Improving Response in Genomic Selection with a Population-Based Selection Strategy: Optimal Population Value Selection

Genomic selection (GS) identifies individuals for inclusion in breeding programs based on the sum of their estimated marker effects or genomic estimated breeding values (GEBVs). Due to significant correlation between GEBVs and true breeding values, this has resulted in enhanced rates of genetic gain as compared to traditional methods of selection. Three extensions to GS, weighted genomic selection (WGS), optimal haploid value (OHV) selection, and genotype building (GB) selection have been proposed to improve long-term response, and to facilitate the efficient development of doubled haploids. In separate simulation studies, these methods were shown to outperform GS under various assumptions. However, further potential for improvement exists. In this paper, optimal population value (OPV) selection is introduced as selection based on the maximum possible haploid value in a subset of the population. Instead of evaluating the breeding merit of individuals as in GS, WGS, and OHV selection, the proposed method evaluates the breeding merit of a set of individuals as in GB. After testing these selection methods extensively, OPV and GB selection were found to achieve greater responses than GS, WGS, and OHV, with OPV outperforming GB across most percentiles. These results suggest a new paradigm for selection methods in which an individual's value is dependent upon its complementarity with others.