Importance of Genomics for Genetic Improvement in Dairy Cows
The greatest improvements in milk production in dairy cows in the past several decades have been due to genetic selection. We have learned more about genetics in recent years. Research has enabled scientists to look at the genome (complete set of genes or genetic material present in a cell or individual animal—all of the DNA for that cell or organism). Genomics is the study of an organism’s complete set of genes (the genome), including how they interact with each other and their environment. This research enables us to harness genetic knowledge we’ve gained, in making genetic selection for the traits and improvements we want in our animals. Francisco Peñagaricano, PhD, Associate Professor, Quantitative Genomics Department of Animal and Dairy Sciences, UW-Madison does research in dairy cattle genomics. His research program focuses on development and application of methods to dissect the genetic basis of relevant traits in dairy cattle. “Our research involves gene mapping, gene-set analysis, genomic prediction, methylome, and transcriptome analysis, multiomics data integration, and network modeling,” he says.
Peñagaricano says that in earlier years the foundation for genetic improvement was performance records and pedigree information. Development and widespread use of national milk recording systems, introduction of artificial insemination, and development of accurate genetic evaluation methods have led to remarkable genetic improvement in dairy cattle populations. The success of these programs was due to close collaboration between dairy farmers, milk recording organizations, dairy records processing centers, breed associations, breeding companies, government agencies, and agricultural universities.
Prediction of genetic values has been through integration and analysis of multiple types of data, including phenotypic records such as milk yield, days open, health events, and more recently, genotypic data. “The most important result of this process, known as genetic evaluation, is the estimate of genetic merit, commonly known in dairy cattle breeding as predicted transmitting ability (PTA). The PTA is an estimate of the relative genetic superiority (or inferiority) a particular animal will pass to its offspring for a given trait. It represents the most important tool for making selection decisions,” according to Peñagaricano. The advent of genomic selection has revolutionized dairy cattle breeding because it allows breeders to make accurate selection decisions at a much earlier age, reducing generation intervals and increasing the rate of genetic progress. Genomic selection also provides a way to improve traits like feed efficiency that were too difficult or expensive to measure in conventional progeny testing schemes.
“In the last six years, 60% of that increase in milk production is due to genetic selection. This is a very powerful tool for achieving lasting gains in dairy cattle performance. Contrary to changes we can achieve with better nutrition, management, or cow comfort, the changes achieved through genetic selection are incremental, cumulative, and permanent. This makes genetic selection a very powerful and cost-effective tool,” says Peñagaricano.
THE MAIN GOAL IS TO INCREASE INCOME – Most dairymen select traits that increase income, such as milk yield and milk composition. In the past, dairy cattle selection programs generally focused on increasing total lactation milk yield, but in many markets, the vast majority of milk is used for making dairy products such as cheese, ice cream, butter, and yogurt, rather than for fluid milk consumption. In these situations, increasing the fat and protein yield is more important than increasing milk volume. “Most breeding programs have increased the fat and protein yield by direct selection for these traits, improving the fat content by approximately 57% and the protein by 66%,” says Peñagaricano. “During recent years there has also been growing interest in milk with specific nutritional value, such as specific protein composition (rich in A2 b-casein) or desirable fatty acid profile (high in unsaturated fatty acids), and improved manufacturing properties (coagulation time and curd firmness). If milk processors start to pay premiums for these traits, then farmers will have economic incentives to select for altered milk composition and manufacturing attributes,” he says. Dairymen can also select for traits that reduce expenses—such as fertility and health. A few years ago, the U.S. dairy industry implemented genetic evaluations in Holsteins for six health traits, including milk fever, retained placenta, metritis, displaced abomasum, ketosis, and clinical mastitis. “These six health traits are considered the most common
and most costly health events impacting U.S. dairy herds,” he says.
USING A SELECTION INDEX – “We now have more than 50 traits under selection. Farmers should not select for just a few traits; if they do, they are making a mistake. We need to consider multiple traits, and this is a challenge, but we have the tools to do it. There are many traits, including production traits (such as milk yield and milk composition) and functional traits (such as fertility, health, longevity, and calving ability), that directly impact the profitability of any dairy farm. It’s easiest to improve multiple economically relevant traits by using a selection index.
“These selection indices perform well regardless of the number of traits selected, and even more importantly allow for selection of animals that are highly superior for one trait and slightly deficient in other traits, which leads to maximization of the selection response. Economic selection indices are updated periodically to include new traits and to reflect price trends. The emphasis on yield traits has declined over time as health and fertility traits, commonly grouped as fitness traits, were introduced. Today economic selection indices include both production and fitness traits,” says Peñagaricano.
