Dairy breeders alert: The 2025 genetic base change reveals hidden inbreeding impacts reshaping PTA values and herd futures.
EXECUTIVE SUMMARY: The April 2025 genetic base update exposes how surging Holstein inbreeding silently distorts PTA adjustments, with proven bulls like Seagull-Bay Supersire-ET showing smaller-than-expected milk drops due to shifting Expected Future Inbreeding (EFI) calculations. As the Holstein population’s average relatedness spikes, EFI adjustments now account for 18% of PTA changes, requiring breeders to prioritize genomic relationship management. Delayed updates for calving traits until August 2025 add complexity, while breed-specific impacts highlight Holsteins’ 404 NM$ drop—double other breeds. Strategic herd management must now balance genetic progress with inbreeding mitigation through EFI monitoring and targeted mating programs.
KEY TAKEAWAYS:
- EFI’s Hidden Power: Every 1% EFI increase costs 64 lbs milk yield, reshaping PTAs more aggressively in Holsteins than other breeds.
- Supersire Shock Example: A 135-lb “missing” milk PTA drop reveals how population-wide inbreeding dilutes individual bull penalties.
- Holstein Crisis: 2020-born base herds show 9.4% EFI (vs. 7.5% in 2015), accelerating inbreeding depression in evaluations.
- Calving Trait Delay: Phenotypic calculation issues push key updates to August 2025, requiring interim breeding adjustments.
- Survival Strategy: Focus on EFI-adjusted NM$, utilize low-relationship genomic sires, and implement mating software to curb profit erosion.
The April 2025 genetic base change isn’t just another spreadsheet update—it’s a genetic reckoning that demands immediate attention from every serious dairy producer. While the headline numbers show significant PTA drops across breeds, the real story lies in how increasing Holstein inbreeding is silently reshaping genetic evaluations and potentially threatening your herd’s future profitability.
The Genetic Time Bomb: Why Your Top Bulls Defy Expectations
When the Council on Dairy Cattle Breeding (CDCB) announced the 2025 base change, most Holstein breeders expected a uniform 752-pound drop in milk PTAs across their animals. Yet something unexpected happened: many proven bulls showed smaller decreases than anticipated.
Take Seagull-Bay Supersire-ET (007HO11351), for example. His milk PTA decreased from 978 to 361 pounds—a drop of only 617 pounds instead of the expected 752. This 135-pound “missing” decrease isn’t a calculation error—it’s a warning sign that inbreeding dynamics are changing rapidly in the Holstein population.
The Base Change Reality Check:
- Holstein milk PTAs dropped by 752 pounds on average
- Fat and protein PTAs decreased by 44 and 29 pounds respectively
- Net Merit (NM$) values plummeted by $404
- Jersey and Brown Swiss breeds experienced smaller adjustments
The magnitude of these changes reflects both genetic progress made between 2015 and 2020 and shifting inbreeding patterns that are reshaping how genetic evaluations work.
EFI Exposed: The Silent Profit Killer in Your Breeding Program
At the heart of this genetic puzzle is a measurement called Expected Future Inbreeding (EFI), which has been used to adjust PTAs since 2008. Think of EFI as your bull’s genetic shadow—the darker it looms over the herd; the more milk profits evaporate in future generations.
EFI measures how closely related an animal is to the current female population. When a bull is mated randomly to the breed, EFI predicts the level of inbreeding expected in the offspring. This matters because inbreeding depression has real economic consequences:
Inbreeding’s Hidden Cost Per 1% Increase:
- Milk yield: 63.9 pounds reduction
- Net Merit (NM$): $25 decrease
- Fat yield: 1.18-1.70 kg decrease
- Protein yield: 0.90-1.45 kg decrease
- Calving interval: 0.19-0.34 days longer
The CDCB adjusts PTAs using a formula that accounts for an animal’s EFI relative to the base population: PTAEFI = PTA0 + b(EFI − EFIbase). This adjustment helps predict the true genetic merit an animal will transmit when accounting for inbreeding depression.
