Characterizing Environmental Associations and Measuring Ploidy in Switchgrass Using Exome-Capture Data

Increasing switchgrass biomass yields is a major goal for developing switchgrass as a bioenergy crop. Environmental stresses, such as drought and cold, limit switchgrass productivity, particularly in marginal lands and regions in which high-yielding cultivars are poorly adapted. As such, improving tolerance to environmental stresses in switchgrass cultivars grown for bioenergy can increase biomass yields. There is extensive natural variation in switchgrass for tolerance to environmental stresses; however, the genetics underlying this variation is poorly understood. Switchgrass lives in diverse habitats and climate conditions throughout its extensive native range in North America. Environmental data for collection locations from across the range provide information about the stresses to which different switchgrass populations are adapted and can be used to better understand the genetics underlying adaptation to different conditions. Here, we use climate data for more that 1000 switchgrass plants collected from across the U.S. range and 5 million SNP markers derived from exome-capture sequencing to identify genetic associations with environmental conditions. Our results provide initial insight into the genetic architecture of and genetic pathways important for adaptation to different environmental stresses in switchgrass. To improve our analysis, we also developed, and demonstrate here, a method to use exome-capture sequencing data to differentiate the major switchgrass ploidy levels (4X and 8X). Our results provide insights into the genetics of adaptation in switchgrass and will inform breeding efforts for producing switchgrass cultivars used for bioenergy production.