The role of deleterious substitutions in crop genomes

Abstract

Historically, it has been postulated that populations carry genetic variants with deleterious effects as segregating variation. Recent advances in DNA resequencing technology allow a new view on this topic, providing a way to identify segregating molecular sequence variants that alter sites that show constrained evolution. Targeted identification and removal of such segregating variants has been proposed as a novel path for improving agronomic performance in plant breeding programs. In this dissertation, I present a brief review of deleterious variation, and why it may be important to plant breeding. Then, I present a tool for classifying single nucleotide polymorphisms into functional classes using public sequence databases. Next, I present a survey of potentially deleterious alleles segregating in two crop species, and a software package that implements a likelihood ratio test for sequence constraint and deleterious prediction. Finally, I present an examination of the contribution of potentially deleterious alleles to yield in a barley breeding experimental population. While potentially deleterious alleles themselves do not explain a larger proportion of phenotypic variation than non- deleterious alleles, genomic prediction of phenotypes may be improved by examining informative subsets of sequence variants, rather than with genomewide markers.