Inbreeding

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Archive for Inbreeding

Inbreeding: Could we be Headed to a Genetic Dead End?

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Tuesday, April 21st, 2015

Inbreeding and the lack of genetic diversity are on the radar screen of milk producers, breeding stock suppliers, A.I. companies and scientists. In some cases, they are barely there while for others it is a major concern. Every year there is new evidence that points to the fact that these factors should not be ignored when it comes to breeding decisions.

A New Approach to Studying Diversity

A recently published article by Yue, Dechow, and Liu, where they studied the limited number of Y chromosome lineages in North American Holsteins, gives discerning breeders serious food for thought. The results of this study appear in this month’s (April 2015) Journal of Dairy Science and is entitled “A limited numbers of Y chromosome lineages is present in North American Holsteins”.

Some Eye-Opening Facts

The researchers found that all current North American Holstein A.I. bulls trace to two sires from the 1880’s, Hulleman, and Neptune H. And that’s just the beginning of the narrowing of the bloodlines! The more in-depth study shows that, of three prominent sires from the 1960’s, Chief, Elevation, and Ivanhoe Star, two remain dominant today. The study reports that, in 2010, Pawnee Farm Arlinda Chief (48.8%) and Round Oak Rap Apple Elevation (51.0%) totally dominate, being present in 99.8% of all North American A.I. bull pedigrees. The data for this study came from Interbull’s files that contained 220,872 bulls worldwide born between 1950 and 2013. Of those bulls, 62,897 were from North America.

Genetic Diversity is No Longer

To say the least, we have severely narrowed the genetic diversity in North American Holsteins. Yue, Dechow and Liu state the obvious “We believe that the extreme lack of genetic diversity of Y chromosome could be a limiting factor toward improvement in Holsteins for male fertility traits that are influenced by the Y chromosome”.

The effects of reduced genetic diversity on male fertility is often not a high priority for breeders. Breeders think of calf liveability and growth, female reproduction, disease resistance, lifetime production and many more traits when it comes to the negative effects that result from inbreeding. The truth is that limiting our effective breeding population to two sires from the 1880’s and two of their descendants from the 1960’s is alarming.

Is this a Ticking Time Bomb?

Most of us ignore the actual situation. We accept, as a fact of life, that the rate of inbreeding in our dairy cattle is increasing every year. Could it be just a matter of time until we are doomed? Do breeds and breeding companies need to take the blinders off?

Finding Solutions

Dairy cattle breeders are usually quite creative when it comes to finding solutions. It means thinking outside the box. So let’s think outside that box!

Sourcing Sires: Now that we have DNA analysis in most countries with significant Holstein populations, it should be possible to find breed improving sires that do not contain Chief and/or Elevation in their pedigrees. Getting the genetics of such outcross sires incorporated into North America Holsteins is now simple enough. Simply IVF top North American Holstein cows and use those non-Chief and non-Elevation sires to produce sons. Then DNA test those sons and identify which ones have the different Y chromosome. The project will need to be large, but amongst the sons without Chief or Elevation Y chromosomes, there will be sires that are high based on genomic testing.

Lower Purity Requirements: North American Holstein breeders have prided themselves on having animals that are 100% pure as to breed. That’s nice but do we need to demand 100% purity at the expense of losing the breed because of lack of genetic diversity? In New Zealand the Kiwi breed, Holstein x Jersey, has been developed and it has gained wide acceptance by milk producers as the animals they want to work with on their pasture-based milk solids per hectare dairy farms. Bringing in genetic diversity from other breeds could produce a strain of Holsteins that suits the needs of bottom line focused dairy farmers everywhere.

Genetic Engineering: I understand that anything to do with altering nature is a controversial topic. However can we not learn from the success of crop breeders where they introduced new and constructive genes into plants? Introducing those new genes has been a major success story in positioning farmers everywhere to produce crops that have fed and will continue to feed our ever growing global population. Genetic engineering is a topic that ne eds serious consideration in dairy breeding.

These three suggested ways of finding a solution only scratch the surface of what’s available to an open-minded, progressive dairy cattle improvement industry

The Bullvine Bottom Line

North American Holstein breeders have been very successful in eliminating unproductive animals. As a result, the average production per cow has doubled in less than fifty years. But with that increased yield has come inbreeding, poorer reproduction, disease resistance challenges and other detrimental factors. Continuing to ignore the facts and refusing to search for ways to increase genetic diversity could take us down a road that leads to a dead end.

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The Truth about Inbreeding

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Thursday, October 30th, 2014

Should breeders be concerned about the increasing rate of inbreeding in today’s dairy cattle? Articles are regularly published about the need to lower the rates of inbreeding by such means as cross-breeding. However for purebred breeders planning to remain competitive in advancing their herds genetically, to increase the inventory value of their herds and to maximize the profit from their dairy operations, the matter of increased rates of inbreeding is more than a single item issue.

Breeder Attention to Inbreeding is Limited.

As I follow breeders’ comments on The Milk House (link) and other Facebook posts, I see little breeder concern or perhaps even awareness of any negative impact from focusing on a limited number of bloodlines that are more inbred than the general population.

Showmen often identify Atwood, a Goldwyn son, as the next great sire to follow Goldwyn as the Holstein breed champion in the show ring. Already, before they even receive their first official daughter proofs in December, I hear breeders talking about the attributes, including breed leading TPIs or LPIs of the many daughters they already have in their herds from two unproven bulls, Mogal and Uno. Supersire may not receive an official proof in December but, in time, all three of these sires will enter into the club of very, very extensively used sires that will lead to a further narrowing of the global diversity of Holsteins. That is what happened with Elevation, Astronaut, Blackstar, Shottle, Goldwyn, Planet and Oman in the past.

The Question is ……

Dairy breeders need to be asking themselves “How do I balance genetic improvement, dairy enterprise profit and increasing rates of inbreeding as I mate my herd?”

What is Inbreeding?

In simplest terms, inbreeding is the mating of related animals. The more closely a bull and cow are related, the higher the frequency that their common genes will be passed on to their resulting progeny. Animals that do not meet the breeding goals of breeders do not get the opportunity to have their genes passed on. As a result, the genetic diversity of the population decreases. In short, focused selection contributes significantly to decreased diversity. It is a double-edged sword.

Varying Degrees of Inbreeding.

The Dairy Cattle Reproduction Council (a proactive organization of professionals interested in enhancing reproduction through technology) has produced the following helpful chart to demonstrate the varying degrees of inbreeding.

Some interesting facts can be extrapolated from this chart. Line breeding has been used by dairy cattle breeders to fix the good genes in their herds. But it can also accentuate any negatives associated with the breeding lines used. Selection within a breed has, by far, been the tool of choice for genetic improvement especially since the introduction of artificial insemination. Its contribution to increasing rates of inbreeding has come through the very extensive use of the top sires. Inbred crosses within species has been promoted by some as a solution to the increasing rates of inbreeding but very often the benefits quoted are for single traits and not for total lifetime profit of the resulting generations.

Level of Inbreeding

For North American Holsteins from 1960 to 2010, the levels of inbreeding have gone from zero to 7% to 8%. Moreover, it is continuing to increase at about 0.3% per year.

Impact of Inbreeding in Dollar Terms

Based on USA studies it is estimated that for each 1% increase in inbreeding there is a loss in lifetime net income of $23.11. That equates to a difference of $96.44 for a 9% inbred cow compared to a 5% inbred cow. Canadian and Irish crossbreeding studies show slight lactation losses for milk, fat, and protein yields, but gains for fertility and health traits when breed crossing is practiced. However, neither study reports a net lifetime profit figure comparing breeding pure to crossing breeds.

The question when making a mating decision comes down to correcting for the loss due to inbreeding between the sires under consideration. A sire with an Inbreeding Coefficient of 8% would need to have a NM$ value of about $70 more than a sire with 5% Inbreeding Coefficient for them to be considered equal.