The Holstein Relationship Crisis
What’s changed dramatically between the 2015 and 2020 base populations is the average level of relatedness among animals. The Holstein breed has experienced a rapid increase in relationships among young animals, driven largely by the intensive use of genomically-tested elite sires.
In Supersire’s case, his inbreeding adjustment changed from -441 to -310 pounds between December 2024 and April 2025. This occurred because while his individual EFI remained relatively stable (13.5% to 13.6%), the base population’s average EFI jumped from 7.5% to 9.4%.
This increasing relatedness in the Holstein population means:
- The new base population (2020-born cows) is significantly more inbred than the previous base
- The difference between an individual bull’s EFI and the population average has narrowed
- Inbreeding adjustments are now smaller relative to the base population
Breed Differences: Not All Breeds Face Equal Challenges
The impact of inbreeding on genetic evaluations varies considerably across breeds:
| Breed | Milk (lbs) | Fat (lbs) | Protein (lbs) | NM$ |
| Holstein | 752 | 44 | 29 | $404 |
| Jersey | 355 | 16 | 14 | $179 |
| Brown Swiss | 381 | 9 | 14 | $130 |
These differences reflect both the genetic progress made within each breed and the varying levels of inbreeding. Holsteins show the most dramatic adjustments, highlighting the more intensive selection and higher inbreeding rates in this population.
Calving Traits: The Delayed Update
While most traits have transitioned to the new genetic base, calving traits (Daughter Calving Ease, Sire Calving Ease, Daughter Stillbirth, and Sire Stillbirth) will maintain their current base until August 2025. This temporary delay resulted from unexpected issues when applying base updates to these phenotypically scaled traits.
This exception means that until August, these traits will continue to be evaluated against the 2015 base population, though new phenotypic data received since December will still be incorporated into evaluations.
Your Strategic Action Plan
The 2025 genetic base change demands a complete reassessment of breeding strategies. Here’s how to adapt:
1. Recalibrate Selection Thresholds
Previous benchmarks for selecting AI sires need upward revision. If you previously selected bulls with +2000 NM$ you might now look for $1600 NM$ bulls given the base change.
2. Focus on Rankings, Not Absolute Values
The relative ranking of animals remains more important than their absolute PTA values. Compare animals within the same evaluation run rather than fixating on specific PTA thresholds.
3. Implement Inbreeding Management
With Holstein inbreeding accelerating, consider:
- Monitoring EFI values when selecting sires
- Utilizing outcross sires with lower relationships to the general population
- Implementing mating programs that optimize for both genetic gain and inbreeding control
4. Prepare for the August Calving Trait Update
Remember that calving traits will maintain their current base until August 2025, requiring another adjustment to selection criteria later this year.
The Bottom Line
The 2025 genetic base change reveals both remarkable progress and new challenges for dairy breeders. The increasing rate of inbreeding in Holsteins has amplified the effect of PTA adjustments, creating a situation where genetic evaluations reflect not just advancement but also changing population relationships.
By understanding how EFI influences genetic evaluations and implementing strategies to manage inbreeding while maintaining genetic progress, you can navigate this genetic reset to enhance your herd’s potential and profitability in the years ahead.
Remember: Genetic progress without inbreeding control is like milking three-legged cows—eventually, the whole operation crashes.
Learn more:
- Inbreeding: Risks and Rewards in Dairy Cattle Breeding
Explore how inbreeding impacts milk yield, fertility, and health, and learn strategies to balance genetic progress with herd diversity. - 2025 U.S. Genetic Base Change: Final Values and Strategic Implications
Dive into the details of the 2025 genetic base change, including breed-specific PTA adjustments and how Holstein inbreeding is reshaping evaluations. - Can You Trust Genomic Evaluations? 7 Facts Exposed
Uncover the truth behind genomic evaluations and how tools like Expected Future Inbreeding (EFI) help refine breeding decisions.
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