Everyone says chase the highest milk yield… but what if that’s quietly draining your profits, one genomic bull at a time?

The numbers on the screen look great, but what are the hidden costs of our genetic choices?

You ever have that moment, late at night, scrolling through bull proofs with a cold cup of coffee, and something just doesn’t add up? On paper, your herd’s genetic merit is off the charts, but conception rates are slipping, and you’re seeing more health issues than you’d like to admit. Trust me, you’re not imagining things—and you’re definitely not alone.

I’ve been talking with producers from coast to coast—big dry lots out in California’s Central Valley, tie-stalls on the rolling hills of Wisconsin, and everywhere in between. There’s a quiet trend building, and it’s not about milk price or feed costs (though, let’s be honest, we all lose sleep over those too). This is something deeper—a multi-billion-dollar genetic reckoning that’s happening right now in all our herds.

Here’s what really sticks in my craw: we’re spending fortunes chasing the top 1% of sires, poring over genomic proofs until our eyes cross, and on paper, our herds have never looked better. So why does it feel like we’re running faster just to stay in the same place?

The $23-Per-Cow Problem That’s Adding Up Fast

Let me hit you with a number that’ll wake you up faster than a fresh cup of dark roast. According to a 2020 study from Penn State, between 2011 and 2019—right as genomic selection was gaining steam—the U.S. Holstein industry lost between $2.5 and $6 billion. That’s not a typo, and it wasn’t a market crash or feed crisis. That was the cost directly tied to rising inbreeding that came with our shiny new genomic tools.

For every 1% bump in inbreeding costs you about $23 per cow annually—and let’s be clear, that’s per lactation, not lifetime. Do the math. If you’re milking 1,000 cows, that’s $23,000 a year for every percentage point of inbreeding. Over five years? That’s $115,000—enough to replace 40 solid cows.

But here’s what keeps me up at night: the very technology we embraced to future-proof our herds could be creating a systemic vulnerability if we’re not managing it with our eyes wide open. Genomic selection has been a game-changer. It’s slashed generation intervals from about 5.5 years to less than two, and according to recent CDCB research, genetic gain has jumped by 12% to over 100% compared to the old progeny testing days.

The problem? That same rocket fuel has driven the effective population size of U.S. Holstein bulls down to a historic low—just 43 to 66 animals. Think about it: the genetic diversity of the world’s most dominant dairy breed now rests on fewer animals than most high school graduating classes.

Pedigree vs. Genomic: Which Inbreeding Number Actually Matters?

Here’s where things get interesting. When we talk about inbreeding, we’re really talking about two different numbers, and the difference matters more than you might think.

Pedigree-based inbreeding is what we’ve used for decades—it’s like cattle genealogy, calculating the odds that an animal inherited identical genes from a common ancestor. But it often underestimates what’s actually happening in the genome.

Genomic inbreeding, measured through runs of homozygosity (ROH), looks directly at the DNA to see where an animal truly has identical gene sequences. It’s the difference between assuming what went into a recipe and actually tasting the final dish.

What strikes me about the genomic approach is how it can distinguish between old inbreeding (from way back in the pedigree) and recent inbreeding (from repeatedly using popular sires). The recent stuff—that’s what’s really hurting us. A 2023 study from the University of Guelph showed that recent inbreeding under genomic selection has a sharper negative impact on both production and fitness traits than the “old” inbreeding our breeds have carried for generations.

So, which should you focus on? My take: use genomic measures for the animals you’ve got data on, and supplement with pedigree for everything else. Genomic tools give you the real picture of what’s happening now.

Where to Actually Find These Numbers (Because That Matters)

You can’t manage what you can’t measure. For U.S. herds, your best bet is the CDCB (Council on Dairy Cattle Breeding) website. They publish Holstein inbreeding reports that give you both pedigree and genomic inbreeding levels for AI sires. It’s free, it’s current, and it’s data you can use.

Canadian producers might have it even better—Lactanet has integrated genomic inbreeding tools right into their genetic evaluation system. You can get inbreeding levels on individual animals as part of your regular genetic evaluations.

Here’s what’s interesting, though: most breed associations don’t routinely publish inbreeding levels in their regular communications. It’s there if you dig, but it’s not as front-and-center as TPI or LPI rankings. That needs to change.

The Wake-Up Call: Genomic vs. Proven Sires

Want something that’ll make you think twice about your next sire selection? Here’s a stat that’s been making the rounds among geneticists but hasn’t gotten the attention it deserves.

