Importance of Genetic Selection in Dairy
Importance of Genetic Selection in Dairy Cattle
Genetic selection and genomic testing in dairy cattle has greatly improved the milk production in cows, along with improved health, fertility, calving ease and other important traits. Genomics involves collecting DNA samples from animals to identify desirable traits and predict the animals’ genetic potential, which can help producers improve herd health, milk production, etc. Genomic information is utilized to make more effective breeding decisions (with predictable results), accelerate genetic progress and contribute to more sustainable and profitable dairy operations.
Scott E. Poock, DVM, DABVP (Dairy), Extension Professor, University of Missouri, says the data bank for dairy cattle is so large that genetic progress can be made very quickly. “We’ve made tremendous progress in a variety of areas, not only in calving ease but also in traits like milk production, increases in fats and proteins. I was recently looking at a herd that I worked with in Wisconsin. They are now routinely at 100 pounds of milk, 4.6 fat and 3.3 protein on Holstein cows,” he says. This is much better than it was a few years ago.
An article entitled “Genomic selection in United States dairy cattle” published in 2022, stated that the genomic selection program for dairy cattle in the U.S. has doubled the rate of genetic gain. Since 2010, the average annual increase in net merit has been $85 compared to $40 during the previous 5 years. The number of genotypes has been rapidly increasing both here and in other countries, reaching more than 6.5 million in 2022 with 1,134,593 submitted in 2021. Evaluations are calculated for over 50 traits.
Feed efficiency (residual feed intake), heifer and cow livability, age at first calving, six health traits, and gestation length have been added in recent years to show the economic value of the animals more accurately. Additional work is currently developing evaluations for hoof health. Evaluations of animals with newly submitted genotypes are calculated weekly.
In April 2019, evaluations were extended to include crossbreds. For these animals, evaluations are initially calculated on an all-breed base and then blended by the estimated breed composition of those animals. For individuals that are less than 90% of one breed, the evaluation is calculated by weighting the contributions of each of the major dairy breeds evaluated (Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey) by breed proportion in that animal.
Nearly 200,000 animals received blended evaluations in July 2022. Pedigree information can be augmented by using haplotype matching to discover maternal grandsires and great-grandsires. A haplotype is a group of genes inherited together from a single parent.
Haplotype analysis is also used to discover undesirable recessive conditions that we want to avoid. In many cases, the causative variant has been identified, and the results from a gene test (or inclusion on a genotyping chip) improves the accuracy of those determinations for the current 27 genetic conditions that have been reported. Recently discovered recessive conditions include neuropathy with splayed forelimbs in Jerseys, early embryonic death in Holsteins, and curly calves in Ayrshires.
The success of the Council on Dairy Cattle Breeding (CDCB) in conducting the genetic evaluation program is the result of cooperation with industry and research groups, including the USDA, breed associations, genotyping laboratories, and AI organizations.
The first official genomic evaluations were released in January 2009 for Holsteins and Jerseys. In 2008 and 2009, more genotypes for bulls were received than for cows, but in later years, the number of bull genotypes received has remained fairly constant while the number of genotypes of females received has increased rapidly. Many dairy producers now genotype all their heifers so they can select their replacements using a range of breeding and management strategies.
Genomic evaluations were rapidly accepted by the dairy industry, using these as the basis for selecting the sires for their herds. In just a few years, most mating decisions were using only genomic evaluation as selection criteria. Bulls are used widely as sires based on analysis of their DNA, even before they have produced any milking daughters.
“The generation turnover has decreased a lot (the time it takes to have reliable data for the next generation),” says Poock. Generation interval is the average age of parents when offspring are born and can impact genetic improvement. The shorter the generation interval, the faster that progress can be made
“It used to be 5 years before you really knew what the offspring of a bull could do and now it’s down to less than 2 years. Not very long ago if you had a good bull and wanted to know his genetic merit he would be 5 years old before he’d have his first reliable sire summary. He had to be at least a year old before you could collect him to breed cows, then by the time he was a 2-year-old you’d have calves on the ground, and as a 3-year-old his daughters were being bred, and when he’s 4, they’d be having calves, and when he’s 5, those daughters have gone through a lactation,” he says.
