Genotyping-by-Sequencing Reveals Genomic Variation Underlying Ecotypic Diversity and Geographic Patterns in Switchgrass

Switchgrass (Panicum virgatum L.), a wide-ranging warm-season (C4) grass, is a major component of many ecosystems and an emerging bioenergy feedstock crop. Ecotypes of switchgrass are adapted to different temperature, moisture, and light regimes, and understanding the genetic basis of this ecotypic variation is crucial for informing management decisions and identifying ecologically and economically important diversity. However, genetic studies in switchgrass have been limited by polyploidy, lack of a reference genome, and modest tractability for many genetic methods. Here, we use genotyping-by-sequencing (GBS), generating 98,042 polymorphisms in 27,666 restriction site-association loci, to measure geographic and genome-wide patterns of genetic variation in 126 switchgrass and other Panicum samples from across their native range. We observe extensive genetic differentiation between the lowland and upland switchgrass ecotypes, regional genetic differentiation within each ecotype, and variable levels of gene flow across the species.  Furthermore, we use genome scans to identify genomic regions associated with ecotypic differentiation and regional adaptation.  These results have direct implications for the design of switchgrass association studies and indicate that natural variation for beneficial traits in switchgrass can be harnessed best if diversity from across the range is included in crop improvement efforts.