a measure of the confidence range around a PTA – say, plus or minus 200 lb of milk or plus or minus $50 for Net Merit. Mathematically, accuracy for genetic evaluations is calculated as the square root of reliability. To put this into perspective, we will compare reliability versus accuracy alongside their corresponding confidence range for Net Merit for the four types of genetic evaluations of bulls – Parent Average (average of the PTA of his two parents), genomic test, first-crop daughters, fully proven (thousands of daughters in hundreds of herds). We will use a confidence range of 68% (which means there is about a two-thirds chance the eventual Net Merit of a bull will fall within the range).

The reliability of the genetic evaluations for Net Merit of most Holstein A.I. bulls is about 38% (Parent Average), 70% (genomic test), 85% (first-crop daughters), 99% (fully proven). These reliabilities suggest the result of a genomic test almost doubles the genetic knowledge known about a young bull without daughters. However, that is NOT the case. The accuracy of the genetic evaluations for Net Merit associated with those four levels of reliability are 62% (Parent Average), 84% (genomic test), 92% (first-crop daughters), and 99% (fully proven).

Use of accuracy instead of reliability demonstrates the gain in genetic knowledge when going from Parent Average to genomic testing isn’t as large as reliability leads one to conclude. The truth is Parent Average is a fairly good predictor (but far from perfect) of eventual PTA for traits of bulls or females. Yes, genomic testing provides improvement in accuracy over Parent Average, but it doesn’t provide the extent of improvement that some have suggested – certainly not, “a doubling of knowledge”. Most people in the dairy industry are likely unaware that reliability and accuracy are different measures and reporting of reliability exaggerates the increase of genetic knowledge when moving from Parent Average to fully proven status for bulls.

Reliability, accuracy, and 68% confidence range for Net Merit of Holstein bulls
Type of evaluation	Reliability	Accuracy	Confidence range
	(%)	(%)	($Net Merit)
Parent Average	38	62	±157
Genomic	70	84	±110
First-crop daughters	85	92	±77
Fully proven	99	99	±20

Over-Evaluation of Highest Ranking Individuals

The greatest frustration has been the over-evaluation of highest-ranking young bulls by genomic testing. This upward bias of PTA for highest-ranking bulls is now well-documented by both researchers and A.I. organizations. The extent of this upward bias has been estimated by some to be at least $150 for the Net Merit index and 200 for the TPI index of Holstein USA. The upward bias is more pronounced if the PTA of the sire of a young bull is also genomic-only (no daughters contributing to the sire’s PTA).

Consequently, most in the dairy industry recommend separate rankings of proven bulls (with daughters) versus genomic-only bulls (no daughters), because the genomic-only bulls are more likely to drop for PTA than bulls with daughters contributing to PTA. Definitely, when genomic-only bulls are selected for use in a herd, a group of them should be used to spread the risk over a larger number of bulls. Proven bulls can be used with more confidence in regard to potential changes of PTA.

Genomic testing of heifers

Some that provide advice to dairy producers recommend genomic testing of all heifers to determine which surplus heifers to sell or to breed to beef bulls. However, routine genomic testing of all heifers in commercial settings should be given very careful consideration prior to implementation. It’s important to keep in mind environmental influences, in addition to genetics, are large on the eventual performance of heifers as cows. For example, differences of heifers due to respiratory illness that causes lung damage, the lack of growth, and structural deficiencies could easily overcome differences for genomic test results versus Parent Average. Also, daughters of genomic-only bulls are more prone to changes of their genomic test results over time compared to daughters of proven bulls with daughters contributing to their genetic evaluations.

Source: University of Minnesoa

Categories : Genomics

Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!

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Friday, August 1st, 2014

There are certainly breeders who are not fans of Genomics and the heavy use of high index genomic young sires. Yet genomic sires now account for 50% of semen sales. That leads me to propose that genomics will soon be used by 84% of the breeders in the world.

The reason for this has nothing to do with the merits of genomic sires versus proven sires. Rather it has to do with the historical patterns of adoption of new technologies. The theory behind this is called the Diffusion of Innovations. According to this theory, consumers differ in their readiness and willingness to adopt new technology. There are the innovators (2.5 percent of the population), the early adopters (13.5 percent), the early majority (34 percent), the late majority (34 percent), and the laggards (16 percent), who are also the people who still don’t have cell phones or who are not on Facebook.

As far as genomics goes, we have seen that it has followed this same pattern. When genomics was introduced, there was a small percentage of breeders who were so excited about the technology, or technology in general, which started using genomic sires instantly. These were the innovators in the dairy breeding marketplace. Since the information was not publically available and held by the A.I. centers, this uptake was very restricted. Then came the public introduction of genomics and the early adopters started using it. For a little while after that genomics seemed to stall. While there was 16% of the marketplace that was excited about Genomics and the possibilities that it held, the majority of breeders were not convinced. They had skepticism about whether genomics would work and if they should be using this new technology in their breeding programs. Regardless, the momentum started to grow.

Malcolm Gladwell describes this point, after early adoption, as “The Tipping Point” in his titled bestselling book of the same name. It’s at this point that it is determined whether something will spread like wildfire or sputter and fade into oblivion. Gladwell’s central argument is that there are actually a number of patterns and factors that are at play. They have an effect in virtually every influential trend, ranging from the spread of communicable diseases to the unprecedented popularity of a particular children’s television show. If you analyze the evolution of any significant phenomenon, Gladwell suggests, you will find that the processes involved are strikingly similar. Based on his in-depth research spanning a number of different fields, industries, and scholarly disciplines, Gladwell identifies three key factors that each play a role in determining whether a particular trend will “tip” into wide-scale popularity or fade. He calls them the Law of the Few, the Stickiness Factor, and the Power of Context.

The following is a closer look at each of these concepts and how they apply to what we have seen in the adoption of Genomics in the Dairy Breeding Industry:

The Law of the Few
Before the tipping point can be reached, a few key types of people must champion an idea, concept, or product, Gladwell describes these key types as Connectors, Salesmen and Mavens. If individuals representing all three of these groups endorse and advocate a new idea, it is much more likely that it will tip into exponential success. Regarding the use of genomics in the dairy breeding industry, these roles were filled by the large A.I. companies, their salespeople as respected high index breeders.
The Stickiness Factor
This refers to the unique quality that compels a phenomenon to “stick” in the minds of the public and then influences their future behavior. Gladwell defines the Stickiness Factor as the quality that compels people to pay close, sustained attention to a product, concept, or idea. In the dairy industry use of genomics, this was the allure of significantly more accurate genetic evaluations for young animals combined with the ability to dramatically accelerate breeding programs.
The Power of Context
This is enormously important in determining whether a particular phenomenon will tip into widespread popularity. Even minute changes in the environment can play a significant role in the likelihood of a given concept attaining the tipping point. If the environment or historical moment in which a trend is introduced is not right, it is not as likely that the tipping point will be attained. Clearly, in order for a trend to tip into massive popularity, large numbers of people need to embrace it. However, Gladwell points out that certain groups can often be uniquely helpful in achieving the tipping point. For genomics, commercial dairy producers were that group. When they started to adopt the use of genomic young sires that marked the point at which genomics fulfilled the three concepts and crossed the tipping point.

