CoPIs: Kevin P. Smith (University of Minnesota - Twin Cities) and Justin C. Fay (Washington University)
Through examination of the prevalence of deleterious mutations, the project will address a longstanding issue of both theoretical and practical importance. Important crops such as barley, rice, soybeans, and wheat are inbreeding and deleterious mutations could be of greater consequence on yield in these crops, as the mutations will more frequently occur in the homozygous state in inbreds than in hybrid cultivars. Once identified, deleterious mutations can be eliminated through marker-assisted selection using genomics tools that are independent of the cost and inaccuracy of phenotyping to increase yield and reduce disease prevalence in crop plants. The barley system to be used in this study is ideally suited to translate our understanding of the nature and importance of deleterious mutations to application within a nationally organized and primarily public sector plant breeding community. USDA regional genotyping laboratories serve barley and wheat breeding programs across the country, using contemporary genotyping platforms to perform selection with informative SNPs. Several large collaborative research projects in barley are developing next generation mapping populations, a centralized trait and genotype database and analysis tools, and other resources that can be employed to further explore the role of deleterious mutations in barley. The public nature of the national barley breeding community will make application of this research in commercially relevant breeding lines broadly visible to the agricultural research community. This provides a uniquely open research system where results can serve as a model for other plant species that are used for food, fuel, and other natural products. Finally, the project will provide interdisciplinary training opportunities for a postdoctoral scholar, a graduate student, and an undergraduate in crop genomics, evolutionary genetics, and computational biology. Through involvement with outreach programs at both universities, the project will engage students from populations underrepresented in the sciences.
The research aims to characterize the potentially conflicting effects of self-fertilization and strong selection on the proportion of deleterious mutations harbored in individual plant genomes. Using resequencing of barley exomes from wild accessions, landraces (local cultivars), and modern elite (high yielding) inbred lines, the project will determine the extent to which selection for yield has affected the proportion of deleterious mutations present across genomes. Given sufficient population sizes, active selection of progeny that are more productive than either parent clearly has the potential to reduce the proportion of deleterious mutations present in elite lines. Nevertheless, strong selection for alleles that improve inbred lines or adaptation to agronomic environments may also increase the frequency of linked deleterious mutations. Genome-level comparisons will permit the identification of loci subject to artificial selection and estimation of the degree to which barley breeding programs have eliminated deleterious mutations across the genome while simultaneously contaminating the genome with deleterious mutations through hitchhiking at agriculturally important loci. All data generated in this project will be accessible through long-term repositories such as the NCBI SRA, GrainGenes and the Triticeae Toolbox (T3) database. Germplasm used in this project will be available upon request and through the USDA-ARS National Plant Germplasm System and Grin-Global.
