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HOME > GENETICS > COMBINING EPD INFO WITH DNA TEST RESULTS IMPROVES GENETIC PREDICTION ACCURACY
Combining EPD Info With DNA Test Results Improves
Genetic Prediction Accuracy
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Fusing EPD information with DNA test results to improve prediction accuracy is now a
reality.
Alison Van Eenennaam
Feb. 1, 2011
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The promise of using DNA information to improve the accuracy of expected progeny differences (EPDs) on
young animals is starting to be realized, at least for Angus cattle
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The promise of using DNA information to improve the
accuracy of expected progeny differences (EPDs) on young
animals is starting to be realized, at least for Angus cattle.
First, there was an agreement between Angus Genetics
Inc.® (AGI) and IGENITY® to calculate genomicenhanced expected progeny differences (GEPDs) for
multiple carcass traits using American Angus
Association® carcass and ultrasound data. Then, in
November 2010, AGI announced an agreement to similarly accept Pfizer Animal
Genetics’ High-Density 50K test results for incorporation into GEPDs.
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Genomic-enhanced EPDs are produced using DNA and traditional (performance
records, pedigree) information sources. The inclusion of DNA information should
improve the accuracy of EPDs, especially for young animals with little performance
data. Producers often ask how much a DNA test improves accuracy. The answer
depends on the amount of genetic variation accounted for by the test, and the accuracy
of the EPD for that trait in the absence of DNA information.
Figure 1 shows the Beef Improvement Federation (BIF) accuracy of a DNA test that
accounts for 25% of the genetic variation in a trait. If no pedigree, individual or parent
records exist for that trait, then the BIF accuracy of an EPD based on the DNA data
alone 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 upon
the 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 accuracy
most (0.11) for the low heritability trait, and least (0.05) for the most highly heritable
trait. In practice, this means that DNA testing is most useful for traits for which no
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Combining EPD Info With DNA Test Results Improves Genetic Prediction Accuracy | Genetics content from BEEF Magazine
other record exists (e.g., meat tenderness), and/or low heritability traits (e.g., calving
ease, fertility).
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To incorporate DNA test information into EPDs, it’s necessary to determine the amount
of genetic variation associated with the test (25% in the example in Figure 1). Ideally
this value would be high, such that DNA tests results would be very predictive of genetic
merit. Independent estimates of this proportion aren’t available for all breeds and tests
on the market.
Some estimates are available for Angus cattle (Table 1). The U.S. IGENITY estimates
were developed in the U.S. Angus population, whereas the U.S. Pfizer estimates were
developed in company-derived populations, and the Australian estimates were
developed in the Australian Angus population. To incorporate Pfizer HD 50K data into
the American Angus EPDs, these estimates will need to be recalculated for the U.S.
Angus population.
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Beyond Angus
Breeds other than Angus are likewise going to have to derive these genetic variations
associated with any DNA test. To date, data suggest that tests developed for one breed
are unlikely to work very well in another.
Even within Angus, tests trained in North American Angus were associated with less
genetic variation when used in the Australian/New Zealand Angus population, and
required regional recalibration for that population and production system. One possible
reason for this is that a portion of the accuracy associated with genetic testing is the
result of linkage – relationships between the animals in the training population (the
population used to develop the test) and the test population. Tests are likely to be less
accurate (explain less of the genetic variation) when used to evaluate more-distantly
related animals, such as those in another country where animals may be several
generations removed from U.S. genetics.
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Combining EPD Info With DNA Test Results Improves Genetic Prediction Accuracy | Genetics content from BEEF Magazine
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The National Beef Cattle Evaluation Consortium (NBCEC) has encouraged discussion
about how to develop DNA tests to improve the accuracies of EPDs for breeds other
than Angus. One of the requirements in DNA test development is access to a large
training population of genotyped animals from the target breed or its crosses. Some
breed associations (Hereford, for example) are starting to develop such populations with
an eye toward developing breed-specific DNA tests. A similar approach is being
implemented in Australia where breed associations are establishing reference
populations to provide training and validation populations for breed-specific DNA test
development.
Bigger panels
It’s becoming increasingly clear that to obtain accurate DNA tests, it’s necessary to train
on large numbers of records. The dairy industry is currently training on records from
tens of thousands of animals including well-proven Holstein sires to obtain their
genomically enhanced predictive values. Obtaining similarly large numbers of records
from breeds other than Angus poses a challenge for the beef industry.
The recent development of a high-density (~700K SNP) bovine marker panels provides
a potential solution.
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Combining EPD Info With DNA Test Results Improves Genetic Prediction Accuracy | Genetics content from BEEF Magazine
With the 50K marker panel, as shown in Figure 2, a marker associated with a trait in
one breed may not have the same association in another breed. The reason is that the
marker is often located a “long way” from the gene and so it’s not found to be
associated in all breeds with the variant of the gene that is causing the effect. By
increasing the number of SNP markers to 700 K, markers are more closely spaced and
there is a greater likelihood of finding SNPs that are close to the gene (red markers in
the diagram), and hence the marker will “work” in both breeds.
These high-density bovine marker panels provide an opportunity for breeds to pool
information. Developing large multi-breed training data sets may collectively improve
the accuracy of tests for all breeds, more than any single breed can do on its own due to
the larger number of combined records.
These high-density panels come with increased cost ($200-$300 each), but this price
will likely drop in the future. Ultimately the availability of high-density arrays may
enable the use of DNA test information to improve EPD accuracy for many breeds of
cattle, including those with a relatively small number of performance-recorded animals.
Although this field is evolving quickly, the ultimate goal for using genomics remains the
same, and that is to cost-effectively improve accuracy of EPD produced in National
Cattle Evaluation (NCE). As outlined by BIF, “information from DNA tests only has
value in selection when incorporated with all other available forms of performance
information for economically important traits in NCE, and when communicated in the
form of an EPD with a corresponding BIF accuracy. For some economically important
traits, information other than DNA tests may not be available. Selection tools based on
these tests should still be expressed as EPD within the normal parameters of NCE.”
a. Heritability from http://www.angus.org/Nce/Heritabilities.aspx; or literature
estimates.
b. MacNeil, M. D., S. L. Northcutt, R. D. Schnabel, D. J. Garrick, B.W. Woodward, and
J. F. Taylor. 2010. Genetic correlations between carcass traits and molecular breeding
values 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.pdf
d. Animal Genetics and Breeding Unit (AGBU). 2010. Evaluation of Pfizer Animal
Genetics HD 50K MVP Calibration. http://agbu.une.edu.au/pdf/Pfizer_50K_September
2010.pdf
--Alison Van Eenennaam is a University of California-Davis animal biotechnology
Extension specialist.
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Combining EPD Info With DNA Test Results Improves Genetic Prediction Accuracy | Genetics content from BEEF Magazine
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