After the use of genomic young sires crossed the tipping point, the rate of adoption accelerated to the point where the limiting challenge was not consumer demand, but rather the ability of A.I. companies to supply the semen. Because young sires produce far less semen than mature proven sires, it is hard for A.I. companies to meet demand. This has actually led to an increase in the number of young sires being sampled compared to the number that was forecast when genomics was first introduced. A.I. companies have had to sample more sires than predicted in order to meet the growing demand. It has also led to a much shorter active use life span for sires than in the past.

The Polled Story

In looking at the three tipping point factors, when applied to the dairy industry, you can see why some trends may not have been adopted as quickly. An example of this is the use of polled sires. Polled sires have been around for years but have failed to gain significant traction until recently. (Read more: Polled Dairy Genetics: The Cold Hard Facts, From the Sidelines to the Headlines, Polled is Going Mainline! and Why Is Everyone So Horny For Polled?) That is because while polled certainly has the concept of the Law of the Few, it has not had the Power of Context. While there have been significant gains in quality of the polled sires available, adoption will not pass that tipping point until it meets the third concept that Gladwell highlights, which is the Power of Context. Until there is significant consumer demand that dairy cattle not be dehorned, the use of polled sires will not pass the tipping point. While there will certainly be polled sires in the top 10 genomic sires within 2-3 years, and proven sires in 5-6 years, polled semen will not account for more than 16% market share until it develops the Power of Context (consumer demand for animal treatment) needed to cross the tipping point. It’s for that reason that I think that widespread polled semen use will not really take off until 10-12 years from now. Until then, it will be the domain of the innovators and the early adopters and stay below 16% market share. In fact, I would argue that it has just recently crossed over in the past couple of years from the innovators to now include the early adopters.

The Bullvine Bottom Line

Throughout history, there have been many excellent examples of products or technologies that have failed for a variety of reasons. Genomics met resistance similar what was faced by artificial insemination in the early days. However, currently genomic usage has crossed the tipping point. It is now inevitable that soon 84% of the dairy breeding industry will be using genomic sires.

Not sure what all this hype about genomics is all about?

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Categories : Genomics, The Bullvine

Tags : A.I. Industry, Genomics, Malcolm Gladwell, Polled Dairy Cattle, Polled Dairy Genetics: The Cold Hard Facts See more at www.thebullvine.com/polled-dairy-cattle/polled-dairy-genetics-cold-hard-facts/ ©www.thebullvine.com, Sire Usage, Tipping Point

The Genomic Roller Coaster – Hold on it’s going to be a bumpy ride

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Friday, July 11th, 2014

Since the very first genomic young sire lists were published in April of 2011, it certainly has been a very bumpy ride for the dairy breeding industry. Top sire lists are changing almost monthly. Contract sires seem to go cold even before breeders have a chance to breed their animals. This has many breeders feeling dizzy and asking “Does this genomic index thing really work?”

We here at the Bullvine decided to take a closer look. We took the Top 20 gTPI sires from April of 2011 and compared them to the Top 20 proven sires from April of 2014 to see who performed better over the past three years. The reason we are using the top 20 sires is that based on semen sales, most breeders, when using high index sires, prefer to stick to the very top of the list. Therefore, doing a comparison on the top 200 or even 100 sires would not be an accurate representation based on actual usage. The following is what we found.

TABLE 1 – Top Genomic Sires April 2011 to April 2014

The top 20 Genomic Sires from April 2011 dropped about 10% upon receiving their official daughter proofs in April 2014. Key areas that saw significant decline were DPR (57%), PTAF (31%), PTAM (27%), PL (24%) and PTAP (26%). This tells us that the genomic markers used in April 2011 for these traits were not as accurate as say SCS, SCE, DCE, UDC and PTAT, which saw less significant declines from April 2011 to April 2014.

TABLE 2 – Top Proven Sires April 2011 to April 2014

On average, the top proven sires from April 2011 held up pretty well on the April 2014 results seeing only 3% decline. Though interestingly we do see the same trend as in the genomic sires where the PL, DPR, PTAF lead the way with the greatest declines. Also of interest are the changes in ranking. In April 2014 the top three sires from this list were Badger-Bluff Fanny Freddie, Regancrest Altaiota, and Lotta-Hill Shottle 41 none of which were in the top 5 in April 2011’s top proven sire list.

TABLE 3 – Comparison of Top Genomic and Proven Sires from April 2011 (April 2014 values)

If you had used the top 20 genomic sires from April 2011 rather than using the top 20 proven sires from April 2011, you would have come out 3% ahead. More importantly let’s look at each sire did in the actual ranking.

TABLE 4 – Ranking of Top 20 Genomic and Top 20 Proven Sires from April 2011 in April 2014 values

Interestingly none of the top 7 sires in April 2014 were from the top 3 on the April 2011 Top Genomic or Top Proven Sires list. In fact, the top proven sire in April 2014 was Robust, who was 14^th on the Top 20 Genomic Sires in April 2011. The top Genomic Sire from April 2011, Shamrock, is actually in 17^th spot on this list. That is more than 200 points behind Robust, who in April 2011 was 169 TPI points behind Shamrock. That is a 370 point swing between these two sires. When you think about this from the effects it has on your breeding program, owners of daughters from Ladys-Manor Pl Shamrock, Mr Chassity Gold Chip, and Wabash-Way Explode who once thought they would have the next list toppers for sure. Now they find themselves (on average) behind daughters of Roylane Socra Robust, De-Su 521 Bookem, Sully Altameteor, RMW Armitage, Co-Op Upd Planet Yano, De-Su Observer, UFM-Dubs Sherac, and Vendairy Wonder. When they were making their mating decisions back in April 2011, breeders thought the first group would surely outperform the second.

Analysis reveals an even more alarming situation than this. What it shows us is that sires that were not even on the Radar back in April 2011, ended up outperforming the top 20 Genomic sires from April 2011. In fact, 4 of the 10 sires from April 2011 were not in the top 20 Genomic or Proven Sires in April 2011, and 25 of the top 30 proven sires from April 2014 were not on the top 20 Genomic or Proven Sires lists in April 2011.

TABLE 5 – Top 10 Proven Sires April 2014

TABLE 6 – Top 40 April 2014 Proven sires that were missed

While a few of these sires may not have been missed because they were about to receive their proven daughter proof shortly, the majority fall into a situation where they were just not as high ranking as the top Genomic sires from April 2011 but they held their values much better.

When looking at the 25 sires that were in the top 40 proven sires in April 2014 that did not find themselves in the top 20 Genomic or Proven Sires in April 2011, a strong trend starts to show itself. All of these sires were within 15% of the top genomic sire from April 2011, Roylane Socra Robust. This tells us is that you can’t only use the top 10 or 20 genomic sires, if you expect to have the best results in your breeding program. In fact, you need to consider sires that are within 15% of the top genomic sire. When you compare the top 20 Genomic Sires from April 2011 to these 25 sires you find the following:

TABLE 7 – Comparison of Top 20 Genomic Sires from April 2011 to Missed Sires

Applying this analysis to today’s breeding strategy shows us that we cannot just use the top 20 Genomic sires that are available, in order to have the best long term results. Instead, we need to use sires that fall within 15% of the top current genomic sire, Cogent Supershot, who has a current gTPI of +2625. That means all sires that are 2231 TPI currently could easily be in the top 10 proven sires in April 2017. That will be a list of sires that has over 600 bulls on it. Even if you remove the two proven sires (Robust and Dorcy) as well as those sires that are older and about to receive daughter proofs shortly, you are still left with over 500 genomic sires to choose from. That means that currently there are over 500 genomic sires that could be in the top 10 proven sires in April 2017.

