Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species
that is native to North America, and is being developed as a future
biofuels feedstock crop. Switchgrass is present primarily in two ecotypes:
a northern upland ecotype composed of tetraploid and octoploid accessions,
and a southern lowland ecotype composed of primarily tetraploid
accessions. We employed high-coverage exome capture sequencing (~2.4 Tb)
to genotype 537 individuals from 45 upland and 21 lowland populations.
From these data, we identified ~27 million single nucleotide polymorphisms
(SNPs), of which 1,590,653 high confidence SNPs were used in downstream
analyses of diversity within and between the populations. From the 66
populations, we identified five primary population groups within the
upland and lowland ecotypes, a result that was further supported through
genetic distance analysis. We identified conserved, ecotype restricted
non-synonymous SNPs that are predicted to impact protein function in genes
that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes
involved in flowering which may contribute to the phenotypic differences
between the two ecotypes. We also identified, relative to the
near-reference Kanlow population, 17,228 up-copy number variants (CNVs),
112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a
total of 9,979 genes, including two upland-specific CNV-clusters. In
total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel
providing a firm foundation to identify functional variation associated
with phenotypic traits of interest for biofuel feedstock production.