2011 Annual Report 1a.Objectives (from AD-416) 1. Germplasm characterization: a. Develop DNA markers that can be used as tools to select switchgrass plants with superior performance for Biofuel and bioenergy uses. b. Develop selection methods and models in which DNA markers can be used to select the best switchgrass plants in segregating populations and as parents for upland X lowland hybrids. 2. Translational research and breeding: a. Identify functional polymorphisms in switchgrass genes that are directly associated with important traits for Biofuel and bioenergy uses. b. Identify candidate genes from maize, sorghum, Setaria, and other species that are homologous to important polymorphic regions in switchgrass, describe the function of these genes, and develop generalized markers that can be used to implement marker selection in switchgrass. 1b.Approach (from AD-416) 1. Conduct amplification and polymorphism analyses using EST-SSR markers on switchgrass association panels, including marker screening, scoring, and analysis. 2. Conduct simulation studies on marker-assisted selection methodologies to optimize the deployment of both laboratory and field facilities to maximize genetic gain per unit of expenditure. 3. Develop SNP markers from sequence analysis of candidate regions. 4. Develop methods by which performance of both half-sib and full-sib family performance can be predicted from genotypic assessment of parents. 3.Progress Report Phase I of the Exome Capture project was partially completed, with data analysis of the upland vs. lowland switchgrass transcriptome underway. Phase II of the Exome Capture project has been initiated with submission of a larger panel of genotypes that include the four major switchgrass taxa: 4x upland, 4x lowland, 8x upland, and 8x lowland. We cloned the caffeic acid O-methyl transferase gene in upland switchgrass and discovered 46 single-nucleotide polymorphisms, i.e. 46 individual DNA nucleotides that show distinct variation between different genotypes. Three of these sites appear to regulate endogeneous genetic variation in lignin concentration, as demonstrated by significant differences across phenotypic selection cycles for lignin concentration. Transcriptome analysis of flowering-time genes in switchgrass has just been initiated, and we expect to complete data collection and a limited data analysis before the end of FY11. ADODR monitoring was accomplished by face-to-face meetings and occasional emails.