The Bullvine Bottom Line

While many breeders battle to get their hands on the early release semen of the top 10 genomic sires, and A.I. units are putting extremely high prices on this semen, analysis of performance data from the top sires in April 2011 shows us that these sires are not necessarily going to outperform the other available sires. Breeders who used sires like Ladys-Manor Pl Shamrock, Mr Chassity Gold Chip and Wabash-Way Explode now find themselves behind sires such as Den-K Altagreatest, Pine-Tree Picardus, and Altaceasar. These were all sires that in April of 2011 were not even on most breeders’ radars. While genomic indices are an excellent tool for helping develop a short list of sires to use. Performance data shows us that sires that are within 15% of the genomic sires can still produce a top 10 sire. For your breeding program, this means that you need to take a look at all sires who are within 15% of the top sires and consider them for use. This will help you develop your own shortlist, and then using corrective mating tools like GPS (Read more: gPs– Genetic Profile Systems – Dairy Cattle Breeding Made Simple), will help you determine exactly which of these sires will perform best on a mating by mating basis. You can’t just use the top 20 Genomic Sires and expect to get ahead of everyone else. Past performance shows this just doesn’t work.

Not sure what all this hype about genomics is all about?

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Categories : Genomics

Tags : Genetic Profile Systems, Genomics

Top 200 New Genomic Females For July 2014

Tuesday, July 1st, 2014

Topping the list of the top 200 new genomics females in the USA is S-S-I MONT 8679 10721-ET a BACON-HILL MONTROSS-ET owned by Select Sires Inc. Also coming out as the top new NM$ daughter is EDG EMLEE FLAME 57856-ET a VIEUXSAULE FLAME-ET daughter owned by Elite Dairy Genomics LLC.

Leading sires of the top 200 are MR WELCOME HILL TANGO-ET (24), VEKIS CHEVROLET-ET (14), COYNE-FARMS JABIR-ET (14), VIEUXSAULE FLAME-ET (13) and COYNE-FARMS JACEY CRI-ET (12).

Top breeders of the top 200 are De Su Holsteins (16), SANDY-VALLEY (15), Elite Dairy Genomics(10), and Bomaz Inc (10).

Lot	UI	Price	Notes
25		$265,000	Calbrett Supersire Barb RDC (GPA LPI +3,386), a Supersire x Rainyridge Super Beth (VG-86 Superstition) x Talent Barbara (EX-95). SOLD BY HOLSTEINWORLD PRODUCTIONS Calbrett Supersire Barb RDC (GPA LPI +3,386), a Supersire x Rainyridge Super Beth (VG-86 Superstition) x Talent Barbara (EX-95). SOLD BY HOLSTEINWORLD PRODUCTIONS Calbrett Supersire Barb RDC (GPA LPI +3,386), a Supersire x Rainyridge Super Beth (VG-86 Superstition) x Talent Barbara (EX-95). SOLD BY HOLSTEINWORLD PRODUCTIONS Calbrett Supersire Barb RDC (GPA LPI +3,386), a Supersire x Rainyridge Super Beth (VG-86 Superstition) x Talent Barbara (EX-95). SOLD BY HOLSTEINWORLD PRODUCTIONS
1		$125,000	Calbrett Goldwyn Layla (EX 95), 1st Mature Cow and Grand Champion of the 2013 Ontario Summer Show. Out of Lylehaven Lila Z (EX
24		$75,000	Rainyridge Super Beth *RDC (VG 86 2y), a Superstition x Talent Barbara (EX
55		$33,500	Flower Brook Gyna
82		$30,500	Blondin Desty Sally-Red (VG-87 2y), 2nd Int. R&W calf at the Royal in 2011, 6th Sr. 2-year-old at Ontario Summer Show 2013. Shes out of Talent Salena (VG-89) x R Marker Supra (VG-89) x Skychief Supra (EX-93). Sold open, ready to flush or breed.
23		$18,500	The 2nd 4-year-old at Ontario Summer Show 2013, Calbrett Airraid Lu (VG-89, 91MS), x Goldwyn Lyndsey (VG-87 2y) x Lila Z (EX-94). Sold open, ready to flush or breed.
89		$15,500	Calbrett Redliner Surprise, a red and white summer yearling for 2013 x Apple Superb (VG-86) then Blondin Redman Sesame (VG-85) x R Marker Supra (VG-89). She was the 2nd summer yearling in the Ontario Summer Show 2013 (in B&W show).
30		$15,500	Tolamika Goldwyn Madeline (VG 89 3y), the Res. All
2		$13,100
53		$12,500
4		$11,200	Three Windhammer Dec. calves out of Goldwyn Layla (EX 95) sold.
20		$11,000	A VG-86 Goldwyn x Lila Z (EX-94), fresh Oct. 1, 2012, and currently on a flush program. Sold open and ready to flush.
62		$11,000
101		$10,700
11		$10,000	A November Numero Uno x Goldwyn Layla (EX 95) x Lila Z (EX
45		$9,500	A fancy Sept. Sid calf x Goldwyn Breezy (VG 87 2y) x Champion Budgee (EX
19		$9,100	A 9/2012 Aftershock from Lila Z (EX 94) herself!
3		$9,000
56		$9,000	The 3rd place Jr. 3 year
6		$9,000	Three Epic October calves sold from Goldwyn Layla (EX 95) x Lila Z (EX
18		$8,200
61		$8,200
17		$8,200	Four May Mascalese heifers sold by Goldwyn Layla (EX 95) x Lila Z (EX
42		$8,000
78		$7,500	A polled Goldwyn 8/2012 heifer out of Golden Oaks Peach
26		$7,000
33		$7,000	A group of 3 March calf full sisters to Goldwyn Madeline (Lot 30) sold.
83		$6,900	A March 2013 Larson x Sally Red. SOLD BY HOLSTEINWORLD PRODUCTIONS
7		$6,600
86		$6,400	Three Dec. Acme calves from Sally-Red.
9		$6,200
22		$6,100
16		$5,500
12		$5,300
14		$5,300	Two December Alexander heifers sold by Goldwyn Layla (EX 95) x Lila Z (EX
58		$5,200	An Atwood x Esteem Kael YN (VG-89 3y) x Karleen Champion (VG-88)
39		$5,200	A VG 87 Man
29		$5,100	Lexis Champion Magnificent (VG 89 4y), the dam of Lots 30
10		$5,000
37		$5,000	Calbrett Manoman Brandy, a Man-O-Man out of Ben-I-Q Champion Bally (EX-95) x Braedale Baler Twine herself! She sold fresh 5/23.
36		$4,900	Gen I
38		$4,700	Calbrett Manoman Bailee sold fresh 7/2 from Bally (EX-95) x Baler Twine. 94).
50		$4,700
76		$4,700	94) herself, Layla sold open ready to flush or breed.
77		$4,700	Canadian & Res. All American 2010, out of Lexis Champion Magnificent (VG 89 4y). Madeline was also 2nd Jr. 3 year old at BC Spring Show 2012.
13		$4,700
15		$4,500
8		$4,300
31		$4,200
68		$4,200
60		$4,100
75		$4,100
70		$4,000
59		$3,900
21		$3,700
79		$3,600
51		$3,500
32		$3,400
71		$3,300
88		$3,300	Red, a Contender x Advent Gia (EX 90) x Lyster Goofy (EX 90) x Milan Gabrielle (EX 93). She was Jr. Champ. RendezVous R&W 2012 and 1st summer yearling R&W at the Royal in 2012. Sold fresh July 25.
5		$3,200
63		$3,200
64		$3,200
85		$3,200	Q Champion Bally (EX 95, 96MS) sold. She was the Res. All Canadian Jr. 3 Yr. Old in 2007, Res. Grand Champ. Expo Quebec in 2009, and Res. Int. Champ. ON Summer Show 2007. Her dam is Baler Twine (VG 86), the mother of Goldwyn. She sold with a #1 Numero Uno (sexed IVF) embryo.
99		$3,200
40		$3,100
41		$3,100
67		$3,100
28		$3,000
66		$3,000
72		$3,000	35A. Shes from Magical Leduc (VG 85) x Mark Cathy (EX CAN).
100		$3,000	O Man x Duplex Bassy (VG 85) x Champion Bally (EX 95), she sold fresh Dec. 2012. Bred July 22 to McCutchen.
84		$2,900	94).
90		$2,800
91		$2,800
80		$2,700
93		$2,700
94		$2,700
54		$2,500	P * RDC polled (VG 85 2y) x Perk Rae Red (EX 90) x Beauty Rae (EX 90). Tested *BYC.
49		$2,400
92		$2,400	95). She has 2 sons in AI and 2 Numero Uno daughters have sold for $46,000 and $64,000 in 2013, both over 2,400 GTPI. Sold open, ready to flush. SOLD BY HOLSTEINWORLD PRODUCTIONS
69		$2,300
55	A	$2,300	Calbrett Larson Gia, Gynas July calf by Larson. 94).
46		$2,100
65		$2,000	87 2y)
74		$2,000
48		$1,600	old at the Ontario Summer Show 2013 sold, Holywell Atwood pocket (VG 87 2y). Shes an Atwood x Pronto Pocket (VG 87) x Lyster Polly (EX 94) x Progress Polly (VG 94) x Progress Polly (VG 88). She sold confirmed safe in calf with a Windbrook heifer due 12/1/13.
47		$1,550	04).
52		$1,550
50	A	$1,050	92) x Allen Bridget (VG 87).
58	A	$1,000
8	A	$800
29	E-12 & 13-	$325 x 12
29	E-9 & 10-	$225 x 11	Lauthority x Magnificent embryos
82	E-3	$800 x 5
82	E-1	$800 x 5	Colt P embryos from Blondin Destry Sally Red (VG
82	E-2	$800 x 5	Colt P x Sally Red
20	E-2	$750 x 5	5 McCutchens from Lot 20 (above).
20	E	$700 x 5	5 Unos from Lot 20 (above).
23	E	$575 x 4	4 Numero Uno embryos from Lot 23.
96	E	$575 x 4
23	E-2	$550 x 5
30	E	$450 x 6	6 Uno embryos from Lot 30.
23	E-3	$450 x 5	5 McCutchen embryos from Lot 23
26	E	$425 x 6
56	E	$425 x 5
29	E-3 & 4	$400 x 8	Bolton x Magnificent embryos
42	E	$400 x 3	3 #1 Sid embryos from Lot 42.
34	-35-35A	$4,400 x 3	A group of 3 June calf full sisters to Goldwyn Madeline (Lot 30).
82	E-4	$375 x 4	Larson x Sally Red
82	E-5	$350 x 2
29	E-2	$325 x 7	Fever x Magnificent embryos
29	E-1	$325 x 6	Fever x Magnificent embryos
95	E	$325 x 6
43	E & 44E	$300 x 10	10 Uno embryos from Lot 42.
98	E	$275 x 2
29	E-7	$250 x 5	Lauthority x Magnificent embryos
29	E-11	$250 x 5	Sid x Magnificent embryos
27	E	$250 x 5
97	E	$250 x 4
29	E-5 & 6	$250 x 10	Lauthority x Magnificent embryos
46	E	$225 x 6
29	E-8	$225 x 5	Lauthority x Magnificent embryos
47	E	$200 x 2

