Most of the benefits from genomic selection can be realized by genotyping a small proportion of available selection candidates

Abstract

We reasoned that marginal returns from genomic selection diminish as the proportion of genotyped selection candidates increases and breeding values (BV) based on a priori information are used to choose candidates that are genotyped. We tested this premise by stochastic simulation of breeding schemes that resembled those used for pigs. We estimated rates of genetic gain and inbreeding realized by genomic selection in breeding schemes where candidates were phenotyped before genotyping and 0 to 100% of the candidates were genotyped based on predicted B V. Genotyping was allocated to male and female candidates at ratios of 100:0, 75:25, 50:50, 25:75, and 0:100. For genotyped candidates, a direct-genomic value (DGV) was sampled with reliabilities 0.10, 0.50, and 0.90. Ten sires and 300 dams with the largest BV after genotyping were selected at each generation. Selection was for a single trait with heritability 0.20. We found that the marginal returns did diminish as genotyping proportion was increased, while the rate at which the returns diminished slowed as DGV became more reliable. With DGV reliability 0.10, genotyping as little as 5% of the selection candidates realized 86% of the additional genetic gain and 67% of the reduction in inbreeding that was realized by genotyping 100% of the candidates. All of the genetic gain and reduction in inbreeding was realized by genotyping 40 and 50% of the candidates. When the reliability was increased to 0.90, genotyping 20% of the candidates was required to realize 76% of the genetic gain and 85% of the reduction in inbreeding. Genotyping 50% of the selection candidates with DGV reliability 0.90 realized 91% of the genetic gain and 94% of the reduction in inbreeding. Regardless of DGV reliability, returns at small genotyping proportions of 0.5 to 10% were maximized when only male candidates were genotyped. At the large genotyping proportions of 20 to 50%, returns were maximized by genotyping both males and females. Our findings indicate that, provided a priori information is available, only 5 to 20% of the selection candidates need to be genotyped to realize most of the benefits from genomic selection. At these genotyping proportions, it is best to target males in schemes when selection intensity for males is greater than females. Our findings should benefit breeders because they suggest that large investments in genotyping are not required to reap most of the benefits from genomic selection. © 2012 American Society of Animal Science. All rights reserved.