It is more than looking at the Inbreeding Coefficient (IC)

An animals IC tells the degree to which the animal is inbred. However in breeding it is the degree to which the progeny of a mating is inbred that needs to be considered. That means that a sire will not likely produce calves with similar ICs for every mating in your herd. It all depends on a sire’s varying degrees of relationship with your females.

In the USA and Canada information is provided for every sire on how he will mate with the national population of females as to inbreeding level. In the USA the terms used in Effective Future Inbreeding (EFI) and Genomic Future Inbreeding (GFI), while in Canada the term used is Relationship Percent (%R). In all cases, they are general guides to which sires will produce more or less inbred progeny.

What is the Ideal?

The are no perfect numbers for EFI, GFI or %R. It depends on both the genetic merit and inbreeding percent of the resulting progeny. Generally speaking, EFIs and GFIs over 10.0% and %R over 15% of the progeny should be avoided by using an alternate sire that is less related to the dam.

Sound Advice

Dr. Nate Zwald of Alta Genetics provides two thoughts relative to inbreeding:

Will the use of genomic sires speed up the rate of inbreeding? – “Yes on a breed level it will, but we are also increasing the rate of genetic gain in an incredible way. So our goal should not be a ‘less inbred’ cow but, instead, the most profitable cow. Over the past 25 years, we have created more inbreeding but also more profit. The same is true now with genomics, except that we should now expect both inbreeding and genetic gain to increase at a rate two to three times what we experienced in the past.”
Does this mean we can soon expect to get to 10 percent inbreeding level on a breed-wide basis? “Yes says Zwald. Geneticists are working on ways to balance the inbreeding level with genetic gain on a breed-wide basis, as a producer you should only be concerned with inbreeding versus genetic gain in your own herd.”

Ways to Select Bulls to Use in Your Herd

In summary, there are basically three ways to address both genetic gain and increased inbreeding:

Use Outcross Sires that are low for EFI, GFI or %R. (Read more: 12 Outcross Sires to help Control Inbreeding)
Use a herd mating program that takes into consideration inbreeding. Most AI studs have such a service.
Use sires that optimize your breeding program that are not closely related to your herd (i.e. GFI below 10% or %R below 16%) (Read more: What’s the plan?)

The Bullvine Bottom Line

As long as breeders plan to rapidly increase the genetic merit of their herds an increasing rate of inbreeding will be with us. Remember when mating a cow and bull it is the genetic merit and inbreeding percent of the resulting progeny that is the focus and not the parents’ values. One breeding program will not suit every breeder, but basing decisions on profit should be part of every plan.

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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?

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Stop Talking About Inbreeding…

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Tuesday, March 25th, 2014

Dairy cattle breeders talk about attempting to keep the level of inbreeding within check in their herds. Poultry, swine and corn breeders talk in terms of inbreeding and producing lines and then crossing the inbred lines to produce the birds, piglets and seeds that are used for commercial production. In beef, breeds have been developed for their specialities and then breeds are crossed to produce the commercial animals. The challenge currently being faced by Holstein breeders is that once again the level of inbreeding is creeping up and that has the potential to be a limiting factor when it comes to on-farm profit. Let’s look at where the level of inbreeding is at and how breeders might address that.

Current Inbreeding Levels

Dr. Filippo Miglior, Canadian Dairy Network, presenting at the February 2014 Advancing Dairy Cattle Genetics Workshop held in Phoenix Arizona, reported of the state on inbreeding in Holsteins born between 1982 and 2012..

It should be concerning to breeders that over the most recent time period, 2007 to 2012, that the Inbreeding Coefficients for Holsteins everywhere, North America and Global, increased at the rate of 0.36% and 0.33% per year respectively. These levels are the highest in modern Holstein breeding history. Levels four to almost seven times large in 2012 compared to 1982 should be a wake-up call for our industry. The inbreeding levels from 1987 to 1997 were a concern back then when only a few sires were being used to produce sons for A.I. progeny testing programs. Breeders and A.I. took the warnings seriously and increased the number and diversity of sires of sons entering A.I.

What Has Been Happening?

There are a number of factors that need consideration.

Limited Number of Bloodlines – Where once the bloodlines often had country or regional focus, Holstein breeding has gone global with only a few total merit indexes in use and TPI dominating. Diverse breeding resulting from the environmental situation or the cheese produced has disminished.

The number of different bloodlines used by A.I. companies has been greatly reduced. The table below is a global report on the Top 20 Sires of Sons since 1986. Half of these sires were born and used prior 2000. However recent sires like Man-O-Man, Planet, Shottle and Superstition are in the top ten. Only one of these sires, Shottle, was first proven outside North America but his pedigree was from North America. The end result is that this extreme use of a limited number of sires of A.I. sons has contributed to the increased inbreeding in the past 25 years.

Rapid Genetic Progress – The significant increases in inbreeding comes about as a result of the very significant increase in the past decade in the genetic merit of the Holstein breed. The following graph produced by USDA shows the change in the annual rate of genetic improvement for Net Merit. This change was a result of intense selection and increased accuracy using genomic information. However the fallout from that is the greatly increased inbreeding that we have now.

Adjusting Indexes for Inbreeding – USDA/CDCB has produced reports on adjusting US production indexes for level of inbreeding. There is much more work to be done on the effects of inbreeding beyond milk production. The truth is that it will take a long time to determine adjustments for traits relating to health and fertility. Note that the field observations for those areas are likely only available in the Nordic countries.

Limited Number of Sires of Sons – The two graphs below show just how short the list of sires of sons has become during. Having only 16 to 19 sires producing 50% of the young sires entering A.I. was great for genetic gain but for inbreeding it was a recipe for major problems. Even in 2011 there was still too much focus on too few sires of sons when only 32 produced half the young bulls entering A.I.

Focus is on Top Genomic Animals –Breeders should be concerned about inbreeding with the extreme focus on only the very top young heifers and bulls. This has also put downward pressure on animal values for high indexing animals that are just outside the top group. Genetic gain for production and type could be almost as good if there was increased selection pressure for other economically important traits. Remember that the very top heifers are full sisters to the young bulls entering A.I. Where is the genetic diversity in that?

Inbreeding of Sire List Toppers –The Bullvine has studied the Expected Future Inbreeding (EFI) for the top forty Net Merit Dollars ($NM) sires on both the Holstein USA Dec ’13 proven and genomic sire lists. Each 1 percent increase in EFI reduces milk proofs by 65.3 pounds. The published proof on a bull with an EFI of 4 per cent would be reduced by 261 pounds (4 X 65.3 = 261). The top 40 proven $NM sires have an average EFI 6.4, the genomic test sires also had an average EFI of 6.4 (Note: Had to be active with NAAB). Sires with O-Man blood all have high EFI’s due to O-Man’s extensive use as a sire of sons. Interesting to note that while both the top proven sires and genomic test sires average the same, this is a far greater range in the proven sires, the lowest proven sire in the top 40, Twist, has an EFI of 5.5, and the highest EFI proven sire in the top 40, Manifold, has an EFI of 7. In the genomic test sires, the lowest EFI, (Rubicon, Mr Max and Magoo all tied at 6), and the highest EFI belongs to Dozer at 6.7.

Breeders looking for the sires with the lowest expected future inbreeding should look up:

Proven Sires

Erdman – Kings-Ransom Erdman Cri-ET – 01HO09800	Twist – Clear-Echo Nifty Twist-ET – 029HO14335
AltaNetworth – Bomaz AltaNetworth-ET – 011HO10767	Dorcy – Coyne-Farms Dorcy-ET – 029HO14142

Genomic Test Sires

Rubicon – Edg Rubicon-ET 151HO00681	Mr Max – Bomaz Mr Max-ET – 151HO00675
Magoo – Bomaz Magoo-ET – 151HO00677	Troy – River-Bridge Co-Op Troy-ET – 001HO11056

Polled not likely to help lower Inbreeding – With more breeders breeding for polled animals, some of us may have thought there could be genetic diversity brought into Holsteins by this route. Well that just isn’t so. What is happening is that the same all too frequently used sires in horned are showing up as the sires or maternal grandsires in polled. The only outcrosses in the polled young sire pedigrees are the generation of sires or dams that introduced the polled gene.

