Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars, three lowland and four upland, to enable comparative analyses between switchgrass cultivars and to identify single nucleotide polymorphisms (SNPs) for use in breeding and genetic analysis. We also generated individual transcript assemblies for each of the cultivars. Transcript data indicate that subgenomes of octoploid switchgrass are not substantially different from subgenomes of tetraploids as expected for an autopolyploid origin of switchgrass octoploids. Using RNA-sequencin...