Provided by Holstein Association USA
* GTPI is a Service Mark of Holstein Association USA

Categories : Genetic Evaluation Review, Genomics

Heifer Genomics and Lactation Performance: Are They Related?

Monday, June 9th, 2014

Over the past few years, we’ve seen many examples of the benefits of genomics on the sire side. Quantifying the advantages of genomic selection on the female side has been slower, primarily due to the cautious adoption of the technology at the herd level. Of the registered Holstein heifers born in Canada in 2013, less than 5% were genotyped. On the other hand, CDN projections show that uptake could increase to surpass the 18% mark by year 2020.

With genomic testing, producers have the opportunity to improve the genetic potential of their herd and decrease costs. This can be done by capitalizing on the herd’s best genetics through the use of sexed semen, flushing or IVF, or by selling the bottom end, breeding them with beef semen or using them as recipients.

Genomic Tested Heifers and First Lactation Performance

Does a heifer’s first genomic prediction provide enough information about future performance to allow confidence in selection and culling decisions at an early age? To answer this question, we examined three Canadian commercial herds that extensively genotyped heifers born in 2011. These animals were chosen since they have had the chance to complete their first lactation and be type classified.

Graph 1 compares the first genomic evaluation for milk yield (GPA Milk) after being genotyped as a heifer calf to the subsequent first lactation 305-day milk production. In total, the chart includes 305 cows born in 2011 from the three herds. Average 305-day milk yield was highest for Herd A, followed by Herd B, and was the lowest for Herd C. In general, within all three herds, the higher the GPA Milk as a heifer calf, the higher the first lactation 305-day milk yield as a cow. This clearly demonstrates the usefulness of genomic evaluations for heifers as a tool for identifying the animals that will perform better in your herd as a cow.

Graph 1 also shows the equations for predicting the first lactation 305-day milk yield in kilograms based on the genomic evaluation as a heifer. While the prediction is not perfect, on average 1 kg increase in GPA Milk resulted in a first lactation milk yield gain of 1.2 to 1.5 kg, depending on the herd. This exceeds the expectation of one kg milk yield per one kg of GPA Milk and presumably results from appropriate management in each herd. The actual yield per kg GPA Milk can be used to gauge whether the management level in a given herd is fully taking advantage of the herd’s genetic potential. If the management level wasn’t taking full advantage of the herd’s genetic potential, we’d expect the actual ratio of milk yield to GPA Milk to be less than one.

GPA LPI and First Lactation Performance

Is a higher genomic evaluation as a heifer calf associated with better first lactation performance? To answer this question the three herds studied above were analyzed separately and their data was subsequently combined to create Table 1. In total, 284 animals with a lactation and classification in first lactation were included in the analysis. These animals were divided into four groups of 71 cows based on their genomic evaluation for LPI as a heifer (GPA LPI). Table 1 compares the actual first lactation performance for production and type for the highest versus the lowest 25% of these animals based on GPA LPI.

The heifers that ranked within the top 25% for GPA LPI in their herd performed better in first lactation on nearly all accounts relative to the bottom quartile. As cows, the heifers that were in the top quartile for GPA LPI produced more milk, fat and protein, and scored higher at first classification for final score, mammary system and feet & legs than those in the bottom quartile. Categorizing heifers into the top and bottom quartiles based on their genomic LPI resulted in no significant difference in the average somatic cell count as cows in first lactation.