What Needs to Happen?

The Bullvine offers the following ideas for how to make progress to reducing or at least holding the inbreeding levels.

Calculate Inbreeding Levels for Every Calf –Remember that it is the inbreeding level for the calf that is to be born that needs to be watched. To achieve a reduction in inbreeding, the sire and dam should not be closely related. A good example where the breeder did his homework is Crackholm Fever, 6.35% inbred. His parents are more inbred than he is but they are from quite different lineage. His sire Goldwyn (James x Storm x Aerostar) is 15.17% inbreed while his dam Fashion (Blitz x Mattie G x Rudolph) is 8.17% inbred. Inbreeding can be managed. Most sire mating services have incorporated the minimization of inbreeding into their programs.

New Total Merit Indexes – At the present time total merit indexes in the United States (TPI and NM$) and Canada (LPI) are under review for updating to include additional economically important heritable traits for which data is captured. Breeders need to have input into the further development of those indexes. Once those indexes are revised, new males and females will come onto the elite lists. Those animals are likely to bring forward the opportunity for breeders to use them to both generate more on-farm profit and to reduce inbreeding.

Develop Lines within Holsteins – A.I. companies have already started to develop lines that place emphasis on traits like health and fertility. No doubt lines will be developed for feed efficiency, once more is known about it. Having such lines available will give breeders the opportunity to specialize the families on their farms or to cross lines to end up with less inbred animals. It could make for the best of both worlds – for the breeders and for the A.I.

More Study of the Genome – As more and more animals are genomically tested there will be more accuracy to genomic results. But it does not end there. By studying each animal’s genome, it will be possible to know the exact level of inbreeding instead of what is currently done, which is only an estimation based on parentage. This will provide for yet another way to help tackle the inbreeding issue. Definitely genomically testing all heifers in a herd will, in the future, have a multitude of benefits for breeders (Read more: Herd Health, Management, Genetics and Pilot Projects: A Closer Look at ZOETIS)

The Bullvine Bottom Line

Holstein breeders and the breed cannot afford to fiddle while Rome burns when it comes to inbreeding. It is time to take action to reduce inbreeding levels. It does require collective action by the breed, on behalf of breeders and A.I. companies. It is not too late to act. The time for procrastination has past.

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Genomics – Opportunity is Knocking

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Thursday, November 28th, 2013

With less than a week until the December 03 index release day I am thinking what more do I want or need to learn about genomics in the world of dairy cattle breeding. I have friends that entirely use genomic information to breed and market while others are riding along and using higher indexing young sires but otherwise remain in the prove it to me “I am from Missouri camp”. Here at The Bullvine we have provided thoughts in the past on genomics (Read more: Genomics at Work – August 2013). Today we decided to further document some areas that we feel are important to watch for and questions we are searching for answers to so that you don’t miss this opportunity.

Verification

“Does it really work?” is the question most often asked. The verdict is still out for many breeders. (Read more: Is the Genomic System Really Working?, The Truth About Genomic Indexes – “show me” that they work! And What Happens If Genomics Doesn’t Work?)

Except for a few preliminary reports by a couple genetic evaluation centers little has been published verifying that using genomics actually works. Breeders need the truth and nothing but the truth based on scientific analysis. We can likely expect the report to say that it assists with increasing the rate of genetic advancement but that: i) on an individual animal basis it is not as accurate as a 99% reliable daughter proven A.I. bull; ii) for young bulls, heifers and cows it increases the accuracy of indexes ; iii) for traits for which we have limited farm data it is still too early to make an accurate assessment; and iv) it is in fact the most important step forward in breeding since we got broadly based proven sires. The message to our scientist and industry leaders is that breeders need to know the facts. The industry depends on breeders being successful. (Read more: CANADIAN BULL PROOFS – You’ve Got to Prove It to Use It!)

With the indexes of young animals today exceeding their older counterparts by a significant amount, breeders need to know the facts so they can decide on the extent to which they should use genomic information in their breeding plan (Read more: What’s the plan?).

Intensity of Use

It is well known that concern exists among all players, from breeders to scientists, on the increased rate of inbreeding. (Read more: Twenty Things Every Dairy Breeder Should Know About Inbreeding, 6 Steps to Understanding & Managing Inbreeding in Your Herd and INBREEDING: Does Genomics Affect the Balancing Act?)

A study of the sires of top ranking young animals shows the following:

Sires of top fifty August 2013 gTPI young bulls – Mogul (21); Uno (8); Supersire (7); McCutchen (3); Facebook (2); Lithium (2),..plus seven others
Sires of top fifty August 2013 NM$ young bulls – Mogul (13); Supersire (10); Uno (8); Robust (3); Shamrock (3); Epic (3); Lithium (2); Facebook (2); ..plus six others.
Sires of top fifty August 2013 gLPI young bulls – Mogul (17); Supersire (9), McCutchen (5); Bookem (5); Mixer (3); Epic (2); Lexor (2); Iota (2); ..plus five others.
Sires of top fifty gLPI heifers (Sept-Nov releases) – Supersire (11); McCutchen (6); Enforcer (5); Mogul (5); Liquid Gold (4); Munition (4); Morgan (3); Cashmoney (2); ..plus ten others

Even though most of these bulls are not themselves closely related it is concerning that only a few bulls come to the top on all these lists. 66% of the above lists are over 6.0% inbred and only one is below 5.0% inbred. Outcross sires (Read more: 12 Sires to Use in Order to Reduce Inbreeding and GOING OFF THE MAP: 14 Outcross Holstein Sires That Don’t Include GPS) has been recommended as a solution yet Oman, Planet, Shottle and Bolton are prominent is the ancestry of the bulls above. It is time that we stop worrying about inbreeding and start finding practical solutions. Do we need to designate breeding lines and then doing line crossing like is done in crops, poultry and swine? Why are A.I. organizations not using alternate sires of sons? Is it that those alternates do not come up as high on total merit index ranking lists? If that is the case should total merit index be the criteria used when selecting young bulls to be sampled or marketed. Should the inbreeding coefficient of every bull be a required number to be published? There are solutions but it takes effort and leadership to stop the runaway train.

Finding the Best

Breeders of very elite indexing animals want to know which bulls will ring the bell for them when they flush their top virgin heifers. Some of those breeders feel that there are certain sires more capable than others at leaving top of the list progeny? Put another way can two bulls be ranked the same for total merit but one leaves progeny that are very consistent for their genomic values while the other bull produces progeny that range more in value. Breeders are willing to gamble and use the bull that appears to be able to produce list toppers. Breeders are asking the question – have our scientists studied this and is their an answer to the question of why some families consistently throw the high outliers?

Which are the Future Parents

As well with more and more emphasis being given to management, health and fertility traits in dairy cattle selection the question becomes which are the young bulls or elite heifers for the future. Could it be that they should be 90%RK for Production and 99%RK for Durability and 99%Rk for Health & Fertility? Attention needs to be given to matter with a view to the needs for the next ten plus years. (Read more: Total Merit Indexes: Are they helping or hurting?, Does Your Breeding Program Save You Labor? and Are Your Genetics Wasting Feed and Labor?)

Health / Disease Resistance

No doubt we have only scratched the surface on what the DNA profile of an animal can tell use about an animal’s ability to remain healthy and disease free. Even though breeders would like to have the answers today, the absence of farm data to match to the DNA will likely mean that this area of breeding will be relatively inaccurate for some time into the future. That does not mean that we should not continue to study this area, it is just that we can not expect answers quickly.

Female Fertility

Here again we are dealing with an area where there is limited farm data, or the farm data is not in connected data bases that can be used to correlate female fertility with DNA profiles. Is there farm data out there that tells us when heifers reach puberty? No. Are there genetic differences in when heifers can be first bred? Likely but we do not know. To go even further what about female conception rates? Biologically up to 90% of the time a sperm fertilizes an egg, yet only 65% of heifers and 40% of cows in Holsteins actually become pregnant. The inability of a fertilized egg to implant is significant but knowing the genetics of that is still a long ways off. Maybe there is research in other species that might be useful for linking female fertility with DNA profiles.

