The Angus Journal is a monthly magazine known for in-depth coverage of American Angus Association programs and services; the Angus business; herd management techniques; and advertising reflecting genetics herd philosophies.
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January 2015 n ANGUSJournal n 137 Calculating a GE-EPD "There's a two-step process whereby the equations are built for genomically enhanced EPDs," Moser said. The frst is the process of building molecular breeding values (MBVs) using archived test results and Association data. The second is incorporating those MBVs into the EPD calculations. "Along all 30 pair of chromosomes in cattle, there are some places where they are exactly the same. Every living, breathing beef animal — or dairy animal — has an 'A' in this spot. There's no variation there," Moser said, referring to a nucleotide, one of the building blocks of an animal's genetic code. "There are a lot of spots — many, many spots — where there is variation." DNA testing using today's high-density genomic tests look for those places in the chromosome where one animal has an "A" and one animal has a "T," Moser explained. "That's a SNP (pronounced snip); that's a single-nucleotide polymorphism, and they exist all over the chromosome. The chips (used in DNA typing) that we work with test for 50,000 or more different SNPs, or points of variation." For cattle that have been tested, we have information on what they have at each of those spots, said Moser. "We also have the data that you folks have submitted — generations of weights and measures, carcass characteristics, docility scores." Actual measurements are more important than they've ever been, noted Moser, "because not only are they being used directly in the EPD equation, but they are also driving the genomic part. We build the genomic equations based on your good data." The SNPs are evaluated for whether they affect traits. When looking at a particular trait, many of the SNPs won't seem to matter, Moser admitted, "but many of them do. They have a signifcant, statistical association with the higher or lower level of that trait. Those are the SNPs that are identifed and tracked." So, for any given trait, whether calving ease or docility, SNPs are selected that are associated with that trait, he said. SNPs selected are not the same for every trait. Some of them don't matter for any trait. Some may infuence several traits. Each one has more or less its own EPD for having an "A" vs. a "T" at that spot. What does that mean to weaning weight? What does that mean to docility? An animal's MBV, the DNA only, is just adding all those up for every trait. In the second step of calculating a GE- EPD, the MBVs are incorporated into the EPD equation like a correlated trait. The molecular value is correlated to actual measurements, such as weaning weights. How well they correlate is an indication of how well the DNA is describing genetic merit. The higher the correlation, the better the DNA test is at describing variation among animals, Moser explained. So, as the correlation gets higher, its impact in the EPD calculation increases. Fig. 3 refects how far the Association has come since unveiling the frst GE-EPDs in 2010. Moser explained that in each recalibration, such as the one released in September, the Association trains the DNA analysis to the current population by recalculating the MBVs using animals in the data set that have both DNA samples and actual data. The original GE-EPDs released in 2010 were built upon a training population of only 2,200 animals, said Moser. The recalibration in September was based on 57,550 animals, increasing almost 20,000 animals in one year. Other breeds are back where Angus started, he added. "There's certainly a healthy advantage due to the effort you folks have made submitting that data." The larger test population provides stronger correlations, explaining a greater share of the genetic variation (see Fig. 4). "Even for a trait like marbling that worked really well in the beginning, you can see the increase each time the recalibrations have occurred; the relationships got stronger," Moser said. "With more data and more samples, we're able to do a better and better job of characterizing the cattle with DNA tests." Moser pointed out that none of the lines in Fig. 4 reach 100%. "That's a message I want you all to take home," he emphasized. "This is a useful tool, just like having the actual measurement on the animal is useful, having the pedigree is useful, but no one item by itself gives us the whole story. We really gain from combining those various sources of information together to get the best picture of the animal." Editor's Note: Moser spoke at the breed improvement workshop at the Angus Means Business National Convention & Trade Show. To listen to his presentation, access his PowerPoint or read summaries of other presentations at the convention, visit the newsroom at www.angusconvention.com. Fig. 3: Increase in data over the four calibrations Fig. 4: Percent genetic variation explained with a common data set with marker effects from different calibrations 70,000 60,000 50,000 40,000 30,000 20,000 10,000 0 80 70 60 50 40 30 20 10 0 2,253 57,550 38,988 BIRTH MILK WW YW CED CEM CWT RIB FAT FAT MARB SC YHT DOCILITY FI MHT MWT HP 11,756 Y_2010 Y_2012 Y_2013 Y_2014 (Calibration 1) (Calibration 2) (Calibration 3) (Calibration 4) No. of head tested EPD %GV_2010 %GV_2012 %GV_2013 %GV_2014 35 Keys to Success Seedstock & Genetic Selection Source: Prashanth Boddhireddy, Zoetis.