Average first lactation performance for the top and bottom 25% for GPA LPI as a heifer

What Does This Tell Us?

These findings validate that heifer calf genomic evaluations can be an indicator of future performance. In addition, they confirm that genotyping heifer calves at a young age can provide producers with useful information for making selection and culling decisions. Lastly, these results show that genomic LPI values for heifers can be used as primary selection criteria as they are related to first lactation performance for both production and conformation traits.
Authors: Lynsay Beavers and Brian Van Doormaal, CDN
Date: May 2014

Categories : Genetic Evaluation System, Genomics

Genomic testing: Feeding the world with profitable cows

Thursday, April 24th, 2014

The dairy industry has greatly evolved over the years with necessity-driven innovation. In order to be efficient in feeding a growing world, it has to.

Dairy producers have to find ways to excel faster and further than they ever have before. Genomic testing, one of the fastest and most powerful breeding tools we have today, does just that.

Genomic testing is no longer a new tool in the dairy industry. However, the innovations for applying this tool are continuing to be discovered at a rapid pace. The practicality and economic logic for utilizing genomic evaluations in commercial female settings is real.

We know more than we ever have about the bovine genome. Even better, we know how to utilize the data for improved profitability and efficiency. Genomic testing is a powerful management tool for realizing maximum gain for return on investment of herd replacements.

The need to increase production efficiency with technology innovation
The agriculture industry needs to continue striving for innovation to meet the nutritional needs of a growing population and increase the average life span with fewer natural resources.

If producers can’t grow larger due to limited space and resources within an operation, they need to strive for efficiency. Growing profitability from a genetics standpoint in replacement heifer groups is one of the most efficient places to experience this gain.

Genetic innovation for increased efficiency within the dairy industry will continue to grow in importance. Genomic-testing calves before making a large initial investment to raise them for replacements reduces resource spending on predicted unproductive cows. Genomic evaluations are a predictive tool for screening herd productivity for the type of cows who will be entering a farmer’s parlor as 2-year-olds.

Applications today in large herds
Since the introduction of genomic evaluations, the Holstein breed has seen an increase of about $80 per year in average net merit value. According to Dr. Paul VanRaden of USDA/AIPL, at the 2014 Advancing Dairy Cattle Genetics: Genomics and Beyond Conference, an increase of $90 per year is realistic.

This expeditious advancement is an example of how powerful the shorter generation interval is at creating higher-profit animals. The female side of genetics has truly had the most benefit from genomic testing technology.

Producers are now able to be more selective for genetics with higher reliability in their replacement heifers, instead of primarily relying on sire selection for genetic advancement.

Producers who are expanding through purchasing large groups of replacement heifers with limited record availability on the group can use the predictive power of genomic testing to obtain a more accurate idea of the type of heifers they are bringing home.

Even if heifers have some pedigree information available, genomic evaluations combined with pedigree information is a much higher reliability prediction of the group’s performance. In addition, a farmer can receive parentage verification for more accurate parent average ranking, genomic inbreeding values and identification of expensive genetic recessive carriers.

Accelerate genetic progress from the female side of your herd with genomic evaluations for breeding program decisions. Depending on your annual needed replacement rate, the cost of testing all or the majority of heifers born can be economically justified from the gain in genetic value and lifetime profitability.

The heifers in a herd are going to be the most genetically valuable animals in a herd because they are one generation further along in progress.

Pre-screening for future high-performing cows gives the ability to shorten the generation interval in your herd with heifer donor selection for ET or IVF procedures. Creating more replacements from the highest heifers in the herd will drastically increase the average genetic value of replacements in just one generation.

Other breeding program strategies include using sexed semen on the top genetically elite heifers to increase the number of future replacement heifers from these higher heifers, culling heifers with lower predicted performance or breeding them with beef semen.

Mating decisions for heifers can be made more accurately using genomic evaluations in sire selection. This data will be more reliable and predictive than solely using pedigree information.

It will also be a stronger line of defense for protecting against potential inbreeding losses. The genomic inbreeding value will be a true measure of how much gene relatedness is in the animal’s DNA.

Testing animals as carriers for expensive recessives and fertility haplotypes will give farmers a better tool to manage the frequency of these genetics in their herd.

It is more genetically efficient to manage the use of carrier sires who do offer profitable mating matches in females than to completely avoid these sires. Genetics can advance aggressively but still protect for recessive dangers.

Managing recessive carriers through a mating program that will protect against two known carriers allows safe use of elite sires who are carriers of the fertility haplotypes.

Herds do not need to completely avoid profitable matings with a particular sire because he is a carrier – but simply to identify and eliminate matings between two carriers. The benefit from reducing losses in abortions and shortening days open intervals would be a high-realized gain from genomic evaluations on replacement heifers.

Ancestor recovery will help producers with data management, which in turn will help them to more correctly identify heifers they believe to be elite based off of pedigree and dam performance compared to herdmates.

The larger a herd, the more calves being born each day and the greater the opportunity for calves to be misidentified at birth. According to VanRaden, more than 50,000 misidentified sires were discovered in genomic sample submissions in 2013.

Applications tomorrow in novel traits
Researchers and academia are pushing forward with hopes of discovering genetic correlation to dairy cattle health traits that will be applicable in everyday herd management. The subjectivity of categorizing health events is the major challenge in advancing these efforts. In order to collect and utilize data from on-farm health events, systems for standardization across the industry need to be established.

The health traits currently in the midst of being researched include a high health immune response for reliability in disease immunity and hoof health traits. Other novel health traits being developed for genetic correlation include a feed efficiency index, heat stress measurement and methane emissions.

As with all new technologies, it takes time to adapt management styles to utilize that information for increased overall herd profitability. The tool will continue to be developed upon and more unrealized potentials for utilizing genomic evaluations on modern, commercial operations will be released.

The dream cow can easily become reality
Writing up a wish list for a producer’s made-to-order ideal cow is easy. A group of moderate-statured, highly productive, feed-efficient cows with sound feet and legs, as well as trouble-free health, paints a general picture of a profitable barn in any region of the U.S.

However, actually, making that dream cow a reality takes a little longer than ordering your next piece of custom equipment. However, thanks to genomics and research efforts, the dairy industry will continue making steps in the right direction at a faster pace with a focus on the commercial producer’s ideal barn cow.

Written By: Mandy Brazil, Program Services Coordinator at Accelerated Genetics

Categories : Genomics

The Genetic “SUPER COW” – Myth vs Reality

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Friday, February 28th, 2014

During the recent “Advancing Dairy Cattle Genetics: Genomics and Beyond”, Paul VanRaden with USDA’s Animal Improvement Programs Laboratory pointed out that “If we took the best haplotypes (genes) from all the cows genomic tested to date, we would have a cow at $7515 Net Merit”. That’s pretty spectacular considering the current top Sire on the $NM list is DE VOLMER DG SUPERSHOT at 1000 $NM.

Now to put that into perspective the current rate of gain is $80 per year. So in order to breed that $7515 animal it would take us 81 years to actually breed that animal. Therefore it raises the question whether such an animal is actually achievable and is there technology out there that could accelerate the process of getting that Super Cow.