Breeders who flush females know that to be financially successful a cow or heifer must give many viable embryos. And that there are differences amongst cow families in how many embryos produced. (Read more: What Comes First The Chicken Or The Egg? And Investing in Dairy Cattle Genetics – Think Outside the Box) One question yet to be answered is by using IVF on poor flushing families are we, in fact, hindering reproduction from a genetic perspective. Yes more questions than answers but remember that the most common reason for cows being culled is infertility. So we do not need bull dams being genetically inferior for reproduction.

Mobility

With lameness in dairy cattle being targeted as a big time problem in animal care circles, is it time that a mobility index be produced? Can we take our current DNA profiles and calculate such an index? It matters little that we know a host of traits about feet and legs when breeders are most concerned about a cow or heifer’s ability to move freely and comfortably in the environment is which she lives. (Read more: Cow Mobility: One Step Forward or Two Steps Back?)

Getting with the Program

Perhaps some of our ‘thought list’ will be possible in the next year or two. One thing we know is that for traits to be able to be evaluated we need more animals both recorded for performance and DNA profiled. Of immediate concern is that without broad based field data for calf and heifer performance we are limited in what we can accurately know about this important cost center. Any breeders not currently DNA profiling all their heifer calves are denying themselves future opportunities to advance their herds. Cost is frequently given as the reason for not DNA profiling, yet the cost is only about equal to officially milk recording a cow for a year. The information obtained can be used early in life including which heifers to keep, how to manage them and which sires to breed them to.

The Bullvine Bottom Line

Like almost everything else in genetic advancement, genomics does not have all the answers. It does not have 100% accuracy but it sure does shorten the generation interval in dairy cattle breeding. Opportunity knocks for the breeders that do profile their animals. And every month with new facts coming out on genomics, the opportunity for greater return on investment increases for participating breeders.

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Genomics – Lies, Miss-Truths and False Publications!

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Tuesday, October 15th, 2013

Recently I read the most disturbing Letter to the Editor that I have read in a long time. It was produced by lr Gerard Scheepens. The concerning part was that it was written by someone working for an A.I. company (K.I. Samen) and was published by a dairy publication (Holstein World) trying to pander to those who spend the most money with them instead of thinking about how accurate the letter was. In typical Bullvine fashion we decided to dispel the lies, miss-truths and false publications, so that you, the dedicated breeder, can see through the BS and understand what is actually happening.

Accurate Prediction or Wishing on a dream

In the article they make the following comment “Looking at the results of the genomic bulls with daughters in production you can see a devastating truth; nearly all of the bulls drop and drop a lot.” The funny part, but not surprising is that they don’t back up this “devastating truth” with numbers. Having painted a bleak picture, they just provide generalities and expect you to accept them as truth. As the Bullvine has published several times in the past (Read more: How Much Can You Trust Genomic Young Sires? and The Truth About Genomic Indexes – “show me” that they work!), 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, will be higher than +3173 LPI, once he has his official progeny proven index that is over 90% reliable and that would make him the highest active proven sire in Canada. 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. This clearly means that they are a better option than the proven bulls available at that time. It’s called genetic advancement.

Columbus disease

Didn’t Christopher Columbus colonize the new world? Wouldn’t America have been different if Columbus had not dared to try new things? If bold thinkers like Columbus had not set out to explore and try new things the world would still be reported to the editor as flat? You see in order to advance we have to try new things. The benefits of a technology such as genomics is that there are educated risks. They are not sure fire guaranteed, they are educated risks. Even using a 99% reliable sire will not give you the same exact result every time. Fear mongers who are afraid of change like to throw out things like bulls’ proofs dropping. Well, guess what people, so do proven bulls’ proofs. Those proofs just don’t get noticed as much and no one is using it to put fear into breeders for no reason other than personal profit. Mother always said that upon hearing outrageous criticism, “Always consider where it’s coming from!”

Equations

I don’t profess to be a mathematician or a geneticist, though there is one fact I know for sure. The more accurate the information you have to work from the more accurate the result. Genomics is not a perfect science, but it is more accurate than just parent averages alone. You think bull’s proofs drop now. Look what used to happen before the introduction of genomics. (Read more: Has Genomics Knocked Out the Hot House Herds? And The Hot House Effect on Sire Sampling). If someone runs a person over with a car, who is to blame? Is it the car manufacturer’s fault for making a machine that can go faster than we can walk and larger than a bike? Or is it the driver’s fault for using the machine in other than the intended way. You see genomics in itself is not solely to blame when the resulting calf does not live up to expectations. (Read more: Who’s to Blame? Why is there a lack of accountability in the Dairy Genetics Marketplace)

Real change is needed

In the published letter to the editor the author highlights the issue of inbreeding, something that has been an issue for a very long time. The thing is you need to put inbreeding into perspective. First data from the US reported that the current cost of inbreeding over an average cow’s lifetime was US$24. (Read more: INBREEDING: Does Genomics Affect the Balancing Act?) That means that a 1% reduction in progeny inbreeding (valued at around $5 per cow). But what if the genetics of that animal also means that their production will drop $10? Inbreeding needs to be kept in perspective. Inbreeding is only an issue when you don’t manage and account for it. (Read more: 6 Steps to Understanding & Managing Inbreeding in Your Herd and Twenty Things Every Dairy Breeder Should Know About Inbreeding) There are times when certain levels of inbreeding can work well. You just need to understand all the factors.

Sire and son

In the article it makes the point that “O Man has 253 sons with daughters tested in the US and only 5 of them score higher than him on Net Merit.” It is funny that for any point you can find one single stat that you might think (or hope) proves your point. In actual fact you need to look at performance over a whole population not case by case. It’s like saying 2% of the population died from the use of penicillin, what about the 98% of the population who are still living as a result of its use?

“150% more progress in what? for whom?”

The number of times the author of this article shows an inability to understand bull proofs is a major concern. In the article he makes the following comments “The top 10 NM bulls from August 2009 with daughters had an average of 702 NM. The top 10 NM genomic bulls without daughters had an average of 814. The genomic bulls without daughters had a 14% lead. In April 2013 the average of the bulls with daughter group dropped to 607 around 13.5%. However the genomic group fell to 515 NM which leads to a drop of 37%. Furthermore, the proven group, which was 106 NM behind now leads with 92 points NM. Where is the speed, and where is the progress?” Again there are two main issues here. First can I introduce you to something that is called a base change? Secondly, the author is again using a selective group versus the whole population. There are published results from across the whole population that shows that the actual rate of genetics advancement has increased rapidly with the use of genomics.

Cows are not pigs

Can pigs fly? The author’s point about how cows are not pigs is almost as irrelevant as the price of eggs in Winnipeg. Yes in pigs the female has a larger role in genetic advancement than the female in cattle (Though the use of IVF on top females in dairy cows is quickly changing that). The point the author makes is about how cows need to also reproduce in addition to produce. That is why we have traits like daughter fertility, calving ability, daughter calving ability, calving ease, maternal calving ease, daughter pregnancy rate, sire still birth and daughter still birth. This has nothing to do with genomics. It has to do with which traits we use to evaluate animals.

Variation is essential

“The new major impact bull always has an original pedigree”, according to the author of the letter. Really? Was Durham that unique (Elton x Chief Mark)? Shottle (Mtoto x Aerostar)? Goldwyn (James x Storm)? Man-O-Man (Justice x Aaron)? I think more time, research and education should be taken by the author. It is much needed before making comments that have no facts to back them up.

Reliability or accuracy?!?

For about 30 seconds I almost agreed with the author on this one point…then they fell off the rails and I was back to how off the mark this individual is. Yes bias is an issue (Read more: Preferential Treatment – The Bull Proof Killer). But then the author’s points fall off the train when he says “The accuracy of the breeding is way too low to take that kind of chance. Accuracy of the proof will become more important than the reliability of the proof.” That logic would then say that we never use an un-proven sire ever again. Then where would our genetic advancement be?

