Estimating the relative contribution of deleterious and neutral SNPs to agronomic phenotypes. Hordeum vulgare subsp. vulgare

Targeted identification and purging of segregating deleterious alleles has been proposed as a novel approach to plant breeding. Recent advances in DNA resequencing technology and sequence constraint-based approaches to predict the functional impact of a mutation now permit the identification of putatively deleterious SNPs on a genome- wide scale. Previous surveys of bioinformatically-identified deleterious SNPs show that individual crop genomes may carry hundreds of deleterious SNPs. However, the contributions of these SNPs to phenotypic variation have not been empirically evaluated. We use exome resequencing and SNP genotyping in three cycles of an experimental spring six-row barley breeding population to compare the phenotypic contributions of putatively deleterious SNPs to those of neutral SNPs. In this population, selection was carried out jointly for increased yield and decreased disease severity. Grain yield remained stable while disease severity decreased. Across functional classes of SNPs from noncoding to putatively deleterious, we find that putatively deleterious SNPs explain more phenotypic variance for grain yield than other classes.