The Role of Deleterious Substitutions in Crop Genomes

Populations experience a continual input of new mutations, with a distribution of fitness effects (DFE) that ranges from lethal to beneficial. While the DFE of new mutations is not directly observable, many mutations likely have no effect on organismal fitness. Among mutations that have non-neutral fitness effects, many mutations are likely to have deleterious effects on fitness. Historically, it has been hypothesized that populations carry many mildly deleterious segregating variants, which contributes to a reduction in the absolute fitness of each individual. Recent advances in resequencing technology and sequence conservation-based metrics for predicting the potential functional impact of a variant permit an examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding would allow deleterious variants to persist and reach moderate frequencies, potentially reducing crop productivity. In this study, we use exome resequencing of eight cultivated barley lines and seven cultivated soybean lines to investigate the prevalence and genomic distribution of deleterious variation in crop plants.