How to stop a runaway train?

And then the author himself slams the brakes on his own runaway line of reasoning! The author categorically states that as an industry we should “spend the money by improving the animal model, spend on better evaluations, less costly and more effectively.” The simple reply: Isn’t that exactly what genomics is designed to do? And is doing?

The Bullvine Bottom Line

Since launching the Bullvine we learned one thing, it’s not wise to spread falsehoods or inaccurate information. That is why whenever possible we have always put facts behind our points or when there are no facts available, such as in the case of dairy cattle pictures, we have gone to the effort ourselves so show how things are working. We don’t believe in treating our readers as if they have no brains by publishing falsehoods or misinformation. Instead we believe an educated breeder is the most valuable asset the dairy industry must have at this time. That is why each day we source, write and share the most educational content in the dairy industry. And we back it up with facts!

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Genomics at Work – August 2013

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Wednesday, August 21st, 2013

Five years ago dairy cattle breeders were first hearing the word genomics. Over many generations of cows they had followed the recommended practice of using plus proven A.I. sampled sires on the majority of their herd with limited use (20-30%) of high indexing young unproven bulls. This practice had made it possible for them to improve their herd, help the breed improve and to generate revenue from the sale of breeding animals. And then along came a new way to look at accuracy for young animals and the merits of a cow without having to wait for her to have many milking daughters.

For most of us it was something that shook the foundation of what we knew about breeding cattle. How could an analysis of the genes change the method of breeding we knew and had been very comfortable with using? As expected breeders have had a variety of reactions. Some instantly adopted genomics. Some cautiously considered and used it to a limited extent. Many took a wait and see approach.

Today much has changed to the point where half the semen used is that of genomically evaluated bulls. We are learning more every month and every index run about genomics. The Bullvine decided to address some of the current questions and thoughts about genomics that we are hearing expressed by our readers.

Learning from Observer

DE-SU OBSERVER

De-Su Observer, a former high ranking genomic bull, born in November 2008, received his first official proof, which included daughter performance, in April 2013 and he had a gTPI of 2332. However with last week’s index release (Read more: August 2013 Holstein Sire Evaluations Highlights From Around the World) his gTPI dropped by 188 points to 2144. Many breeders are asking why? Can we trust genomics and the very first proofs with daughter performance included? Let’s think this one through.

High genomic bulls are now used by A.I. and breeders as mating sires for the next generation mostly using ET. The female mates of these bulls, with few exceptions, are also high indexing. Their progeny’s genetic evaluations will be adjusted for their parent’s high genetic merit by the genetic evaluation centres. However the extra care and treatment breeders give to these future star females, from birth to the end of their first lactations, cannot be totally adjusted for in the genetic evaluations. This means we can expect these young bulls to be over-evaluated in their first official proof based on the performance of their first 30-60 daughters. Until we can capture more details at the herd level for yields, health, reproduction, herd management, type assessment and heifer performance we can expect that high genomic bulls, after they get their very first official proof, will subsequently fall back slightly in some part of their proof.

This just happened to Observer. Between April and August he added 582 milking daughters to reach 800 and 283 classified daughters to reach 349. In April he was and in August he still is a 99%RK gTPI sire but he dropped from #1 to #21 on the TPI list (#8 among those with 99% reliability for MF). His breeding pattern for type did not change. His daughters have outstanding mammary systems but are only average feet and legs and below average dairy strength. His ratings for fertility and longevity were essentially unchanged. If anything they are up slightly. However Observer’s ratings for the yield traits dropped. The decreases were milk -14%, fat -26% and protein – 21%. He is still a top proven bull and a good bull to have in the pedigree or to use to make productive profitable cows. With the high number of daughters now in his proof we can expect he will not changed to a similar extent in December.

Considering a bull’s rank on a total merit index list is the first step in selecting bulls. However knowing how his strengths and limitation match your herd’s genetic needs is the important second step.

What about Robust, Bookem, AltaMeteor and AltaRazor?

All these bulls had their first official proofs in August after being highly rated on their genomic information. Their August Reliabilities range from 89% to 91%. So we can expect some movement in their indexes, as they have information added on daughters, the same as happened with Observer. Remember they can go up as well as down. They are all top of the class graduates but like all new graduates we can expect to know their attributes more exactly come December or next April. For discerning breeders this means use them but not any one of them to an excessive amount. Between them these four bring to the industry high NM$, high protein yield, high udder composite and high fat yield. All things commercial breeders include in their breeding plans (Read more: What’s the plan?).

What about Inbreeding?

Some breeders are asking the Bullvine – “so where are the bulls that are below 5% for inbreeding”? Readers have taken seriously the need to decrease the inbreeding level in dairy cattle (Read more: 6 Steps To Understanding & Managing Inbreeding In Your Herd and Twenty Things Every Dairy Breeder Should Know About Inbreeding). It is not easy to find bulls to use that are low for their inbreeding coefficient. To readers it seems that the high genomic bulls come from the same sire lines – Planet, Shottle, Oman, Goldwyn, Bolton,..etc. From time to time the Bullvine does produce lists of outcross sires (Read more: Going off the map: 14 outcross Holstein sires that don’t include GPS and 12 Sires to Use in Order to Reduce Inbreeding) so check those out. It would be a benefit to breeders if CDCB or CDN would produce listings for genomically evaluated bulls over 2000 PA gTPI of +2500 PA gLPI but under, at least, 5-6% for inbreeding coefficient. (Read more: Crossbreeding: Breed Help or Hindrance?).

Can more Genomic Related Information be Published?

To most breeders, it seems that genomic indexes are high, and constantly increasing. It is almost impossible to keep up. Go to an auction sale and hear the pedigree person say that ‘this bull is leaving many high genomic progeny” and what is the average breeder to take that to mean. It can be confusing even for people “in the know”. But what about people who do not follow the results closely? Furthermore for breeders that follow more than one breed, they see what is top numbers in one breed may seem ordinary in another breed. Has the time come to consider changes such as:

Publishing the %RK for indexes – that way an animal’s strengths and limitations was be easily seen
Widely publishing the levels for all indexes for 99%RK, 90%RK and 50%RK
Identifying animals that leave top genomic progeny for all traits not just for the total merit indexes.

Keep moving Forward

Genetic Evaluations Centres around the world are studying ways to use the records from bulls’ daughters where the bull may not have been randomly sampled. Excluding records from analysis is not as easy as not using the data from ET daughters or for the first 50 to 100 daughters born. These steps could be well and good if this matter only involved the genetic side of our business. But it impacts marketing and revenue generation from top animals and therefore it gets complicated. It could well be some time before we have a solution.

Breeders need a breeding and marketing plan for their herd. And then they need to use the most up-to-date genetic indexes for both bulls and cows. It does not change the process: first sort the bulls by your preferred total merit index; and then correctively mate your cows or group of cows with the best mate on your selected list. It is up to each breeder to decide whether to use the genomic information or not. The advantages from using genomic information are a faster rate of genetic improvement by having more accurate indexes on young animals and the use of the very top animals, especially bulls.

The Bullvine Bottom Line

Breeding is about creating animals that are genetically superior to our current herd of animals. It does not simply happen by adding one and one to get two. It involves using all the skills including planning, cow awareness, genetic theory, accurate information, the turning of generations,..etc. Genomics is proving to be a good new tool. No doubt it and genetic evaluations will improve considerably over the next five years. More knowledge is always a good thing.

To see all the latest proofs be sure to check out our Genetic Evaluation Section.

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6 Steps to Understanding & Managing Inbreeding in Your Herd

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Monday, June 3rd, 2013

Many articles and various approaches have been written over the past couple of years on how to deal with inbreeding in dairy cattle (Read more: 20 Things Every Dairy Breeder Should Know About Inbreeding and INBREEDING: Does Genomics Affect the Balancing Act?). However the herd breeding approach towards inbreeding that is best suited for individual dairymen is not a one size fits all.

