Get ready for the new and improved “black box,” as genomic selection is upon us!

Genetic evaluations (i.e., predicted transmitting abilities or PTAs) for sires and cows will soon be enhanced by direct information from DNA. The addition of this DNA information in the calculation of PTAs will have an important impact on breeding programs and will influence decision making at the dairy farm level, so producers need to be ready for these upcoming changes. Official USDA Predicted Transmitting Abilities that contain genomic information may be available in the U.S. as early as January 2009.

Genetic programs in dairy cattle have been extremely successful at improving the productivity of our dairy cattle populations over the last 50 years. Our traditional approach of using selective breeding (based on sophisticated quantitative selection principles) has been very successful, even though we do not know the exact genes that have increased or decreased in frequency in our populations. We often describe our approach as a “black box” approach, since we do not know exactly what genes have been affected. The use of very effective progeny testing programs and the heavy use of well-proven, elite bulls has indeed been very successful. Several advances have improved the basic approach (e.g., the adoption of contemporary comparisons and later the adoption of the animal model for calculating genetic evaluations), but most of these advances have resulted in incremental improvements in the process. In recent decades, dairy producers and geneticists have recognized the importance of breeding for improved health, reproduction and longevity, so health traits, reproduction and productive life have become a larger part of selection in dairy cattle. The new and improved “black box” approach that we call “genomic selection” signals a new era in genetic improvement and will allow us to do a faster job of improving productivity as well as health, reproduction and longevity.

Genomic selection sounds scary to some of us but the reality is that genomic selection actually just extends our current approach to selection. We are not “ditching” tested and proven basic methods used for genetic improvement. Instead we are just enhancing these proven methods by using more information to calculate PTAs. Genomic selection does not eliminate the need to have good data on important families and individuals within our populations. Good, complete data (including data on health, reproduction, production and all other important traits) are still essential for improving our dairy cattle in the future, so do not discount the value of your data collected on your farm for future improvement.

So how does genomic selection work? Why is genomic selection now possible? Genomic selection is selection based on actual DNA sequences where the variation in DNA sequences among individuals is used, along with pedigree and individual performance data, to predict the PTAs of individuals with increased reliability. Improved technology now allows for relatively inexpensive DNA screening of individuals for thousands of locations along the 30 pairs of chromosomes.

The USDA and a small group of universities in cooperation with a major technology company (Illumina Inc.) have developed a very efficient “chip” that is used to identify specific patterns of DNA at over 50,000 locations along the cattle chromosomes. Variability at these locations across the chromosomes is identified (flagged or marked) by single nucleotide (nucleotides are bases that make up DNA) changes at the locations. (There are a total of about 3 billion pairs of these nucleotides in DNA of cattle.) The specific nucleotides that are present at these locations (which are called single nucleotide polymorphisms or SNPs – pronounced “snips” in conversation) can be used to predict how good the genes are that an animal possess. These locations represent important segments of the chromosomes where the actual genes reside. Cattle have 30 pairs of chromosomes and these 50,000 locations are located on all the chromosomes and provide enough coverage to distinguish important differences among animals.

Currently, in Holsteins, almost 40,000 of these locations are valuable for estimating PTAs for animals. You can think of all these locations as having specific genetic values associated with the specific nucleotides that reside at these locations. In the calculation of PTAs, these values for the nucleotides are essentially summed, and this information is then combined with the pedigree and performance information to arrive at PTAs that are considerably more reliable than the PTAs without the genomic information for most animals. These PTAs that include genomic information are much more reliable, especially for young animals that traditionally would have only had pedigree information.

Estimation of the values for each of the nucleotides at each location is beyond the scope of this article, but it should be noted that modern computing capacity along with some ingenious approaches to data analysis have been critical to the development of genomic selection. One of the most important advances of genomic selection is that it will probably make the value of current genetic markers or quantitative trait loci (or QTLs) obsolete. Genomic selection will solve the problem of using a limited number of QTLs whose effects were difficult to estimate. With genomic selection, all the nucleotide effects are estimated simultaneously, which overcomes a major problem associated with QTLs. We should have much more confidence in genomic selection, compared with the use of only a few QTLs.

1. What will genomic selection do for our populations?
If the industry readily accepts genomic selection and we properly apply genomic selection, then we can expect to see faster rates of genetic progress for all the important traits in dairy cattle. We expect that annual genetic trend in most important traits will increase by at least 30 percent and maybe as much as 50 percent. The actual increase will depend on the industry uptake of the new information and the actual average increase in reliability for the primary animals used for selection decisions.

Currently, as an example, the genetic trend for milk yield is almost 200 pounds per year. This means that the average heifer born this year is expected to produce approximately 200 pounds more per lactation than the average heifer born last year, just due to improved genetics. With genomic selection, we expect annual rates of genetic improvement to increase, perhaps to more than 300 pounds per year. For traits like daughter pregnancy rate and productive life, the expected improvement in genetics may be relatively more substantial. More dramatic improvement in productive life and daughter pregnancy rate is likely because genomic selection substantially increases reliability for young animals, so we will not be required to wait as long for daughter information on productive life and daughter pregnancy rate to have PTAs with acceptable accuracies. With the proper emphasis and the use of genomic selection, daughter pregnancy rate will actually improve and this will reverse an undesirable trend seen during the last three decades. The bottom line is that we will be able to have more reliable proofs at a very early age and can use these younger animals, especially younger bulls, in our breeding programs.

