Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.)

To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation based on the phylogeny of wheat and investigations were made to: (1) assess the benefit of including deleterious alleles into MPH prediction models and (2) understand the genetic underpin-nings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite x elite (Exp. 1) and elite x plant genetic resources (PGR; Exp. 2). In our study, we found a lower allele frequency of moder-ately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH pre-diction models: modelling their additive-by-additive effects in Exp. 1 and dominance as well as associ-ated digenic epistatic effects in Exp. 2 significantly boosts prediction accuracies of MPH. Furthermore, heterotic-quantitative trait loci's underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles con-tributes to grain yield heterosis in elite crosses (Exp. 1).(c) 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).