Out-Crossing

Frequently the method recommended is to find out-cross sires and to use them on a herd rather than closely related or inbred sires. The Bullvine produced such a list a few months back (Read more: 12 Sires to Use in Order to Reduce Inbreeding). However totally out-cross sires are almost non-existent as very few Holstein A.I. breeding bulls do not contain, in their first three generations, a cross to, at least, one of Bolton, Blitz, Durham, Goldwyn, Oman, Planet, or Shottle.

Sires From the Past

But we should not despair. This problem has been the same challenge for the past century. In the past there were concerns about too much concentration of the Holstein bloodlines when Rudolph, Blackstar, Valiant, Elevation, Astronaut, Rockman, the Burkes and the Montvics were in their hay days. It is not new in 2013. A few years back Holstein International produced an article on the extreme focus, around the world, on Blackstar as he had a few hundred sons that were sampled in A.I. But we moved on past the Blackstar focus and outcross sires came along and saved the breed from a one sire focus.

Recent Out-Crosses

The most recent ‘heroes’ to assist with avoiding inbreeding Holsteins have been Shottle, Oman and Planet. They themselves have average to below average inbreeding percentages – 6.25%, 5.06% & 7.27% respectively. We must remember that it was not their lower inbreeding percentages that attracted breeders to them it was what their daughters could do in every breeder’s herd. They were all out-crosses when they arrived on the scene. However, they were all used heavily, perhaps too heavily. In fact it is not the bulls that are the problem. It is our over abundant use of sires on close relatives that lead to them becoming inbreeding concerns.

Why Inbreeding was Practiced in the Past

Before the era of genetic evaluations, inbreeding was employed in what was called ‘Line Breeding’. The concept was to find a family that had the attributes a breeder wanted and then to double, triple or even quadruple up the cow or bull in the pedigree of the next generations. Breeders persist in using the line breeding approach even though we now have very accurate genetic indexes. As a result we are creating an inbreeding problem for ourselves. Especially for traits like fertility, immunity, vigour and longevity. In 2013 these traits are coming to the forefront in the breeding of dairy cattle.

What is Average for Inbreeding?

In the USA inbreeding is expressed by a term called Inbreeding Coefficient, whereas in Canada it is called Inbreeding Percent. The average value for each appear to be similar with the average inbreeding in Holsteins in Canada being 5.87% in 2009.

Here are some examples of inbreeding percent that can be expected from within family matings:

Brother- Sister 25%
Half Brother – Half Sister 12.5%
First Cousins 6.25%
Second Cousins 3.13%

In other words, the average animal in the Canadian Holstein populations was almost equivalent to being the result of mating first cousins.

Sire Selection & Inbreeding

Choosing sires to minimize inbreeding is not as simple as going to CDN.ca or DairyBulls.com and finding the top (lowest) bull for inbreeding percentage or inbreeding coefficient. Thus eliminating from your breeding program any bull that is over average for inbreeding. You must also consider the bloodlines in your herd and the inbreeding of your females.

It can happen that a cow and a bull each have low inbreeding percents but due to being from similar bloodlines the resulting progeny are inbred. Take Goldwyn for example. His sire, James, has an inbreeding percent of 3.67%. His dam, Baler Twine’s value is 9.74%. Yet when mated because of the intense line breeding to both Grand and Aerostar, Goldwyn’s inbreeding value is 15.69%. The line breeding did allow for his genetic make-up to be homozygous at many loci. We all know how he stamps out show type. However breeders planning to line breed further with Goldwyn in the pedigree should be concerned about the definite possibility of inbreeding depression for health and fertility traits. Sire stack does not show inbreeding as accurately as inbreeding coefficient or percent does.

For breeders interested in some bulls with below average inbreeding values, The Bullvine offers the following lists. Note that we have chosen bulls with high total merit indexes and above average for Daughter Pregnancy Rate and Daughter Fertility. There is no benefit to using a sire that has a low inbreeding number yet produces daughters that have low fertility or are lacking in any of healthy fast growing calves, immune animals, SCS, Feet & Legs or Mammary System. Of course the lack of heifer information across herds could be our Achilles Heel in the not too distant future in genetically advancing our heifers.

Tables 1 – Top Sires with Lower Inbreeding Levels

Name	Inbreeding	Index	Fat	Protein	UDC/MS	FLC/F&L	SCS	DPR/DF	Net Merit	Sire Stack
USA Sires
Amighetti Numero Uno	3.6	2456 (GPA TPI)	89	47	2.7	2.21	2.59	1.3	836	Man-O-Man x Shottle x
Co-op O-Style Oman Just	4.1	2246 (GTPI)	47	56	1.21	2.11	2.71	2.4	728	Oman x Teamster x
Farnear-TBR-BH Cashcoin	5	2470 (GPA TPI)	78	52	2.88	1.24	2.56	1.4	904	Observer x Goldwyn x Shottle
De-Su Observer	5.5	2332 (GTPI)	61	52	3.02	0.89	2.76	0.6	792	Planet x Oman x BW Marshall
Canadian Sires
Regan-ALH Diplomat	5.34	2905 (GPLI)	49	73	8	10	2.81	101	327	Mr Burns x Oman x Durham
UFM-DUBS AltaEsquire	5.69	2864 (GLPI)	110	63	1	4	2.79	103	466	Oman x Sam x Patron
Genervations Lexor	5.79	3291 (GPA LPI)	90	84	11	14	2.89	100	652	Man-O-Man x Goldwyn x Durham
Swissbec Brekem	5.85	3227 (GPA LPI)	72	80	13	10	2.87	102	641	Bookem x Man-O-Man x Mr Burns
Other Sires
O-Man End-Story	3.81	2915 (Mace LPI)	80	69	6	7	3.13	103	483	Oman x Besn x Luke
Bertaiola Mincio	4.3	2927 (Mace LPI)	74	45	16	11	3.06	100	460	Bolton x Iron x Mtoto
Koepon AltaClassman	5.29	3180 (Mace LPI)	94	73	8	10	2.71	103	721	Man-O-Man Shottle x Aerostar
KNS Reminder	5.74	3199 (Mace LPI)	106	79	7	10	2.86	101	681	Sudan x Oam-O-Man x Goldwyn

The Bullvine cautions breeders using genomic sires to not use just one sire. Many of the top sires on the genomic listings have average to above average inbreeding numbers. So it is best to use many genomic sires. Many breeders wisely use from 5 to 20 doses of a genomic sire and then move to another high genomic sire.

Six Suggested Practices

Avoid using any sire that has above average inbreeding numbers especially if his pedigree has similar sires to the females in your herd.
After identifying sires with average to below average inbreeding numbers, make sure they are superior for traits important in your breeding program like fat yield, protein yield, feet & legs, mammary system, udder health and fertility.
Use a sire’s genetic and inbreeding indexes when selecting sires and do not practise line breeding.
If there is a sire that you would like to use but his inbreeding index is on the higher side then use his top two non-inbred genomics sons.
Use computerized sire mating programs as they consider inbreeding when making sire recommendations.
A.I. organizations should publish the inbreeding values for the sires they sample, prove and market.

The Bullvine Bottom Line

Inbreeding is a consideration but not the driving force when it comes to improving the genetic merit of a dairy herd. Line breeding served its purpose in the past but now can be detrimental to lowering inbreeding in dairy cattle. By following the suggested practices you will not only be able to better understand inbreeding, you will actually accelerate you genetic advancement, by not avoiding those sires that you thought would have been a inbreeding problem. It’s important to remember just how much effect inbreeding will have, and how does that compare to the difference in genetic merit between the sires you are choosing from.