Today, once a herd has its genomic evaluation, you can make decisions whether to keep a bull or not. “Years ago, people didn’t really start collecting a bull very much until they had that data back, but now they just keep collecting him, once they start, if they think he’s a good one,” says Poock. Today, by the time he is 5, a bull might have sons siring calves, and shortly after he might have grandsons providing semen.
“Now we also have health traits to select for. Just like the beef industry, today the dairy industry has indexes for evaluating net merit, dairy wellness, profit, etc. putting traits together to get an index to evaluate a bull. You can evaluate things like diseases, mastitis, lameness, etc. Before these bulls even produce daughters, you already have an idea about what those daughters will be like,” says Poock.
Improvement in health in dairy animals, improvement in production in terms of components (fat, protein), calving ease, reduction in stillbirths, etc. has made huge strides. “At our university dairy we participate in Select Sire’s program called NxGEN. We can use the best young bulls they have on hand, before they go out for general use.”
There is a wealth of data available today. Years ago people mainly just looked at milk, and maybe cow type. Today we keep adding more traits to evaluate.
Production traits include milk yield, fat yield and percentage, and protein yield and percentage. Milking speed has been collected through the Brown Swiss program and is only evaluated for that breed. Eighteen conformation traits are included for non-Holstein breeds; Holstein conformation evaluations are calculated by the Holstein Association USA.
Longevity traits include productive life, cow livability, and heifer livability (birth to first calving, added in 2020). Fertility traits include daughter pregnancy rate, cow conception rate, calving to first insemination, gestation length, and early first calving (added in 2019); male fertility is evaluated phenotypically as service-sire relative conception rate. The calving traits of dystocia (calving ease) and stillbirth rate are combined into a calving ability index.
In addition to traditional evaluations for somatic cell score as a measure of mastitis resistance, evaluations for other health traits were introduced in 2018: displaced abomasum, ketosis, mastitis, metritis, milk fever (hypocalcemia), and retained placenta. In 2020, the trait of feed saved was added as a measure of genetic merit for feed efficiency; it combines evaluations of body weight composite and residual feed intake. Most traits make a direct contribution to economic value. Gestation length is not included in the economic indexes but it is correlated with calving traits and may be useful in pasture-based systems to assist in determining calving dates.
Lifetime genetic-economic indices are provided to the dairy industry for net merit, fluid merit, cheese merit, and grazing merit. Those indices rank the animals based on their combined genetic merit for economically important traits. Multiple indexes can support selection in a wide range of management and milk payment schemes. The indices are updated periodically to include new traits and are changed to reflect the prices expected in the next few years.
The CDCB provides information on the genomic relationships between potential dams and currently marketed bulls–the actual portion of genetic variants (alleles) in common, in contrast to simple pedigree analysis, which can only give an average based on relationships. This can help dairymen avoid inbreeding.
In any breed—whether in cattle, horses, dogs, sheep—inbreeding occurs, and it’s more likely to occur in a smaller gene pool. “If you can find something that’s more of an outcross, it is better. In dairy we don’t have nearly as many crossbreds as in the beef world. Only 4 or 5% of dairy cattle in the U.S. are crossbred. This number has grown and is continuing to grow, but crossbreds are still the minority,” says Poock.
The CDCB also provides predictions for many recessive conditions; carrier-to-carrier matings can be avoided even without testing an animal. The haplotypes that affect fertility were discovered through genomics and can now be considered. Future mating programs may also consider the effects of dominance, which causes some sire-maternal grandsire-grandsire combinations to do better than expected and others to do worse.
In years past, for traditional genetic evaluations, an animal could only receive an evaluation for a trait observed for the animal or its offspring. Evaluation were limited to traits where large-scale collection of data was possible, with milk, fat yield and type traits collected by breed associations. With genomics, evaluations can be generated for all genotyped animals if enough animals have genotypes and traditional evaluations for the trait (the reference population) to give reasonably accurate estimates.
Feed efficiency is an example of a small population of animals with feed intake measured providing the basis for feed saved evaluations for all genotyped animals. Efforts to collect data for more traits are ongoing. Foot health and milking speed are currently in the research phase. Mid-infrared spectroscopy of milk samples is expected to provide data related to traits of economic importance.
