Data from: Extensive genetic diversity is present within North American switchgrass germplasm

Switchgrass (Panicum virgatum L.) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice (Oryza sativa L.), maize (Zea mays L.), soybean [Glycine max (L.) Merr.], and Medicago truncatula Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.

柳枝稷（Panicum virgatum L.）是一种北美本土多年生草本植物，存在两种生态型：高地生态型主要分布于柳枝稷栖息地的北部区域，低地生态型则多分布于其南部范围。既往研究多聚焦于以北部柳枝稷为主的多样性群体，为拓展对北美更广范围柳枝稷遗传多样性的认知，研究人员对新增的632份主要为低地生态型的个体开展了外显子组捕获测序。本研究共鉴定出超过3700万个单核苷酸多态性（single nucleotide polymorphisms, SNPs），并从140个种群（其中高地型67个、低地型65个、混合类型8个）的1169个个体中筛选得到190万个高可信度SNPs，用于后续的遗传多样性与种群结构分析。研究共鉴定出7个独立的种群类群，低地与高地种群间存在中等程度的遗传分化[固定指数（fixation index, Fst）均值为0.06]。同时，本研究鉴定得到生态型特异性与种群特异性SNPs，可用于种质资源评价。相较于水稻（Oryza sativa L.）、玉米（Zea mays L.）、大豆[Glycine max (L.) Merr.]以及蒺藜苜蓿（Medicago truncatula Gaertn.），核苷酸多样性分析显示所有个体的整体核苷酸多样性达0.0135，这与柳枝稷的异交繁殖方式及多倍体特性相符。本研究支持如下假说：反复发生的冰期事件、倍性障碍以及开花时间差异导致的基因流受限，使得不同生态型与地理区域间形成了独特的基因库。本数据集可为柳枝稷饲用、生态修复及生物燃料原料相关研究中，等位基因与目标性状的关联分析提供资源支撑。