2. What about the costs of genomic selection?
The DNA testing for each animal for genomic selection is approximately $250, which adds to a large sum if we were to do the entire cattle population. However, DNA testing will not be done on all animals in the population. The DNA testing will be done on prospective young bulls and on heifers and cows that are likely to be important contributors of bulls and heifers for breeding programs. This still involves a large number of animals because not all the animals DNA tested will be used for breeding. As a specific example, we will likely DNA test many young bulls and eliminate most of them from breeding based on DNA results, much like we do currently with progeny tests. Fortunately, DNA testing only needs to be done one time on each animal. (DNA does not change.) As far as cost savings for genetic improvement, significant savings in the cost of progeny testing programs may result from genomic selection because the number of bulls that go through formal progeny test programs may be reduced. Of course, all the young bulls that were selected with PTAs based on pedigree information and genomic information will eventually get PTAs with offspring information just like they would if they had gone through a progeny test program. At this point, it is too early to know exactly how progeny testing programs costs will change or adapt to the new opportunities that are provided by genomic selection.

3. Will there be any changes in the policies or decisions on the use of A.I. bulls within our herds and at the breeding company level?
Yes, the breeding industry and the herd owners and managers will need to change their thinking on how to use bulls with PTAs that include genomic information. Very young bulls (at approximately 1 to 3 years old) will likely become a much larger share of the A.I. bulls used in our herds. As indicated earlier, reliabilities for PTAs for these yearling bulls will be considerably higher than reliabilities with just pedigree information (current situation). The increase in reliability will be substantial but will vary from one trait to another. At this point, reliabilities for PTAs on yearling bulls with genomic information will not get to the level of reliabilities for well-proven bulls, but the reliabilities for yearling bulls will be high enough to justify widespread use of these yearling bulls without waiting for PTAs that include progeny information. It looks like reliabilities for these yearling bulls with genomic information will average about 70 percent across all traits with genetic evaluations calculated by the USDA. This is considerably higher than the average current reliabilities of yearling bulls across these same traits (essentially double current reliabilities, which are about 35 percent). Reliabilities of yearling bulls with genomic information will likely be about 75 percent for production traits and 60 to 70 percent for traits like somatic cell score, daughter pregnancy rate and productive life. As you can see, these reliabilities are slightly lower than the reliabilities of proven bulls with their first-crop progeny. (Reliabilities for progeny tested bulls with first-crop progeny are in the 70 to 85 percent range, depending on the trait.) We expect that breeding companies will likely still offer well-proven progeny tested bulls but that breeding companies will shift much of their emphasis to supplying semen from yearling, 2-year-old and 3-year-old bulls for major use within herds. These yearling bulls will have moderately reliable PTAs, which will be based on pedigree information and on genomic information. Ultimately, we expect to see a major shift in the age of the A.I. bulls used in our herds to where much, if not most, of the semen used in herds will be from bulls that are less than 3 years old.

We can expect producers to change their strategy at different rates with some producers adopting the use of these moderate reliability young bulls (with PTAs based on pedigree and genomic information) for their entire herd to a more limited use of these moderate reliability young bulls with PTAs based on pedigree and genomic information and a continuation of the use of well-proven bulls in some herds. There will be slightly more risk for the PTAs of these moderate reliability young bulls with PTAs based on pedigree and genomic information to change compared with the PTAs of well-proven bulls, but the increased level of risk can be easily managed by using a group of these young bulls. (We should probably avoid just using semen from one or two bulls.) Over time we expect that the industry confidence in these young bulls will grow because all these young bulls will eventually have PTAs with daughter information. As we see more proof that the PTAs for these young bulls are much more reliable than PTAs with just pedigree information, producer and industry acceptance is likely to grow.

Reliabilities for PTAs on young heifers and cows will also increase substantially. These much higher reliabilities on females will boost genetic progress considerably because we will be able to more accurately identify the genetically elite females to use for young bull production. Breeder herds involved in intense embryo transfer programs to try to produce elite females and elite bulls for A.I. companies will have much more accurate information to use in decision-making. Higher reliability PTAs on females for traits like productive life, daughter calving ease and daughter pregnancy rate will especially be noticeable. Currently, accurate selection in females for traits with low heritabilities and traits that take considerable time to measure like productive life and daughter pregnancy rate is not possible. However, the incorporation of genomic information into PTAs (or parent averages) for heifers and cows will substantially increase reliabilities for these traits in cows. This should lead to effective selection of females for these lowly heritable traits and provide breeders with much more accurate PTAs for use within their herds.

4. What about any other concerns with the use of these young bulls with PTAs based on pedigree information and genomic information?
The largest somewhat unknown consequence of genomic selection is the impact that genomic selection will have on inbreeding. It is possible that genomic selection could hasten inbreeding; however, genomic selection may also allow us to better handle inbreeding concerns by allowing us to choose more animals with outcross pedigrees. For sure, producers will need to have to plan to manage inbreeding within their herds. Herd mating programs that limit inbreeding may become more important to producers. In addition, the development of strategic line mating programs or the use of crossbreeding may increase to help avoid inbreeding at the farm level. Of course, inbreeding levels will be closely monitored as we adopt genomic selection, and actions to mitigate increased inbreeding will be implemented at the breeding company level, if needed. The bottom line is that producers should be aware of the current potential for inbreeding in their herds and the possibility that this could be a more important issue in the future.

You will hear more and more about genomic selection in the near future, but be assured that genomic selection is not something that should startle you. Genomic selection is just a new tool to help the dairy industry breed better cattle in a shorter time period. Genomic selection is not a replacement for our current procedures and programs, but it will enhance our current programs by providing more reliable PTAs for young animals (especially bulls). This will lead to more use of younger A.I. bulls with moderately reliable PTAs and increase genetic progress for production traits as well as for health traits, reproductive traits and longevity. PD

References omitted but are available upon request at editor@progressivedairy.com

Dr. Gary W. Rogers
Professor of Animal Science
grogers2@tennessee.edu

Gary W. Rogers, Curt P. Van Tassell, Paul M. Van Raden and George R. Wiggans for Progressive Dairyman