The interesting fact here is the greatly accelerated rate of genetic gain since the introduction of genomics. This results for the most part from the greatly shortened generation interval. Females are now being used as bull mothers 18 months sooner than in the past (as yearlings vs mid 1^st lactation), and sires of sons are now being used 24 and sometime 36 months sooner than they were in the past. (Genomic indexes vs waiting for proven sires). The almost 40% increase in reliability of estimated transmitting ability has breeders and AI companies contracting and working with these elite animals at a significantly younger age.

An interesting comparison is found by taking the top 8 proven sires from April 2010 and comparing them to the top 8 genomic sires from April 2010 with their current daughter proofs. You see that the genomic sires are 99 $NM (704 vs 605) higher than the proven sires. These top genomic sires, that have been heavily used as sires of sons, are 16% higher than if we had used their proven counterparts from the same time.

This reminded me of a discussion stemming from an article we wrote over a year ago, “Are You Ready For Genetically Modified Cattle?”. We discussed about how many larger and larger corporations are entering the dairy genetics marketplace and the fact that technology is advancing at such a rate that some time in the not so distant future it will be possible to take the best haplotypes in the Holstein population and produce progeny that would have an estimated breeding value of $7515 as VanRaden proposes. But at this point it’s just like the “Perfect” Holstein Cow picture, it does not exist at this time. (Read more: The Perfect Holstein Cow)

Not only does the potential exists to produce high $NM progeny, but what about creating or developing traits that are not yet available in nature. Things like Epigenomics, Nutrigenomics and Transgenics will make this possible. (Read more: Forget Genomics – Epigenomics & Nutrigenomics are the Future)

The Bullvine Bottom Line

There is no question that great breeding has always been part art and part science. However as technology grows and new discoveries seem to happen almost monthly as opposed to yearly, the balance between art and science is starting to shift drastically. I often hear many breeders comment about the failures of genetic predictions in the past. That was when reliabilities were in the 30% and 40% range. As the systems are refined and biases removed, these rates are now approaching the 70% and 80% range. Given more time, there will come a point where we have over 90% reliable information for animals on the day that they are genomically tested. Add to this the ability to genetically preselect or even manipulate the embryo and there is no question that, before long, numbers like 7515 $NM will not seem to be so astronomical. They will be the expected.

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.

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Categories : Genomics

Tags : Advancing Dairy Cattle Genetics, Epigenomics, Genetically Modified Cattle, Genomics, Nutrigenomics, Paul VanRaden, Perfect Cow, Super Cow, USDA

Forget Genomics – Epigenomics & Nutrigenomics are the Future

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Tuesday, January 14th, 2014

Two months ago I had one of those conversations. A friend said to me “you know Murray I am moving on from just simple genomics”. That perked my ears up and I listened more intently. “Yep I am now thinking about epigenomics”, he said. Well that was enough to set me off investigating what is out there that is beyond what our industry is currently considering and using when it comes to genomic. Relax a little, this may seem like rocket science today, but it is in tune with what our industry has always done in the past. We look to find more accurate ways of indentifying the elite animals. Then we figure out how knowing that information gives us ways to make dairy breeders and dairy farming more profitable.

Already Many Steps Too Far?

So now ‘epigenomics’ was pinned to my clipboard. But I didn’t get any further before I had a Master Breeder husband and wife corner me for half an hour and ‘inform’ me that “The Bullvine was leading the industry astray”. They stated to me that “they were from Missouri” and perhaps we should “still only be using the actually officially authenticated information – DHIR records and breed classification results – when it comes to selecting bulls and marketing females. They asked how can we know that the hair pulled and submitted for DNA testing actually came from said animal.” I have known this couple for almost forty years so I took the discussion on to a review great cows of the past and how they would not compare to the great show and brood cows of today. As we started to conclude our conversation the lady, who had been somewhat quiet during our sharing, commented “You (Murray) have a good point about how the genetic evaluation results over our lifetimes have resulted in the fact that we have far superior cows for both conformation and production, but our herd’s current biggest genetic problem is cows not getting back in calf. We just do not now get to have very many ten year old and older cows in our herd, liked we used to.” That gave me the opportunity to talk to them about genomics and having fairly reliable information, early in an animal’s life, on its genetic merit for reproductive traits.

The husband’s concluding comment warmed my heart. “Our grandson plans to come home to our family farm and he tells us that at university his professors are saying the information we have today on genomics is just the start. So don’t give up on us old guys. You folks at The Bullvine just keep giving us the facts and helping the industry do an even better job of breeding dairy cattle. We don’t own a computer but our family keep us quite up-to-date on what The Bullvine is writing about.” Obviously this couple are not as set in their ways as they led me to understand at the start of the conversation.

So if we have just scratched the surface, let’s delve a little deeper.

Epigenomics – What’s That?

By definition, epigenomics is the study of modification of the expression of the genetic material in a cell. Sounds rather out of the norm. Something can alter what the DNA says is the genetic merit of an animal? Let’s think that through a bit more.

As cattle breeders we can all think of times when three full sisters all had very similar performance. And I expect many of us can also remember situations where two of the sisters were very similar but the third sister just did not measure up to the other two. The question that breeders always ask is did the third one not get the good genes, or did she get the good genes but something inhibited her from being able to express them. I have even heard very knowledgeable breeders say that the third one will breed just a good as the other two. How they arrived at that conclusion I am not really certain. But I have seen it happen as they predicted.

Research in mice has shown that the diet of a sire can influence the gene expression of their progeny. So that fits under the definition of epigenomics. Dr. Jacques Chesnais of Semex feels that “there is a definite possibility that epigenomics plays as important role in adaption to the environment. In particular, in our industry, the way we feed and treat a cow in the early stage of pregnancy could affect the calf for a lifetime and therefore affect the future productivity of the herd.” Hearing that made me wonder if the recipient dams of ET calves may have an influence on how those calves pass on their genetics.

Leaders in the study of epigenomics in livestock Dr Marc-Andre Sirard and Dr Claude Robert, Laval University, are currently investigating how epigenomics applies to the bovine and in particular to female reproduction and embryo development. It will be interesting to follow their reports.

There is obviously much to be studied and learned about epigenomics in the bovine. Definitely traits like reproduction, health and immunity are ones that dairy breeders wish to know more about as they relates to inheritance.

So then – What is Nutrigenomics?

The second new kid-on-the-block, so to speak, is nutrigenomics. The study of the effects of foods and food constituents on gene expression. By definition “Nutrigenomics can be described as the influence of genetic variation on nutrition, by correlating gene expression or SNPs with a nutrient’s absorption, metabolism, elimination or biological effects.” Think about it. If we know the genetic make-up of our dairy cows we would be able to design their diets accordingly. Are there cows out there that can make better use of lower quality forages? Wouldn’t that be a boon for the economics of dairy farming. Especially given that feed costs are 52-58% of total dairy enterprise costs and low quality forages are less costly.

I asked two nutritional consultants about this. I got two very different responses. The first one said – “don’t bring that on too quickly I still have another ten to fifteen years in my working career”. The other consultant said “Well it would change my job but if it means dairy farming can be profitable and sustainable and if we can feed the hungry world – well bring it on”.

Expect Genetics to Play an Even Bigger Role in the Future

Investigation by Canadian Dairy Network (CDN) has predicted that, in stable milk pricing times and on milk production focused farms, half of the increased on-farm profits comes from increasing the genetic merit of sires and cows used to produce the next generation of females. With a better understanding and more definitive knowledge of epigenomics and nutrigenomics it could possibly be that 60+% of on-farm profits could be as a result of the genetics used.