The top 10 TPI genomic sires—the young bulls everyone’s chasing—are averaging around 4–6% inbreeding. Proven sires typically run 3–5%. It’s easy to misread these numbers. That 4–6% inbreeding on a top genomic bull isn’t an additional amount; it’s his total inbreeding. Considering the average Holstein cow is already at 11%, this shows that AI companies are actively managing this trait, selecting elite bulls that are often less inbred than much of the female population. So, when you see those numbers on a bull proof, it’s showing you the bull’s own calculated inbreeding, not how much higher (or lower) he’s compared to the average cow in the population. This distinction matters because it means that even the most popular young sires are typically being selected with inbreeding management in mind, not just raw genetic merit.

Why are the genomic bulls a little more inbred than the proven ones? It comes down to selection intensity. When you can spot the “best” animals at 6 months old instead of waiting 5 years for daughters to freshen, the temptation is to concentrate selection on a smaller and smaller group of elite animals. The math works—until it doesn’t.

Holstein vs. Jersey: A Tale of Two Breeding Philosophies

This trend reveals something fascinating when you compare breeds. Current Holstein populations average around 11% genomic inbreeding, while Jerseys typically run closer to 9%. The economic impact? That $23-per-cow hit I mentioned earlier applies to Holsteins. Jerseys, with their more regional breeding patterns and less reliance on a handful of global sires, tend to experience less inbreeding and, as a result, see smaller economic losses from inbreeding depression.

What’s the difference? Scale and global reach. Holstein genetics flows globally—a popular sire in the Netherlands is used heavily in the U.S., Canada, and a dozen other countries. Jersey breeding, while international, tends to be more regionalized with more diverse sire usage patterns.

A Tale of Two Neighbors

Let’s bring this down to something you can picture—a real-world scenario that’s playing out in more herds than you might think.

Imagine two Holstein herds, each milking 80 cows. Both are run by savvy managers who keep a close eye on their numbers and aren’t afraid to try new things. For the last five years, both have used genomic selection, but their breeding philosophies have diverged.

Farm A is laser-focused on maximizing milk volume. They’ve chased the highest-ranking genomic bulls for milk yield, and their cows average 100 pounds per day. On paper, that looks impressive. But their herd averages 4.1% butterfat and 3.0% protein, which works out to about 7.2 pounds of combined fat and protein per cow per day.

Farm B takes a different tack. Their goal is to maximize component yield and herd health, not just volume. They select bulls based on fat and protein percentages, aiming for a more balanced cow. Their cows average 90 pounds of milk per day, but with 4.6% butterfat and 3.4% protein, also 7.2 pounds of combined solids per cow per day.

Now, here’s where it gets interesting. Even though Farm B’s cows are producing less milk by volume, they’re matching Farm A on actual solids shipped per cow. And with higher component percentages, Farm B’s milk checks are more resilient to market swings that reward fat and protein. Plus, their cows are under less metabolic stress, which means fewer health issues, better fertility, and less burnout for the staff. There’s less time spent in the hospital pen and more time with cows in the parlor where they belong.

Over time, Farm B’s approach pays off. Their vet bills are lower, cows stay in the herd longer, and staff turnover drops because the work is more manageable. When you pencil it out, Farm B’s cows are just as profitable—if not more so—than their higher-volume neighbors, all while running a less stressful, more sustainable operation.

The lesson? Chasing maximum milk yield isn’t always the path to maximum profit or herd health, especially when you focus on what really matters: pounds of fat and protein shipped, cow well-being, and a system that works for both people and animals.

The Numbers That Tell the Real Story

This isn’t just philosophical—there are hard numbers behind these observations. Research from multiple countries paints a consistent picture of what inbreeding depression actually costs:

• Production hits: Every 1% increase in inbreeding typically reduces annual milk production by 26–41 kg (that’s 57–90 pounds). For fat and protein, you can expect losses of 1–2 kg each. Doesn’t sound like much? Multiply it across your entire herd and calculate the results over a full lactation and for longer productive lifetimes per cow.
• Fertility takes the biggest hit: This is where inbreeding depression really shows its teeth. Calving intervals stretch out by about a quarter-day for every 1% of inbreeding. I know that sounds tiny, but when you’re already struggling to get cows bred back, every day matters.
• The hidden costs: Here’s what really gets expensive—increased somatic cell counts, higher culling rates, more stillbirths, and what I call “mystery ailments.” These are cows that aren’t clinically sick but don’t thrive as they should.

