ARS | Publication request: Range-wide genomic variation and population structure of switchgrass (Panicum virgatum L.) measured using genotyping-by-sequencing (GBS)

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 7, 2011
Publication Date: January 13, 2012
Citation: Grabowski, P., Morris, G., Casler, M.D., Borevitz, J. 2012. Range-wide genomic variation and population structure of switchgrass (Panicum virgatum L.) measured using genotyping-by-sequencing (GBS). Plant and Animal Genome Conference. http://pag.confex.com/pag/xx/webprogram/Paper1297.html.

Technical Abstract: Geographic patterns of genetic variation are shaped by historical and contemporary processes including migration, genetic drift, and natural selection. Natural populations of Panicum virgatum, a warm-season (C4) perennial grass and emerging bioenergy crop, are found in a variety of habitats that vary widely in vegetation, soil type, temperature, and moisture regimes. Characterizing patterns of genetic variation in P. virgatum can identify centers of diversity and genetically unique varieties, and quantifying population structure is essential to selecting appropriate panels for association mapping studies for the improvement of lines for bioenergy production. However, P. virgatum is polyploid and wind pollinated, which makes studies of genetic variation more difficult, particularly when using traditional genotyping techniques. Therefore, we adapted a next-generation sequencing approach, Genotyping-By-Sequencing (GBS), to genotype P. virgatum at thousands of loci in order to augment and further resolve patterns of genetic variation. We genotyped 119 P. virgatum individuals from across the native range, generating ~50 million bp of genotyping data and discovering 140 thousand candidate SNPs. We used these data to measure isolation-by-distance and population structure, and because polymorphisms are identified and called in the same step when using GBS, ascertainment bias is essentially eliminated from our results. These results confirm previous range-wide estimates of population structure in P. virgatum while providing much greater genome-level detail of the genetic variation that exists throughout the species.