From the DNA analysis using hair follicles, breeders now know with 50-70% accuracy the genetic merit of their animals for a host of important traits. Think what might be possible if by including epigenomics and nutrigenomics information. The accuracy levels could rise to 70-80%.

The Bullvine Bottom Line

The research phase of studying how epigenomics and nutrigenomics relate to the dairy cow is well underway. We can expect refinements to our genetic evaluation procedures based on what the research tells us. And in time breeders will have information so they can better breed, feed and manage their herds. Stay tuned to the Bullvine for more great insight into these two future changing technologies.

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

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Categories : Genomics

Tags : Dairy Cattle, dairy cattle breeding, Dairy Cattle Genetics, Epigenomics, Genomics, Nutrigenomics

The Genomic Bubble Has Burst?

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Friday, January 10th, 2014

Well that is what some would have you believe. They cite the decreased prices at the top sales, and that genomic young sires are no longer much higher on the list then their proven counterparts. (Read more: An Insider’s Guide to What Sells at the Big Dairy Cattle Auctions 2013) The truth is that, instead of just citing observations, true breeders are looking at the facts. For them, the facts show that Genomics is here to stay.

Almost daily I read warnings in other “leading” dairy publications against the use of genomic sires. This panders to the old school mentality that fosters breeder concern about using Genomics. Instead of basing their comments on facts, they use hearsay, conjecture and outright fear mongering to defend their comments.

Here at the Bullvine we have always worked to let the facts guide what we write. That is probably the biggest reason that we have been proponents of Genomics from the start. There are several key points that we think many breeders and our fellow media are missing. Let’s summarize them here to help put an end to nonsensical comments.

Genomics is a Tool
It drives me nuts on a daily basis the number of breeders who refer to Genomics as a selection tool. Genomics increases the reliability of individual traits and indexes. That’s it. The term “Genomics” is miss-used by many when they should be referring to “High Index” sires, meaning list toppers on the gTPI, gLPI and other lists. This may seem like a minor thing. I am even guilty of it myself from time to time. However, it’s really a huge error when you look at it from a breeder viewpoint. Over the past week, I looked at more than 100 comments about Genomics from naysayers. Every single one of them would have been more accurate if they had used the term “High Index” rather than Genomics. Most of the reservations against Genomics have more to do with the use high index sires. The debate between selecting for “High Index” or “Proven” pedigrees will go on for years to come. The thing that many miss is that Genomics is a tool that can help both strategies. Since Genomics helps increase the accuracy of the indexes in both strategies, it will help both strategies excel into the future.
The Numbers Don’t Lie
It’s always easy to state a case-by-case example and find a few cases that help prove any point. It takes a look at the full spectrum to truly get an accurate assessment on how any program or tool is working. The facts are pretty clear that Genomics increases young sire’s reliability by 30% and 1^st crop proven sires by 5%. In effect that says that a young sire with a 50K genomic test and a proven sire will now have reliability comparable to an early 1^st crop proven sire pre-genomics. This would indicate that if you were willing to trust a 1^st crop proof prior to the introduction of Genomics, you should now be willing to trust a genomic young sire with a proven sire as their reliabilities are very comparable. Furthermore, the genetics marketing is also supporting this. Genomic young sires are set to outsell proven sires as most breeders are confident in the numbers and are making sound breeding decisions based on them. As we mentioned in our article Genomics – Lies, Miss-Truths and False Publications, genomically evaluated bulls with 65% reliable gLPIs, breeders can expect 95% of the time that their official proof will be within 670 LPI points (within about 18-20%) (Please note that with change in Canadian LPI formula this number is more like 400 LPI points). This means that we can be 95% sure that the current top gLPI sire, SILVERRIDGE V EXTREME (gLPI of +3544), will be higher than +3000 LPI, once he has his official progeny proven index that is over 90% reliable and that would make him the top 3 active proven sire in Canada. In the US sires like ZAHBULLS ALTA1STCLASS (gTPI of +2598) will end up over +2200 gTPI placing him in the top 10. (Editor’s note: Prior to the regression to bring high genomic young sires closer to proven sires, sires like Extreme and Alta1stclass would have actually been higher than the current top proven sire). Yes genomic young sires do on average drop below their original predicted values, but, they are on average still higher than the proven sires of that time.
Falling Numbers are not an Indicator of System Failure
Whether it’s young sires indexes dropping or semen prices going down, neither of these two events accurately predict the status of Genomics. You see Genomics is new to the industry and, with anything that is new, there is a period of figuring out how the “new world” will work. During that period aggressive breeders and semen companies have sought to maximize revenues for themselves and the breeders they represent. This has meant testing the market to see just what is the maximum revenue price for each animal or dose of semen. Simple economics teaches us that we need to test that point that maximizes revenue, that is either sell at a high prices and reduced quantity or sell at a medium price at increased quantity. Both are sound strategies. At times due to exclusivity and extreme unique genetics, young sire semen has sold for $10,000 a dose and, with the removal of the exclusivity and other sires coming out after the fact, that semen is now available at a greatly reduced price. (Read more: $10,000 a dose Polled Semen). The breeder who purchased this semen, Ri-Val-Re Holsteins from Michigan, actually made out very well with his investment as he had a clear plan with the use of IVF to maximize his return. (Read more: Breeding R-Val-Re: Where looking good in the stall is just as important as looking good on paper) It has also led to other attempts and premium pricing or pricing models. This is not a failure of the system. This is progressive individuals trying to discover how the new system is going to work. Does it always return maximum profits?….No. But does it help those individuals understand the new market and how they can operate to maximize efficiency in the future? ….Yes. Just because you are not able to justify these prices for your breeding program goals, does not mean that it will not work for others. The big thing is for you to understand your genetic plan and goals and make sure you are constantly evaluating and improving them. (Read more: What’s the plan?). It is interesting to note that since the introduction of Genomics the rate of genetic advancement has more than doubled. Coincidence? I don’t think so. Since more breeders can make more sound decisions, the industry as a whole is benefiting.

The Bullvine Bottom Line

Genomics will not make every breeder an instant Master Breeder. Nor does it profess to. What it will do is help each breeder make sound breeding decisions based on the most accurate information available. There is still the need to have a breeding strategy the works for your specific management and financial goals. You cannot simply use the entire list topping sires and expect to end up with the greatest herd in the world. You need to take the time to choose the sires that work best for each specific mating and understand the issues of each cow or sire daughter group (i.e. inbreeding, strengths and weaknesses). That is exactly what great breeders of the past did. . They took the time to assess their animals and planned how to end up with the best progeny possible. That, and not Genomics, is what will lead to the greatest genetic advancement. Genomics is simply a tool that enables breeders to make improvement happen faster!

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.

