Symposium review: How to implement genomic selection

Authors: Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2020
Publication Date: 6/1/2020
Citation: Van Raden, P.M. 2020. Symposium review: How to implement genomic selection. Journal of Dairy Science. 103(6):5291-5301. https://doi.org/10.3168/jds.2019-17684.
DOI: https://doi.org/10.3168/jds.2019-17684

Interpretive Summary: Genomic prediction methods developed for dairy cattle are now applied widely to many other animal, human, and plant populations. The DNA predictions adopted 10 yr ago have improved rapidly. Accuracy improves as datasets expand and more traits are included. New uses for genomic information include pedigree discovery, genomic mating, and avoiding recessive defects. Future predictions will use more gene tests discovered from sequence data and more international genotypes.

Technical Abstract: Genomic selection was adopted very quickly in the 10 yr after first implementation, and breeders continue to find new uses for genomic testing. Breeding values with higher reliability earlier in life are estimated by combining DNA genotypes for many thousands of loci using existing identification, pedigree, and phenotype databases for millions of animals. Quality control for both new and previous data greatly improves by comparing genomic and pedigree relationships to correct parent-progeny conflicts and discover many additional ancestors. Many quantitative trait loci and gene tests have been added to previous assays that used only evenly spaced, highly polymorphic markers. Imputation now combines genotypes from many assays of differing marker density. Prediction models have gradually advanced from normal or Bayesian distributions within breed and trait to single-step, multitrait, multibreed, or other more complex models. Genomic selection was initially applied to males to predict progeny performance but now is widely applied to females or even embryos to predict their own later performance. The initial focus on additive merit has expanded to include mating programs, genomic inbreeding, and recessive alleles. Many producers now use DNA testing to decide which heifers should be inseminated with elite dairy, beef, or gender-sorted semen; be embryo donors or recipients; or be sold or kept for breeding. Because some of these decisions are expensive to delay, predictions are now provided weekly instead of every few months. Predictions from international genomic databases often are more accurate and cost-effective than from the within-country databases that were previously designed for progeny testing unless local breeds, conditions, or traits differ greatly from the larger database. Selection indexes include many new traits, often with lower heritability or requiring large initial investments to obtain phenotypes, which provide further incentive to cooperate internationally. The genomic prediction methods developed for dairy cattle are now applied widely to many other animal, human, and plant populations.