Genome-Wide Association Study in Oat for Increased beta-glucan Content

We have performed two genome-wide association studies for beta-glucan content in oat. Both used Diversity Array Technology (DArT) markers. In the first, lines were obtained from the USDA-organized Uniform Oat Performance Nurseries (UOPN), and therefore represent the diversity of elite North American oat.  In the second, oat accessions from the National Small Grains Collection (NSGC) and divergent for beta-glucan content on the basis of data from Germplasm Resources Information Network. were obtained. In both cases we had close to 450 lines scored with about 1,000 markers. In addition to historical data (either from the UPON or GRIN), the lines were evaluated for beta-glucan content in Ames, IA in 2009 and 2010. Markers associated for beta-glucan content were identified using a standard mixed-model approach and using a mixed-model LASSO approach. To validate markers associated with beta-glucan content, we have aligned the associations with QTL previously-identified using linkage mapping. We have also BLASTed the sequences of associated DArT markers against the rice genome to determine if likely candidate genes reside nearby. In the NSGC population, but not in the elite North American population, association between markers homologous to genes near the cellulose synthase like F (CslF) genes of rice were identified. Thus, natural polymorphisms at this locus that are favorable for beta-glucan content may exist in gene bank accessions that were lost in the elite oat population.