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Categories : Genomics

Tags : Genetic Evaluation System, Genomics

Top 200 New Genomic Females For January 2014

Wednesday, January 8th, 2014

Leading sires of the top 200 new genomic TPI sires where PINE-TREE ALTAOAK-ET (19), COYNE-FARMS SROCK MACK-ET (16), and COYNE-FARMS JABIR-ET (15). Leading owners of the top 200 where De Su Holsteins LLC (37), Elite Dairy Genomics LLC (17) and Oakfield Corners Dairy (10)

Reg. No	Name	Class	Score	Sire Name	Owner(s)
HOCANF106651028	FERRE BOLTON MATINALE	VG	88	SANDY-VALLEY BOLTON-ET	FERME H.P. GAGNON & FILS INC, LATERRIERE, PQ, (418) 543-4999
HOCANF106028819	AGRIVENTE GOLDEN BOY BIANKA	VG	87	DENISTEINS GOLDEN BOY	FERME AGRIVENTE, ST. ALBAN, PQ, (418) 268-3922
HOCANF105584390	BEAUVIDE SAMUELO MARJO	VG	87	REGANCREST-MR SAMUELO-ET	FERME BEAUVIDE INC, STE. ANGELE DE MONNOIR, PQ, (450) 469-4546
HOCANF10817083	BIGMAPLE LOU LARA	VG	87	JENNY-LOU MARSHALL P149-ET	DUNPHY'S HOLSTEINS, KESWICK, NB, (506) 363-3092
HOCANF11046839	BIRKENTREE DENISON RAFA	VG	87	JERLAND DENISON-ET	EAST RIVER FARMS, MARSHFIELD, PE, (902) 629-1579
HOCANF10950808	BOSDALE SHOTTLE LIBERTY	VG	87	PICSTON SHOTTLE-ET	BOSDALE FARMS INC, CAMBRIDGE, ON, (519) 740-7904
HOCANF11137375	CRAGGAN DENZEL GALA	VG	87	LA PRESENTATION DENZEL	ELMER WEEKS, BREADALBANE, PE, (902) 886-2152
HOCANF11043491	CRATER SKYS THE LIMIT GOLDWYN	VG	87	BRAEDALE GOLDWYN	CRATER FARM, HARTINGTON, ON, (613) 532-0661
HOCANF10946579	CROVALLEY GOLDWYN KEISHA	VG	87	BRAEDALE GOLDWYN	CROVALLEY HOLSTEINS, HASTINGS, ON, (705) 696-3277
HOCANF10946561	CROVALLEY SANCHEZ MICKEY	VG	87	GEN-MARK STMATIC SANCHEZ	CROVALLEY HOLSTEINS, HASTINGS, ON, (705) 696-3277
HOCANF10917454	DONNANVIEW SHOT SHOLLY SUE	VG	87	PICSTON SHOTTLE-ET	DONNANVIEW FARMS LTD, STIRLING, ON, (613) 395-3697
HOCANF10917463	GILLETTE GRT 2ND THRILL	VG	87	SCHILLVIEW GARRETT-ET	ARCADIA FARMS, CODRINGTON, ON, (613) 475-1705
HOCANF11049215	GOLDENFLO SANCHEZ HANDSOME	VG	87	GEN-MARK STMATIC SANCHEZ	MACBEATH FARMS LTD, MARSHFIELD, PE, (902) 628-8348
HOCANF11052059	GOLDSTREAK DUPLEX LUXURY	VG	87	MESLAND DUPLEX-ET	J. GUY THOMPSON & SON, FRENCHFORT, PE, (902) 629-5176
HOCANF11093260	GREENLARK ROSES WANDA	VG	87	GILLETTE WINDHAMMER	DONNANVIEW FARMS LTD, STIRLING, ON, (613) 395-3697
HOCANF106443533	JACOBS ATWOOD MELODY	VG	87	MAPLE-DOWNS-I G W ATWOOD	FERME JACOBS INC, CAP SANTE, PQ, (418) 285-2674
HOCANF105687784	JANOT GOLDWYN ITALIA	VG	87	BRAEDALE GOLDWYN	FERME JANOT, ANGE GARDIEN, PQ, (450) 293-7931
HOCANF106042803	LIATRIS LHEROS FRAISINETTE	VG	87	COMESTAR LHEROS	FERME LIATRIS SENC, ST. FELICIEN, PQ, (418) 679-5892
HOCANF10892741	LOCKRIDGE ROSS RAE	VG	87	PLAIN-O DURHAM ROSS-331-ET	LOCKRIDGE FARM, NEWBURGH, ON, (613) 378-6148
HOCANF8906559	LOVSHIN DENISON KENSINGTON	VG	87	JERLAND DENISON-ET	LOVSHIN FARMS LTD, COBOURG, ON, (905) 372-8337
HOCANF106582820	MABEL OUTBOUND DIVINALE	VG	87	SCHILLDALE OUTBOUND-ET	FERME MAGUY ENR, NORMANDIN, PQ, (418) 274-2065
HOCANF105086179	MARSO DOLMAN SAVITA	VG	87	REGANCREST DOLMAN-ET	FERME MARTIN BOUCHARD S.E.N.C, ST. BRUNO, PQ, (418) 343-2140
HOUSAF140538603	MS CHASSITY SNCHZ CARLY-ET	VG	87	GEN-MARK STMATIC SANCHEZ	CRASDALE FARMS, HUNTER RIVER, PE, (902) 963-3515
HOCANF11110374	OSCROFT PARAMOUNT JADEN	VG	87	STANHOPE PARAMOUNT	OSCROFT FARMS, SHANNONVILLE, ON, (613) 962-3693
HOCANF11050132	PLOEGSWAY NUTFOUR HANNAH	VG	87	PLOEGSWAY FORTUNE NUT FOUR	JOHN VANDERPLOEG, PETERBOROUGH, ON, (705) 295-2681
HOCANF11044926	QUALITY ATWOOD FOLFOE	VG	87	MAPLE-DOWNS-I G W ATWOOD	BRACKLEY FARM, BRACKLEY, PE, (902) 368-8234
HOCANF106117529	ROSIERS BONNA GOLDWYN	VG	87	BRAEDALE GOLDWYN	FERME DES-ROSIERS, ST. FRANCOIS DU LAC, PQ, (450) 568-6202
HOCANF10973122	SMYGWATYS SHOTTLE WATERMELON	VG	87	PICSTON SHOTTLE-ET	FRANCIS COLIN CAMPBELL, CAPE BRETON, NS, (902) 945-2735
HOCANF105934493	STEPIDO STERLING SACHA	VG	87	ARDROSS STERLING	SEBASTIEN FONTAINE, ST. BARTHELEMY, PQ, (450) 835-3705
HOCANF9990388	SUNNY PLAINS WONDERFUL	VG	87	WILCOXVIEW JASPER-ET	SUNNY PLAINS FARMS, JOYCEVILLE, ON, (613) 382-4919
HOCANF10979847	TREKILI W A LAURIENIA BRAXTON	VG	87	REGANCREST S BRAXTON-ET	WALTZ ACRE FARMS, CONSECON, ON, (613) 392-3164
HOCANF11009881	VALLEYVILLE GOLDWYN MADA 921	VG	87	BRAEDALE GOLDWYN	FRIZZELLS VALLEYVILLE FARM INC, HUNTER RIVER, PE, (902) 964-3235
HOCANF106337471	VIEUXSAULE DESTRY DREAMY	VG	87	SCIENTIFIC DESTRY-ET	FERME DU VIEUX SAULE, ST. ESPRIT, PQ, (450) 839-7190
HOCANF11073554	WINTERBAY GOLDWYN LADEEDA	VG	87	BRAEDALE GOLDWYN	WINTERBAY FARMS, MT. STEWART, PE, (902) 629-1800