Discovery and Validation of SNPs for Association Mapping in Switchgrass.

Switchgrass (Panicum virgatum) has been recognized as a model plant species for biofeedstock production.  The identification of molecular markers that are tightly linked to biomass-related trait loci would enable marker-assisted selection and greatly accelerate breeding efforts for enhanced biomass production.  Our aim is to develop SNP markers because they are amenable to high-throughput approaches and are found at a high enough density to potentially tag every gene in the genome.  In the first stage of our research, we downloaded and assembled 73,575 public EST sequences from a single heterozygous tetraploid switchgrass cultivar into contigs, of which 518 (600 kb total sequence) were found to contain 2,998 potential SNPs (1 SNP/200 bp).  Resequencing 20 amplicons across 12 diverse switchgrass lines indicated that less than 50% of the potential SNPs were valid.  We are continuing to make improvements to the SNP discovery pipeline in order to minimize the false positive rate, which is challenging in this complex, polyploid genome.  This research will result in a SNP-based genetic map of switchgrass for QTL studies and association mapping, and will ultimately provide breeders with a tool for marker assisted selection for biomass quality and quantity traits.