Advances in Holstein Milk Production and Fertility
Holsteins still make up the majority of dairy cows in the U.S. although Jerseys have made a big increase in numbers the past decade and are now up to about 14% of the nation’s cow herd. They have always been known for high butterfat and protein content but now the Holsteins have improved in those traits.
“Holsteins, with their numbers and huge genetic base—and how much data they have—are increasing in milk components swiftly,” says Poock. “Today it is phenomenal what the Holstein cow will do. She can make 100 pounds per day at 4.5% fat and 3.4% protein and stay healthy and get pregnant. This makes it harder for Jerseys to compete.”
He recently looked at the Centralstar Cooperative’s top herd list that covers a lot of the Mid-West (Michigan, Indiana, Illinois, Iowa, Wisconsin, etc.) “They had 147 herds listed, and in the top herds the lowest production energy-corrected milk was 103 pound of milk per cow. The highest was 132. Who would have imagined this much milk, 25 years ago? Holsteins’ improvement in fertility is also phenomenal. One of the herds I work with has broken their animals down into quartiles. The difference in first service conception rate was 23% between the top and bottom quartiles. Thus the highest genomic animals, compared to the lowest 25% had a conception rate 23% higher, on average,” he says.
“That’s huge! Looking at days open, the difference between the top 25% and the bottom 25% was also huge. The bottom 25% had 25 more days open than the most fertile cows. Those top cows are breeding back quickly.”
People have always felt that fertility in cattle is not highly heritable, yet this kind of progress has been complete with genetic selection. We can make a big difference when evaluating these genetics and making selections accordingly. The top cows today are producing more milk, yet they are fertile, healthy and staying in the herd longer.
“Who would have imagined this possibility, 25 years ago? We would have said, ‘With that much milk, there’s no way we are going to get them pregnant!’ We have a cow here at the University’s Foremost Dairy that I call Queenie. Through her first 3 lactations she averaged 112 pound of milk a day, and has settled to first service every time. She’s had no health problems except for one day in her third lactation when treatment was given for upset stomach. Otherwise, no problems. Most of the time, no one at the dairy knows who she is, because she doesn’t bring any attention to herself.” says Poock.
No one notices her because there are never any problems. “She’s good in the parlor, she milks out quickly, and never gives any reason for concern. That’s the kind of cow you want! We have two daughters from her, and they are both milking. Last year she had a bull. This year she’s going to calve soon, and her oldest daughter will, too; they were both bred the same day. Unfortunately, Queenie is going to have a bull but her daughter will have a heifer, sired by a polled bull. I probably should use sexed semen on Queenie just to make sure we get more heifers,” he says.
“Improvements in the dairy industry that we’ve made are phenomenal in genetics, forage management, cow health and comfort. American farmers and ranchers are doing a tremendous job. If you set a challenge before them, they will tackle it, and exceed it. My respect for the American farmer and rancher is very high. My career, working with them, had been a great pleasure—to see how they meet a challenge and go above and beyond it. This has been a joy, and I hope it continues.”
Sidebar: Genetic Improvement in Fertility
An article published March 14, 2024 in Clinical Theriogenology, entitled “Genomic selection in dairy cattle: impact and contribution to the improvement of bovine fertility,” stated that genomic selection has revolutionized dairy breeding, with ripple effects that have greatly impacted dairy herd management.
Genomic testing of young bulls and heifers provides greater accuracy of selection decisions involving traditional fertility traits such as daughter pregnancy rate, and has created opportunity to improve additional traits, such as fetal loss. Cameras, wearable sensors, and other precision technologies have allowed selection for traits such as estrus duration and intensity.
Female fertility, measured by a bull’s daughter pregnancy rate (a function of days open), declined each year, from 1975 to 2000. This downward trend in female fertility then slowed and began to reverse after genomic selection became available in 2009, indicating that genomic selection can aid improvement in female fertility and augment the gains achieved through improved reproductive management practices.
Fifteen years before the advent of genomic selection, dairy cattle breeders realized that selection higher production traits such as milk, fat, and protein yields was not the best way to improve profitability. Genetic evaluations of physical conformation, such as udder and foot and leg structure, had been available for decades, but no direct measures of fitness or soundness were part of breeding goals until 1994. That year, national genetic evaluations for somatic cell score and length of productive life were provided to dairy farmers. This enabled indirect selection for improved reproductive performance through favorable genetic correlations with traits such as conception rate and days open.
