Combining EPD Info With DNA Test Results Improves Genetic ...Combining EPD Info With DNA Test Results Improves Genetic Prediction Accuracy Fusing EPD information with DNA test results

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Combining EPD Info With DNA Test Results ImprovesGenetic Prediction AccuracyFusing EPD information with DNA test results to improve prediction accuracy is now areality.

The promise of using DNA information to improve the accuracy of expected progeny differences (EPDs) onyoung animals is starting to be realized, at least for Angus cattle

The promise of using DNA information to improve theaccuracy of expected progeny differences (EPDs) on younganimals is starting to be realized, at least for Angus cattle.

First, there was an agreement between Angus GeneticsInc.® (AGI) and IGENITY® to calculate genomic-enhanced expected progeny differences (GEPDs) formultiple carcass traits using American AngusAssociation® carcass and ultrasound data. Then, in

November 2010, AGI announced an agreement to similarly accept Pfizer AnimalGenetics’ High-Density 50K test results for incorporation into GEPDs.

Genomic-enhanced EPDs are produced using DNA and traditional (performancerecords, pedigree) information sources. The inclusion of DNA information shouldimprove the accuracy of EPDs, especially for young animals with little performancedata. Producers often ask how much a DNA test improves accuracy. The answerdepends on the amount of genetic variation accounted for by the test, and the accuracyof the EPD for that trait in the absence of DNA information.

Figure 1 shows the Beef Improvement Federation (BIF) accuracy of a DNA test thataccounts for 25% of the genetic variation in a trait. If no pedigree, individual or parentrecords exist for that trait, then the BIF accuracy of an EPD based on the DNA dataalone would be 0.13 (red line). If an animal and its parents have records for the trait(blue line), then the BIF accuracy would range between 0.07 and 0.35 depending uponthe heritability (h2) of the trait (see Table 1 for h2 estimates of common traits).

In that situation, the addition of DNA test information would boost the BIF accuracymost (0.11) for the low heritability trait, and least (0.05) for the most highly heritabletrait. In practice, this means that DNA testing is most useful for traits for which no

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HOME > GENETICS > COMBINING EPD INFO WITH DNA TEST RESULTS IMPROVES GENETIC PREDICTION ACCURACY

Feb. 1, 2011Alison Van Eenennaam

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other record exists (e.g., meat tenderness), and/or low heritability traits (e.g., calvingease, fertility).

To incorporate DNA test information into EPDs, it’s necessary to determine the amountof genetic variation associated with the test (25% in the example in Figure 1). Ideallythis value would be high, such that DNA tests results would be very predictive of geneticmerit. Independent estimates of this proportion aren’t available for all breeds and testson the market.

Some estimates are available for Angus cattle (Table 1). The U.S. IGENITY estimateswere developed in the U.S. Angus population, whereas the U.S. Pfizer estimates weredeveloped in company-derived populations, and the Australian estimates weredeveloped in the Australian Angus population. To incorporate Pfizer HD 50K data intothe American Angus EPDs, these estimates will need to be recalculated for the U.S.Angus population.

Beyond Angus

Breeds other than Angus are likewise going to have to derive these genetic variationsassociated with any DNA test. To date, data suggest that tests developed for one breedare unlikely to work very well in another.

Even within Angus, tests trained in North American Angus were associated with lessgenetic variation when used in the Australian/New Zealand Angus population, andrequired regional recalibration for that population and production system. One possiblereason for this is that a portion of the accuracy associated with genetic testing is theresult of linkage – relationships between the animals in the training population (thepopulation used to develop the test) and the test population. Tests are likely to be lessaccurate (explain less of the genetic variation) when used to evaluate more-distantlyrelated animals, such as those in another country where animals may be severalgenerations removed from U.S. genetics.

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The National Beef Cattle Evaluation Consortium (NBCEC) has encouraged discussionabout how to develop DNA tests to improve the accuracies of EPDs for breeds otherthan Angus. One of the requirements in DNA test development is access to a largetraining population of genotyped animals from the target breed or its crosses. Somebreed associations (Hereford, for example) are starting to develop such populations withan eye toward developing breed-specific DNA tests. A similar approach is beingimplemented in Australia where breed associations are establishing referencepopulations to provide training and validation populations for breed-specific DNA testdevelopment.

Bigger panels

It’s becoming increasingly clear that to obtain accurate DNA tests, it’s necessary to trainon large numbers of records. The dairy industry is currently training on records fromtens of thousands of animals including well-proven Holstein sires to obtain theirgenomically enhanced predictive values. Obtaining similarly large numbers of recordsfrom breeds other than Angus poses a challenge for the beef industry.The recent development of a high-density (~700K SNP) bovine marker panels providesa potential solution.

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With the 50K marker panel, as shown in Figure 2, a marker associated with a trait inone breed may not have the same association in another breed. The reason is that themarker is often located a “long way” from the gene and so it’s not found to beassociated in all breeds with the variant of the gene that is causing the effect. Byincreasing the number of SNP markers to 700 K, markers are more closely spaced andthere is a greater likelihood of finding SNPs that are close to the gene (red markers inthe diagram), and hence the marker will “work” in both breeds.

These high-density bovine marker panels provide an opportunity for breeds to poolinformation. Developing large multi-breed training data sets may collectively improvethe accuracy of tests for all breeds, more than any single breed can do on its own due tothe larger number of combined records.

These high-density panels come with increased cost ($200-$300 each), but this pricewill likely drop in the future. Ultimately the availability of high-density arrays mayenable the use of DNA test information to improve EPD accuracy for many breeds ofcattle, including those with a relatively small number of performance-recorded animals.

Although this field is evolving quickly, the ultimate goal for using genomics remains thesame, and that is to cost-effectively improve accuracy of EPD produced in NationalCattle Evaluation (NCE). As outlined by BIF, “information from DNA tests only hasvalue in selection when incorporated with all other available forms of performanceinformation for economically important traits in NCE, and when communicated in theform of an EPD with a corresponding BIF accuracy. For some economically importanttraits, information other than DNA tests may not be available. Selection tools based onthese tests should still be expressed as EPD within the normal parameters of NCE.”

a. Heritability from http://www.angus.org/Nce/Heritabilities.aspx; or literatureestimates.b. MacNeil, M. D., S. L. Northcutt, R. D. Schnabel, D. J. Garrick, B.W. Woodward, andJ. F. Taylor. 2010. Genetic correlations between carcass traits and molecular breedingvalues in Angus cattle. 9th World Cong. Genet. Appl. Livest. Prod. Leipzig, Germany.August 2010.c. Pfizer Animal Genetics. 2010. Technical Summary.http://www.pfizeranimalgenetics.com/sites/PAG/Documents/50K Tech Summary.pdfd. Animal Genetics and Breeding Unit (AGBU). 2010. Evaluation of Pfizer AnimalGenetics HD 50K MVP Calibration. http://agbu.une.edu.au/pdf/Pfizer_50K_September2010.pdf

--Alison Van Eenennaam is a University of California-Davis animal biotechnologyExtension specialist.

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