The Power of Genomics in Dairy Cattle
The Power of Genomics in Dairy Cattle
Genetic improvement is inarguably one of the biggest drivers that has built American agriculture and food abundance as we know it today.
Dairy producers were among the earliest adapters and innovators in this regard. And when you have some as far as many breeders have, it can be difficult to continually improve upon what is already the best. One of the biggest shifts that has happened is moving beyond the limitations of more “traditional” breeding practices on pedigree-based selection and waiting on long genetic intervals to review data.
Genomics has changed a lot of that, making informed breeding decisions easier than ever before, but also having some new pitfalls that breed associations and academics are still navigating.
The Power and Pitfalls of Genomically Enhanced Selection
According to the Council on Dairy Cattle Breeding (CDCB), genomic evaluations have accelerated genetic progress in U.S. herds by increasing the accuracy of selection decisions early in life, reducing reliance on parent averages and long generational intervals. This is perhaps one of the biggest changes that genomics brought to the table. And for all its benefits, it has brought with it some debate among producers if this is always best.
This increases selection accuracy and shortens generation intervals, speeding genetic gain for key traits such as milk production and growth potential.
Genomics are also notable for the ability to identify superior genetic potential even for traits that are difficult or expensive to measure on-farm. These metrics include things like feed efficiency or disease resistance when proper reference populations exist. Likewise, early genomic insights can help cull inferior animals sooner. This reduces the ever increasing cost of raising heifers to mature cows and is another way to build up herd quality faster.
Despite these advantages.
There is a vigorous discussion in both dairy and beef sectors about the limitations and temptations of relying too heavily on genomic data alone.
The crux of the issue is that genomic predictions are entirely dependent on the data (see reference population) they are built on. Practical phenotypes, especially for traits that need to be physically observed as proof-of-concept, do have their place in building more reliable genomic evaluations. Some traits that are good examples of this are fertility, hoof health, disease resistance and longevity. To increase accuracy, these need to be incorporated into accurate datasets to train genomic evaluation models. Naturally, these things are tricky to measure and report accurately, as pointed out by Este van Marle-Köster and Carina Visser in their research Unintended consequences of selection for increased production on the health and welfare of livestock.
Some academic work, like the 2024 Journal of Animal Science article Potential negative effects of genomic selection by Ignacy Misztal and Daniela Lourenco, suggests that strong genomic selection for high production traits can inadvertently magnify negative responses in secondary traits, like fertility or fitness, especially if those traits aren’t adequately included in selection indexes.
Genomic predictions tend to be more accurate where large, recorded reference populations exist. In crossbred herds, the reliability of genomic predictions might not be quite up to par with mainstream breeds like Holsteins and Jerseys.
And on the anecdotal side, there is no shortage of producers who make a point that all the genomics in the world can’t predict how a specific animal will perform on any given operation.
Genomics in the Details
Just how far have genomics in dairy cattle taken us?
According to the CDCB report Genomic selection in United States dairy cattle genomic selection programs in the U.S. have doubled the rate of genetic gain in dairy cattle. Since the implementation of genomics, the average annual increase in Net Merit has risen from about $40 per year to approximately $85 per year — a clear, measurable impact of using genomic data to guide breeding decisions. The review also notes that millions of genotypes have been collected, and evaluations now include over 50 traits such as feed efficiency, health traits, and reproductive measures, illustrating the scope and complexity of modern genomic selection efforts.
Production Traits
In a large genomic association study of North American Holsteins from 2021, researchers identified over 6,000 SNPs significantly associated with milk yield and component traits including specific genomic regions linked to milk volume, fat yield, and protein yield. (Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data)
Health Traits
A meta‑analysis combining data from 30,689 cows for clinical mastitis and 119,438 cows for somatic cell score identified 58 lead genomic markers associated with mastitis resistance across six dairy breeds. These variants provide concrete targets for selecting cattle with improved health resistance. (Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance)
Reproductive Traits
A 2024 open‑access genomic study in Holsteins detected more than 2,700 SNPs associated with reproductive traits (including fertility measures) across more than 90 genes, highlighting the complex genetic architecture of reproduction and giving breeders insight into which regions of the genome influence fertility. (Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes)
A2/A2 Milk Production
In a genomic survey of nearly 2,000 Holsteins from organic herds, 46% of cows were A2/A2 genotype, while 43% were A1/A2 and 11% were A1/A1 — quantifying the prevalence of the A2 variant in a real commercial population. Although this study didn’t find direct production differences between genotypes, it provides measurable data on how common the A2 allele is in U.S. Holstein populations. (Relationships of beta-casein genetics with production, fertility, and survival of purebred organic Holstein dairy cows)
Using Genomics in your Herd
In many ways, genomic familiarity in dairy cattle at the bare minimum is becoming the status quo for successful breeders. Even if it is not a primary driver for mating decisions, it is a tool that can be used
Genomics in dairy cattle has transformed dairy breeding from a slow, reactive process into a precise, proactive strategy. By leveraging genomic insights, producers can select animals that enhance production, improve health and optimize reproduction all done years before traditional methods would allow. But that said, there is reason for a healthy dose of caution in its over reliance.
June 2026
By Jaclyn Krymowski for American Dairymen