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

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12 Sires to Use in Order to Reduce Inbreeding

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Thursday, March 14th, 2013

Inbreeding, and more importantly its consequences, has long been a concern of breeders as it reduces production, lowers fertility, results in more stillbirths and leads to fewer days in the herd. When genomics was first introduced, the theory was that it could help limit the amount of inbreeding in Holsteins. In reality it has done the exact opposite. Research indicates that relationships within respective breeds could be accelerating even faster since genomics’ introduction five years ago and there is also evidence that genetic diversity, another factor of inbreeding, is shrinking.

When you look at the sires of the top 100 genomic young sires lists, you notice a decent variety of sires with 30 bulls siring the top 100 sires. However, a pedigree analysis on only the paternal side reveals that 90 percent of the bulls either have Oman, Planet or Shottle represented as the sire or grandsire. The remaining 10 bulls represent genetic diversity. However, the list needs further refining because 3 of the 10 remaining bulls have Oman’s sire or Shottle’s sire in the pedigree. That leaves seven bulls with unique sires among the Holstein breed’s elite.

To help guide breeders in dealing with this inbreeding issue, we decided to look for outcross sires either proven or genomic tested sires that would offer breeders the near maximum genetic gain while providing needed diversity. The word outcross or what constitutes an outcross sire can be tricky depending on where you are located. For our purposes, we are calling an outcross sire to be one that does not have Oman, Goldwyn, Planet, and Shottle anywhere in the 1st, 2nd or 3^rd generation of their pedigree.

Balanced Overall Performance Improvement

When looking for the sire that will help improve your herd across the board, we looked for sires that have a balance of production and longevity. We also wanted great health and fertility traits that will deliver a low maintenance cow (Read more – Fact vs. Fantasy: A realistic approach to sire selection). Here are our top three.

CO-OP BOSSIDE MASSEY
MASCOL x PECKENSTEIN FORM BRET x HA-HO CUBBY MANFRED
Massey is a popular sire of sons combining elite indexes with a great outcross opportunity. Massey daughters are snug uddered with strong attachments. Though they should be protected for rump angle (high) and dairy strength, his low somatic cell score, high herd life/productive life and strong fertility make Massey a great sire for your breeding program.
COYNE-FARMS DORCY
SANDY-VALLEY BOLTON X PECKENSTEIN FORM BRET x STARTMORE RUDOLPH
Look for Dorcy to sire balanced dairy cattle that have great udders and very good feet & legs, though he will need to be protected for dairy strength, fat percent and specifically his body depth and chest width. While his productive life and low somatic cell score make Dorcy very strong longevity sire, you will want to use him wisely on virgin heifers as he is not a calving ease sire.
CO-OP BOOKEM YUXI
DE-SU 521 BOOKEM x END-ROAD PVF BOLIVER x PECKENSTEIN FORM BRET
Yuxi is a great sire for feed efficiency, based on his strong milk production from smaller framed and stature cattle (Read more: 30 Sires That Will Produce Feed Efficient Cows). While he needs to be protected on loin strength and body depth, his high productive life, low somatic cell score and great calving ease will have his daughters producing milk in your herd for a long time.

Production Improvement

It might be easy to just take the top milk lists or combine the fat plus protein and say those sires are the best for overall production. We here at the Bullvine would not want to totally forgo type as well as health and fertility, so we are looking for the sires that give you the maximum production gain, without sacrificing everything to get it.

KINGS-RANSOM B RUBLE
SANDY-VALLEY BOLTON x END-ROAD PVF BOLIVER x B-Y-U MANDEL BOMBAY
A proven sire that maybe has not caught the eye of many breeders, Ruble offers outstanding production improvement from solid type. While certainly not a calving ease sire, Ruble will greatly increase production from strong uddered cows that have good feet and legs.
OCONNORS JAY
SANDY-VALLEY BOLTON x REGANCREST ELTON DURHAM x HENKESEEN MARCIS MARVELOUS
Coming from a strong maternal line (Read more: The Bloom is on Oconnors Goldwyn Jasmine) Jay offers great component improvement from solid production. He also has the ability to improve overall type, especially udder attachments and texture, but should be protected on pin setting.
CO-OP MASTER GENO
BOSSIDE MASSEY MASTER x BADGER-BLUFF FANNY FREDDIE x JOSE
Talk about a challenge. In order to find a genomic sire that met our requirements we had to go the 95^th sire on our list of production improvement genomic sires. Much like Yuxi, Geno will also produce feed efficient daughters (Read more: 30 Sires That Will Produce Feed Efficient Cows). His strong components, especially fat, combined with great udders and strong health and fertility makes Geno a great sire to look at for a solid outcross sire.

Longevity Improvement

For those of you that are looking to breed cattle that stay around lactation after lactation or maybe you are having problems with your 2 year olds not coming back for a 2nd lactation, we recommend the following outcross sires, in addition to Dorcy mentioned earlier:

SILDAHL JETT AIR
EMERALD-ACR-SA T-BAXTER x MARA-THON BW MARSHALL x HA-HO CUBBY MANFRED
This outcross sire offers great longevity improvement combined with strong health and fertility. While he does need to be protected on protein and milking speed, his great feet and legs, udders and health and fertility, make him an outcross sire you don’t want to miss.
BERTAIOLA MINCIO
SANDY-VALLEY BOLTON x BOSS IRON x CAROL PRELUDE MTOTO
With Boss Iron daughters such as Decrausaz Iron O’Kalibra catching the eyes of the world in the show ring (Read more: The All European Champion Show: The Greatest Show On Earth), there are also Iron daughters that are getting the job done as bull mothers. A great example of this is BEL IRON IRENE, the dam of Mincio. This high fertility Bolton son combines high type with great production, which is resulting in outstanding results in his current daughter performance. Watch for MINCIO to sire great udders and feet & legs though you may want to watch him on somatic cell score.
RONELEE DORCY DELIGENT
COYNE-FARMS DORCY x END-ROAD PVF BOLIVER x COMESTAR OUTSIDE
This outcross genomic sire just spells longevity. Deligent was bred to deliver long lasting daughters. With outstanding Herd Life/Productive Life, breed leading mammary systems scores and strong Feet and Legs scores, Deligent is a longevity specialist, though he does need to be somewhat protected for dairy strength. Look for DELIGENT to combine this longevity with strong production and type numbers.

Health and Fertility Improvement

One area that is not getting enough attention from most breeders is health and fertility. While there is no question that every breeder knows that more pregnancies equals more profits many of the top ranking sires actually have negative values for health and fertility. The following are some outcross specialist sires that should help you change that:

PENN-ENGLAND STOCKTON
PURSUIT SEPTEMBER STORM x FUSTEAD EMORY BLITZ x PEN-COL DUSTER
While you certainly would not use Stockton as a production improvement sire. His high daughter pregnancy rate, productive life and low somatic cell make Stockton the perfect sire for that high production cow you are looking to breed some health and fertility traits into.
CERVI PHONIC
LATUCH ROLEX x OLMO PRELUDE TUGOLO x SHEN-VAL NV LM FORMATION
While not a name that most breeders know, Phonic is certainly going to get some attention from breeders looking to breed to where the industry is headed. With extremely low SCS and high daughter fertility combined with functional type and above average production, Phonic is leaving daughters that are extremely low maintenance. Tracing back to the great Italian brood cow Cervi FIRESTONE, this family has produced such sires as BUXON, WOODSTOCK and PADERNUS. Given his high rump angle, it is interesting that he is such a good calving ease sire.
BLUMENFELD LEWIS TRUE
LATUCH FREDDIE LEWIS x LEIF x RAMOS
Similar to finding an overall performance improver on the top genomic lists, finding a health and fertility genomic sire had us going to number 55 on our list. Look for True to sire outstanding udders with strong feet and legs. He will need to be protected on loin strength.

The Bullvine Bottom Line

Choosing the correct sire can be challenging enough. Finding a sire that also offers an outcross from the main Goldwyn, Planet, Shottle and Oman can be almost impossible. That is why we compiled these 12 sires to bring to light some outcross pedigrees that many breeders may not have heard of. It is, certainly worth taking a look at many of these sires, when looking to combat inbreeding in your herd.

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.

INBREEDING: Does Genomics Affect the Balancing Act?