GENOTYPING AND GENETIC MARKERS – Genomic selection is the latest revolution and refers to selection decisions based on genomic-estimated breeding values. “These genomic breeding values are calculated using genetic markers across the entire genome. This technology has revolutionized dairy cattle breeding because it allows breeders to make accurate selection decisions at a much earlier age, even when neither the animal nor its offspring have been assessed for the phenotypes of interest,” he says. “Three major developments allowed widespread use of DNA information in dairy cattle breeding: identification of many thousands of single nucleotide polymorphism (SNP) markers spanning the entire bovine genome, development of SNP-chip genotyping technologies that allow the genotyping of thousands of SNP markers in a cost-effective manner, and development of suitable statistical methods where genome-wide SNP effects are estimated simultaneously,” says Peñagaricano.
“Genomics has caused the most change in dairy cattle breeding since the introduction of artificial insemination. Hundreds of thousands of animals have been genotyped worldwide, including nearly every potentially elite young animal, and this genomic information is integrated into national genetic evaluations. Young bulls and potential elite females are typically genotyped using mostly medium-density (roughly 50,000) or even high-density (roughly 700,000) SNP genotyping arrays, while most heifers in commercial farms are genotyped with low-cost, low-density genotyping arrays with roughly 10,000 to 20,000 SNP,” he says.
“The first genomic evaluation for U.S. Holsteins occurred in January 2009. We now have almost 16 years of the use of genomic information in our dairy cattle selection. We have about 8.5 million genotypes of Holsteins in the national database. The genomic testing is a tool that is now routinely used by farmers in this country,” says Peñagaricano. Genomics is very simple. “We estimate the genetic merit of an animal based on its genome. This is revolutionary in dairy where most or all economic traits are observed on the females, and observed late in life (after they are adults and producing milk). Now we can estimate the genetic merit of an animal at birth, and do it accurately—and this has a huge impact.” Instead of having to wait until the animal grows up and begins lactating—to know if she has the genetic merit we want—we can make our selection of heifers at birth.
FASTER PROGRESS BY REDUCING GENERATION INTERVALS – Genetic selection works by identifying and selecting the animals with the highest genetic merit to be the parents of the next generation, resulting in the genetic (and phenotypic) improvement of the population in each generation.
Genomic selection has the potential to increase genetic progress considerably—and quicker–by reducing generation intervals. “At least 4.5 years are required for collecting the semen of a potentially elite bull, rearing his offspring, and finally predicting his genetic merit based on his offspring’s performance. Instead of waiting at least 4.5 years, breeders can use genomic-tested young bulls before 1 year of age. This drastically reduces the generation interval,” says Peñagaricano.
Similarly, genomic testing of heifer calves allows accurate selection decisions at an early age. Superior females can be utilized in invitro fertilization programs even before they reach sexual maturity. By shortening the generation interval and increasing the accuracy and intensity of selection, genomic selection in dairy cattle can at least double the annual genetic gains for economically important traits, even before they reach sexual maturity. The benefit of genomics is greatest for improving lowly heritable traits such as fertility, and traits that can only be measured late in life such as longevity. “Genomic selection in U.S. Holstein cattle has doubled the annual rates of genetic gain for production traits, but the changes have been larger–increased three to four times more–for what we call fitness traits such as female fertility, udder health, and productive life that were earlier very hard to improve,” says Peñagaricano.
FEED EFFICIENCY – Feed represents more than 50% of a dairy’s total production costs. “At the same level of production, cows with reduced feed intake requirements are more profitable. It has been suggested that the U.S. dairy industry could save $540 million per year with no loss in milk production by breeding for cows that are more feed efficient,” says Peñagaricano.
“Our ability to select for feed efficiency, because of genomics, was implemented in December of 2020. Now farmers can select more feed-efficient animals. Basically, we can produce the same amount of milk, with the same cow body weight, but using less feed. In the end, this is less cost and less manure to deal with, and less methane emission, etc.” he says.
AVOIDING GENETIC DEFECTS – “With genomics, we can also control genetic defects. A common problem in dairy breeds is haplotypes that impact reproductive performance. Haplotypes are segments of the DNA that appear frequently in the population, but we never observe any animals that have two copies of that segment. This genetic defect seems to play a major role in pregnancy losses—some in early gestation and some of them later. “Now, however, with genomic testing, we know which animals are carriers. In the cattle population, we only have carriers, with a single copy, and this has no phenotypic impact. But if you mate two carriers there will be a 25% chance of early pregnancy loss or abortion,” he says.
SUMMARY – The advantages of using genomics include the ability to progress faster. “If your animals have better genetic merit, they will have better performance and make more money. They will have better production, reproduction, health, etc.,” says Peñagaricano.
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By Heather Smith Thomas
