Article by Wes Ishmael | Beef Magazine
As the art and science of genomics becomes more accurate, cow-calf producers benefit. While cow-calf producers won’t directly participate in genomic evaluation now that single-step evaluation is a reality, they’ll be able to buy bulls with more accurate and reliable EPDs from their seedstock suppliers.
“If you’re a breeder doing a lot of genotyping and phenotyping — you’re measuring all of the data in all of the traits — single-step genomic evaluation lets you leverage the accuracy from that immediately,” says Stephen Miller, director of genetic research for Angus Genetics Inc. (AGI). “I think that’s a strong component of why breeders may become even more active in genotyping than they have been so far.”
Miller is describing what he believes will be one of the results of the single-step beef cattle genetic evaluation currently being refined and tested by organizations with massive databases, including AGI and International Genetic Solutions (IGS), which is a collaboration of 12 breed associations.
For the American Angus Association (AAA), AGI conducts a single-breed genetic evaluation. AAA’s registry grows by about 300,000 annually. The AAA database for genetic evaluation includes weaning weights for 8.3 million animals and birth weights for 7.6 million, among a host of various phenotypes.
Conversely, Mahdi Saatchi, lead genomicist at IGS, explains the organization’s database includes more than 16 million animals — the largest multibreed beef cattle genetic evaluation system in the world — adding more than 400,000 each year.
Single-step genetic evaluation is meant to replace what is currently and usually a multistep process used to incorporate genomic information into the calculation of expected progeny differences (EPDs).
As Alison Van Eenennaam, University of California, Davis, Extension beef geneticist, explains in the report titled “Recent Developments in Genetic Evalua-tions and Genomic Testing” (available at ebeef.org), “Currently, the incorporation of genomic information into genetic evaluations is statistically complex, and often involves a multistep approach that requires 1) traditional genetic evaluation with an animal model, 2) estimation of the marker effects and development of the prediction equation, and 3) a blending of those two pieces of information using a variety of approaches to develop a genome-enhanced EPD [GE-EPD].”
With this multistep approach, GE-EPDs are available only for genotyped animals. Including their information in genetic evaluation requires what’s termed a “training population” used to recalibrate prediction equations periodically. Suffice it to say, this is an added step that requires lots of time.
A shortcoming of the multistep approach is that selection bias can creep into the evaluation, since animals superior in genetic merit are the most likely ones to be genotyped. Saatchi adds that weighting estimates for the information included can be a primary source of biases.
Keep in mind that EPDs were already the gold standard of genetic prediction, even before genomic data was included in genetic evaluation.