What’s particularly concerning, based on recent research from Australia and Europe, is that the inbreeding we’re accumulating now under genomic selection appears to be more detrimental than the traditional inbreeding from past generations. This suggests we’re making genetic changes faster than natural selection can keep up with.

Managing the “Junk” in Our Gene Pool

The thing about genetics is you get the whole package—the good, the bad, and the downright ugly. There are over 130 known genetic defects in cattle, and that’s just the stuff we’ve identified so far and can test for. A significant portion of the real damage stems from early embryonic losses, which we often attribute to “didn’t settle” or “bad heat detection”.

This is where organizations like Lactanet in Canada and the CDCB in the U.S. earn their keep. They’re tracking these genetic defects and building tests to identify carriers. Most AI companies now provide carrier status for about 22 known genetic defects as part of their standard genetic evaluation reporting package.

But here’s what keeps geneticists up at night: new mutations keep popping up. When an influential AI sire carries a new deleterious mutation—especially if he’s a mosaic, meaning only some of his sperm carry it—that mutation can spread like wildfire before anyone notices. Remember the “Pawnee Farm Arlinda Chief” situation? One sire, one mutation, over 500,000 spontaneous abortions, and nearly $420 million in global industry losses.

Smart Strategies That Actually Work

Alright, enough about the problems. Let’s talk solutions—real ones that producers are using right now with good results.

Optimum Contribution Selection is the technical term for what amounts to informed genetic planning. Instead of just using the highest-ranking bull for every breeding, OCS figures out the optimal genetic contribution from a whole group of candidates. The goal is to maximize genetic gain while keeping inbreeding under control.

Think of it this way: you might use the #1 TPI bull on 40% of your herd, the #5 bull on 30%, and a few others to fill out the genetic diversity. You’re still getting tremendous genetic progress, but you’re not putting all your eggs in one genetic basket.

The research backs this up. Multiple recent studies—including work involving Cornell and other major universities—have shown that OCS programs can achieve higher long-term genetic gain than traditional selection, all while keeping inbreeding rates in check. It’s not just theory; the scientific consensus is growing as more research teams publish real-world results.

Crossbreeding is another tool that’s gaining traction, especially among commercial producers who get paid on components. A well-planned three-way cross with Holstein, Jersey, and maybe Montbéliarde or Brown Swiss can deliver significant improvements in fertility and health through hybrid vigor. I know it’s not for everyone—especially if you’re in a market that demands Holstein cattle—but for commercial operations focused on profit per cow rather than genetic prestige, it’s worth considering.

Gene banking might sound like science fiction, but it’s actually a practical form of insurance. Storing and using semen and embryos from a diverse group of animals provides options down the road if current breeding trends create unforeseen problems.

The Reality Check: Implementation Hurdles

Here’s where theory meets the real world, and it’s not always a pretty picture. I’ve spoken to numerous producers who have attempted to implement these advanced breeding strategies, and the feedback is consistent: it’s more challenging than it sounds.

• Logistics matter. If you commit to an OCS program, you might get a breeding plan that calls for very specific matings—Bull A to Cow 123, Bull B to Cow 456. That requires meticulous record-keeping and a well-organized semen tank. For operations where one person is responsible for all breeding, especially in larger herds, this can be a significant challenge.
• Inventory costs add up. Using a diverse group of sires means keeping more bulls in your tank, which ties up capital and requires more careful inventory management than just ordering the “bull of the month.”
• The human element is huge. It takes discipline to stick to a long-term plan when there’s a chart-topping TPI bull available. The mindset shift from maximizing every single mating to optimizing the long-term health, production efficiency, and welfare of the whole herd requires buy-in from everyone—owner, herd manager, AI technician.

That said, the producers who’ve made this transition tell me it gets easier with time, and the results speak for themselves.

Looking Forward: What’s Coming Next

The future of genetic diversity management is getting more sophisticated every year. Artificial intelligence is beginning to play a role in optimizing breeding strategies, not only for genetic gain but also for managing inbreeding and diversity across multiple generations.

Whole genome sequencing is becoming more affordable, which means we’ll be better in the future at identifying harmful mutations before they spread. The cost has dropped from thousands of dollars per animal to hundreds, and it continues to decline.

What’s particularly exciting is the development of combined strategies that use multiple approaches simultaneously—OCS, weighted selection for rare beneficial alleles, strategic outcrossing, and active management of genetic defects. Early research suggests these combined approaches can deliver the best of both worlds: continued genetic progress with better diversity maintenance.