A direct measure of female fertility–daughter pregnancy rate–was added to the breeding goal in 2003, along with calving ability that included direct and maternal aspects of calving ease and stillbirth rate. Two more direct measures of female fertility, cow conception rate and heifer conception rate, were added to breeding objectives in 2014. Several other countries, particularly in Scandinavia, already had national veterinary recording systems, implementing national genetic improvement programs for traits such as fertility, calving ability, and mastitis resistance.
Data from research farms has been combined with genomic testing information, allowing implementation of national genomic evaluations for new traits that can’t be readily measured on commercial farms. Enlisting research farms or contract herds has helped in measuring specific aspects of female fertility.
At first, genomic testing was only for potentially elite animals that were expected to be superior based on pedigrees, performance, or progeny. AI companies tested their current and prospective bulls, as well as most current and prospective donor dams, but the impact of genomics on commercial dairy farms limits indirect gains. In turn raising the merit of bulls inside their semen tanks. That changed between 2015 and 2020, when farmers began using semen from beef bulls to breed cows that were genetically too inferior to be of use as dams of the next generation of replacement heifers. This allowed more mature cows to stay in the herd for additional lactations if they were still producing milk at a high level, as well as creating crossbred calves that were worth more when entering the beef supply chain, especially from Jerseys.
Selection for improved female fertility using national genetic evaluations for daughter pregnancy rate, heifer conception rate, and cow conception rate has slowed the decline in reproductive performance observed in previous decades. Many commercial dairy farms today are achieving levels of reproductive success that would have been unimaginable 20 years ago, using a combination of genetics and management such as heat synchronization and timed AI).
One aspect of female fertility that has eluded direct genetic selection is pregnancy loss. Pregnancy losses during the first 42 days referred to as embryonic loss, whereas losses after 42 days are known as fetal loss. Rates of embryonic loss are typically higher, around 25 to 40%, than rates of fetal loss that usually range from 8 to 14%. However, fetal losses have a greater economic impact because they occur later in pregnancy. This is a heritable trait that could be a consideration during selection programs. There may be some potential for improvement through genetic selection.
Opportunities may also exist to select for estrous behavior, duration, or intensity, which could improve insemination and conception rates. High-producing dairy cows tend to have shorter estrus than low-producing cows or yearlings. In one study, cows producing 102 pounds of milk per day had estrus of shorter duration (about 6.2 hours) than cows producing 74 pounds of milk per day (10.9 hours), with fewer standing events (6.3 versus 8.8). High-producing cows also had lower intensity of estrus, as measured by number of standing events per hour. Estruses that are short in duration or low in intensity make visual heat detection challenging, and can lead to missed estrus events when using pedometers or accelerometers for automated estrus detection. This can lead to greater reliance on hormonal synchronization and timed AI programs.
With all the data accumulating regarding estrus, there is possibility of enhancing the duration and intensity of estrus through genetic selection that could lead to less reliance on hormonal synchronization programs. Female fertility traits have been under study by the research group at the University of Wisconsin-Madison and others. Some are looking at different traits that may also be candidates for improvement through genomic selection.
Sidebar: Selecting for Polled Animals
“I don’t think the dairy industry will move as quickly to polled animals as the beef industry did,” says Poock. “There are a few polled bulls available but most of them are heterozygous, and you’d still have to do some dehorning.” It will take longer to have very many polled animals to choose from because there are more important traits for dairy cattle, and the gene pool for polled is still small.
“We don’t have a dairy breed that is homozygous polled, that would only sire polled offspring even when bred to other breeds. There are a few polled dairy cattle, however, and genomics has helped us select for that trait.” We can maybe find polled bulls that are better (in other traits) than what their pedigree indicates and breed them to progeny of the top horned bulls and gradually come up with some good polled animals.
“At our University dairy, we’ve used some polled bulls and we have some polled cows, but it’s hard to develop a very large group. It’s a bit like the red and white Holsteins (red being recessive), because the genetic base is so narrow,” says Poock.
By Heather Smith Thomas
January 2026
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