TBD6

Switchgrass (Panicum virgatum) is a native North American grass grown primarily as a forage crop and is currently being developed as a biofuel feedstock for lignocellulosic ethanol. Two ecotypes of switchgrass, upland and lowland, differ in phenotype, habitat, and ploidy (tetraploid and octoploid). Switchgrass is self-incompatible and due to its large, repetitive, heterozygous and polyploid genome, we developed an exome capture probe set from transcribed sequences to perform reduced representation sequencing of  ~50 Mb of exonic regions of the switchgrass genome. Following probe optimization, a final set of probe sequences were designed and used to survey genome diversity in a set of seven switchgrass cultivars.  Alignment of reads from each capture experiment to the Alamo AP13 reference genome revealed robust representation of probe-targeted genic regions in both lowland and upland ecotypes. Single nucleotide polymorphisms and copy number variants were readily identified among the surveyed cultivars demonstrating the utility of the exome capture probe set for revealing genetic diversity in switchgrass. Identification of the allele composition at the genome level permitted identification of preferential allele specific expression in the switchgrass transcriptome. Characterization of an upland diversity panel is underway to reveal genetic variation in natural populations.