The Bottom Line: Your Genetic Legacy

Look, we’re at a crossroads. We can continue to chase maximum short-term genetic gain and accept the hidden costs of genetic erosion as just the price of doing business. Or we can get smarter about how we breed cattle—capturing genetic progress while building herds that are resilient enough to handle whatever comes next.

The evidence is clear: producers who take genetic diversity seriously don’t sacrifice genetic progress—they optimize it for the long haul. They’re not accepting lower profits; they’re building more sustainable competitive advantages.

The tools exist. The research is solid. The question is whether we’ll be among the early adopters who see the writing on the wall, or whether we’ll wait until the problems are too big to ignore.

Your genetic decisions this year will impact your herd’s productivity and your farm’s profitability for generations to come. That multi-billion-dollar hit the industry has already taken? It’s both a warning and an opportunity. The producers who heed the warning will be the ones who capture the opportunity.

So here’s my challenge to you: next time you’re selecting sires, ask yourself—and your genetics advisor—some tough questions. What’s our herd’s current inbreeding level? How can we apply OCS principles to strike a balance between our goals? Which outcross sires would be suitable for our system?

The real question isn’t whether you can afford to implement these strategies. It’s whether you can afford not to.

Bottom line: Don’t just follow the crowd. The smartest producers in 2025 are protecting their herds—and their profits—by thinking beyond the next bull proof. Give these strategies a shot and let your milk check do the talking.

Coming up in our next article, “Part 2: A Deep Dive into the Data,” we’ll dig deep into the shocking statistics every breeder should know, including detailed comparisons of top genomic versus proven sires and breed-specific benchmarks to help you assess where your herd stands.

KEY TAKEAWAYS

• Stop silent profit leaks: Every 1% rise in inbreeding costs you $23 per cow, per year.
  Action: Check your herd’s inbreeding numbers on CDCB or Lactanet today—don’t wait for a consultant.
• Genomic testing is a double-edged sword: Yes, it boosts genetic gain by 12–100%, but it’s also shrinking your genetic base fast.
  Action: Ask your genetics rep for the inbreeding coefficient on every bull you buy—aim for below the breed average (currently ~11% for Holsteins).
• Components beat volume for real ROI: Two herds with the same solids shipped (7.2 lbs/cow/day) can have wildly different stress, health, and profit—don’t chase milk pounds alone.
  Action: Shift your sire selection index to prioritize fat and protein percentages, not just yield.
• Diversify or pay the price: Herds using optimum contribution selection (OCS) or crossbreeding are seeing lower vet bills and longer cow lifespans, even with lower daily milk.
  Action: Try OCS planning or introduce a crossbred bull—see how it impacts your cull rate and staff workload.
• 2025 is all about resilience: Feed and labor costs aren’t dropping, so your genetics program needs to deliver more than just big numbers on paper.
  Action: Review your breeding plan with a focus on genetic diversity and operational sustainability—don’t get left behind.

EXECUTIVE SUMMARY

Let me lay it out straight—chasing the top 1% of genomic bulls might be costing you more than you think. According to a Penn State study, U.S. Holstein herds lost between $2.5 and $6 billion from inbreeding tied to aggressive genetic selection. Every 1% jump in inbreeding knocks $23 off your annual revenue per cow, and with herds averaging 11% inbreeding, that’s real money. Sure, genomic testing slashed generation intervals and doubled genetic gain, but it also shrank the effective bull population to just 43 animals. That’s not just a U.S. thing—global trends show the same squeeze on diversity, from Europe to Australia. The kicker? Herds focusing on fat and protein yield, not just milk pounds, are matching or beating their high-volume neighbors in profit and cow health. If you want to protect your margins in 2025’s tight market, it’s time to rethink your breeding strategy—try mixing in optimum contribution selection or crossbreeding, and watch your bottom line thank you.

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

Learn More:

• Genomic Inbreeding: How Much Is Too Much? – Offers practical strategies for monitoring and managing inbreeding at the farm level, including step-by-step guidance on using genomic data to make smarter breeding decisions and immediately reduce risk in your herd.
• The Dollars and Sense of Dairy Genetics – Reveals how genetic choices impact long-term profitability, with actionable insights on navigating market trends, economic trade-offs, and the real-world financial implications of different breeding strategies in today’s volatile dairy industry.
• Dairy Breeding Innovation: Are You Ready for What’s Next? – Explores cutting-edge technologies and future opportunities, demonstrating how forward-thinking producers can leverage emerging tools and innovations to stay ahead of genetic challenges and build a more resilient, productive herd.

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