The Role of Deleterious Substitutions in Crop Genomes

In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.

Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Kono, T. J. Y., Fu, F., Mohammadi, M., Hoffman, P. J., Liu, C., Stupar, R. M., Smith, K. P., Tiffin, P., Fay, J. C., Morrell, P. L. Tags: Discoveries Source Type: research