Genomic EPD’s, The next step in using technology to improve livestock

Genomics have been used in the livestock industry to determine parentage for years, but today Merial-Igenity and Pfizer Animal Genetics both offer DNA tests that measure an animal’s genotype for any number of economically viable traits.
“We have a big challenge in the next 50 years. With the global increase in population, we’ll need to produce 100 percent more food, and we have to do so with 70 percent of that coming from enhancing technologies. After all, they’re not making any more land, and lots of land is getting gobbled up and used for other purposes. We’ll have to be all the better at managing our animals’ health, reproduction, performance and nutrition, and at building animals with the appropriate genetic potentials to squeeze more efficiency out of our livestock production system,” says Kent Anderson of Pfizer.    
“Today we still use visual appraisal and common sense when it comes time to selecting animals, and that will be as important in the future as it is today. But, historically, we’ve carried out pedigree and parentage information with performance data to produce EPDs. We’ve married that with economic information to produce selection indexes to simplify multiple trait selection for genetic merit. Now, with genomics, it’s just a natural evolution to be able to look at gene markers associated with performance. To be able to jump start the accuracy of animals early in life so we can more accurately select animals, practice more intense selection and turn generations faster to make genetic improvement,” continues Anderson.
“We use chips, and each chip is a little bigger than the size of a microscope, and contains 12 wells to test 12 animals. Within each well there are beads that are pre-programmed with very special chemistry, so when those beads are exposed to an animal’s DNA, they react and tell you whether animals are homozygous or heterozygous for that marker at that location. They’re also replicated, so more than one bead represents a particular genotype. Fancy computer technology reads those beads, and produces a computer printout, where different colors represent different genotypes,” says Anderson.
“When we have known performance productivity information on animals, and lots of animals with those genotypes, we can determine the average effect of those genotypes in the population, for different traits,” continues Anderson. “Then we summed those effects up over the animals, and produced what is called a molecular breeding bed. It uses nifty technology, and is what I term quantum leap technology that has enabled us to get lots of genotypes on animals at relatively less cost.”
“There are two kinds of genetic profiles, or panels. There are those that are specific to a breed, and there are others that can basically be applied across all breeds,” adds Jim Gibb of Merial-Igenity.
“You may ask the question that, if you have one that applies to all breeds, why do you need one that’s breed specific? The answer is that today the breed-specific profiles are much more accurate for that breed than an all-breed profile would be,” he continues.
This technology is being used within some breeds to produce genomic enhanced EPDs, which are derived by combining the individual animal’s records, pedigree information and progeny data with genomic data.
“When you see the term ‘GE EPD,’ that’s what it’s referring to,” explains Gibb, adding that genomic data adds its value in a few key ways.
“The first is in those traits that are difficult or expensive to measure. Contemporary groups aren’t required for genomic data, because environment doesn’t affect DNA. You don’t have to wait until a sire has enough daughters to measure their pregnancy rates for a trait, You can have much higher accuracy EPDs for non-parent animals, and provide reliable EPDs for traits that are expensive or difficult to measure,” says Gibb.
“Number two is it gives us more information on young animals, so we can get a better genetic assessment on those young animals early in life. You can pull a DNA sample on a two-day-old calf and get an estimation of that animal’s genetic value as if it had 14 to 15 progeny,” explains Gibb.
He adds that incorporating genetic data can increase the rate of genetic progress by 20 to 41 percent, depending on the trait being measured.
“In the summer of 2009, we made an agreement with the American Angus Association (AAA) to provide them with genomic data, so they can incorporate that into EPDs and get GE EPDs.
“AAA calculates pedigree estimates, which is the average of an animal’s sire and dam, and has an accuracy of .05, which is the equivalent to them having about two progeny. Accuracy goes from zero to .99, and is an indicator of how good that EPD predicts the actual genetic value of the animal,” explains Gibbs.
He adds that additional factors can be incorporated to increase accuracy, but that genomic information makes the biggest difference.
“If we add genomic data, that gets accuracy up to about .35, which is equivalent to about 16 progeny. You can see that, on a two-day-old calf, if you add pedigree and genomic data, you have the equivalent of that calf having roughly 16 progeny,” explains Gibb.
He adds he isn’t suggesting the discontinuation of collecting phenotypes, because without those people would be out of business.
“We rely on genotypes to train these DNA panels, which can actually be used to further enhance the phenotype. We need both, and the best case scenario is to have both,” he states.
“We see genomics as part of the evolution of how we do business,” adds Anderson.
Anderson and Gibbs spoke during the 2011 International Livestock Congress, in Denver, Colo. on Jan. 11. Heather Hamilton is editor of the Wyoming Livestock Roundup and can be reached at heather@wylr.net.