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Tuesday, May 29th, 2012

If you are like many of us you are alternately amazed, overwhelmed and confused by the barrage of information that is fed to you through your breed organizations, cattle committees and industry publications. As part of The Bullvine`s commitment to be an informative and understandable resource for cattle breeders, I have spent considerable time trying to get my non-scientific head around the 2011 paper in the Journal of Dairy Science entitled, “Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information.” Was it worth the bother? Yes. Definitely.

What You Don’t Know Can Hurt You

We can all agree that Genomic information is a tremendous breakthrough for cattle breeding. With all the potential, it didn’t take long for the concern to arise that greater rates of genetic gain could lead to higher annual rates of inbreeding. My wild imagination skipped to a picture of everyone breeding to the top bulls and ending up with a single family. Even if that seems outrageous, it is definitely possible that generation intervals could be halved through taking advantage of the accurate GEBV’s available at birth and this could increase the inbreeding per year. Therefore, I definitely wanted to find out from this paper published by Pryce, Hayes and Goddard in Australia on how genomic information offers possibilities to control the level of progeny inbreeding.

Concern: Are we moving from homogenized milk to homozygous cows?

Let’s take a look at the indicators that might lead us to believe the answer is, “Yes!”

Genomic predictions are both cost effective and highly accurate. Therefore there is the very definite potential to accelerate the rate of genetic gain beyond that achieved through progeny testing.
Shorter generation intervals could result in large numbers of animals who are similar in genetic makeup due to the sires used.
It’s human nature to aim for the best. The uptake of genomics has been beyond anything previously predicted or imagined. Not only is the playing field being leveled it is being dramatically narrowed down.

Strategies to Control the Rate of Inbreeding

An important part of this Australian study was to evaluate the effect of the three strategies tested on the homozygosity of deleterious recessives. In other words, what can breeders do to limit the potential for negative effects of inbreeding? Before, we go further, it is interesting to note, that these researchers referenced more than twenty other research papers. The focus on this subject is concentrated and that can only be good for the eventual outcome for breeder decision making.

The main limitation of comparing methods to predict progeny inbreeding is that, at this time, there is no best practice for measuring inbreeding. Pedigree is flawed by errors and gaps and often, particularly in commercial herds, the depth of pedigree. Genomic relationships calculated using SNP data could have errors from incorrect identification of samples.

The goal of these researchers was to compare 3 strategies for controlling progeny inbreeding in mating plans:

Pedigree inbreeding coefficients
Genomic relationships
Shared runs of homozygosity.

The Good News Is….

I know this all sounds very complex, but relax there is good news. The study found that both genomic relationships and pedigree relationships were successful strategies to control the rate of inbreeding under genomic selection. They also concluded that using genomic relationships instead of pedigree relationships “appears to be better at constraining genomic inbreeding under genomic selection.” The unique part of their study was that they went a step further and proposed “using runs of homozygosity to control the rate of inbreeding.”

Again I know sounds very complex. So let’s try and break it down. One of the underlying processes of inbreeding is that it increases the frequency of both favorable and deleterious homozygotes. ROH stands for run of homozygosity. If the occurrence of deleterious homozygotes is more likely to arise as a consequence of recent inbreeding (which is the potential of heavy use of genomics) then strategies to minimize ROH could be a way of reducing them. A novel approach, don’t you agree?

What did they do?

In the research simulation they used 300 cows with 20 sires available for mating, replicated 50 times. Each of the 300 individuals allocated as dams were matched to 1 of 20 sires to maximize genetic merit minus the penalty for estimated progeny inbreeding and given the restriction that the sire could not be mated to more than 10% of the cows. In the discussion part of the paper, which, of course, is the easiest part to understand they offer this: “The results presented here show that using A GRM instead of pedigree in a mating plan is an effective way to reduce the expected inbreeding in progeny, with minimal effect on the genetic gain for the inbreeding objective.” The breeding objective in Australia is expressed as APR and in Canada it is LPI and in the US is TPI.

What can YOU do Today?

Before we go on to look at the financial aspect of this discussion, you should refer to the Genomic Evaluation Details which are available from CDN (Canadian Dairy Network) or from your breed association. In the CDN report there is a column that gives the percentage inbreeding (%ING) numbers for the Sire; Dam and MGS. In general it could be agreed that 0-8 is good; 8 to 10 is okay: 11 to 14 watch and 15 or more take action.

What is the Dollar Difference of Inbreeding?

Inbreeding affects profitability by adversely affecting traits related to fitness and production. Data from the US reported that the current cost of inbreeding over an average cow’s lifetime was US$24. For this study a conservative value of $5 per year was used as the economic value per 1% increase in inbreeding. “These results demonstrate that using GRM information, a 1% reduction in progeny inbreeding (valued at around $5 per cow) can be made with very little compromise in the overall breeding objective. These results and the availability of low-cost, low –density genotyping make it attractive to apply mating plans that use genomic information in commercial herds.”

By itself this economic benefit does not currently justify the investment in whole herd genotyping, if one considers that pedigree information is free and appears to do a pretty good job of controlling inbreeding, However, it may be economically worthwhile for dairy farmers to invest in whole-herd low-density genotyping in conjunction with other uses of genotyping. Examples could include confirming parentage, selecting the best heifer calves to keep as herd replacements, managing genetic defects, flushing and selling high-value pedigree stock. These researchers conclude: “Based on our calculations the value of genotyping to control inbreeding could be worth between $5 and $10 per cow.” You do the math.

THE BULLVINE BOTTOM LINE

So this is my untrained, non-scientific understanding of this single paper on a subject that is growing faster than gossip on a grapevine. Having said that, it is each dairy breeder’s job to be informed. Use your network to find out who has the best answers to this question because when it comes down to the affect of inbreeding on YOUR breeding bottom line it’s YOUR money!

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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Archive for Inbreeding

A New Approach to Studying Diversity

Some Eye-Opening Facts

Genetic Diversity is No Longer

Is this a Ticking Time Bomb?

Finding Solutions

The Bullvine Bottom Line

Other posts you might like:

Breeder Attention to Inbreeding is Limited.

The Question is ……

What is Inbreeding?

Varying Degrees of Inbreeding.

Level of Inbreeding

Impact of Inbreeding in Dollar Terms

It is more than looking at the Inbreeding Coefficient (IC)

What is the Ideal?

Sound Advice

Ways to Select Bulls to Use in Your Herd

The Bullvine Bottom Line

Other posts you might like:

Only Very Moderate Uptake – So Far

Known Benefits

Genomics Will Make the Future Brighter

Heifers:

Feed Efficiency:

Inbreeding:

Disease Resistance:

Reproduction:

Misconception:

In Another World

Will Genomic Testing Pay?

The Bullvine Bottom Line

Other posts you might like:

Current Inbreeding Levels

What Has Been Happening?

What Needs to Happen?

The Bullvine Bottom Line

Other posts you might like:

Verification

Intensity of Use

Finding the Best

Which are the Future Parents

Health / Disease Resistance

Female Fertility

Mobility

Getting with the Program

The Bullvine Bottom Line

Other posts you might like:

Accurate Prediction or Wishing on a dream

Columbus disease

Equations

Real change is needed

Sire and son

“150% more progress in what? for whom?”

Cows are not pigs

Variation is essential

Reliability or accuracy?!?

How to stop a runaway train?

The Bullvine Bottom Line

Other posts you might like:

Learning from Observer

What about Robust, Bookem, AltaMeteor and AltaRazor?

What about Inbreeding?

Can more Genomic Related Information be Published?

Keep moving Forward

The Bullvine Bottom Line

Other posts you might like:

Out-Crossing

Sires From the Past

Recent Out-Crosses

Why Inbreeding was Practiced in the Past

What is Average for Inbreeding?

Sire Selection & Inbreeding

Tables 1 – Top Sires with Lower Inbreeding Levels

Six Suggested Practices

The Bullvine Bottom Line

Other posts you might like:

Balanced Overall Performance Improvement

Production Improvement