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（Switchgrass，*Panicum virgatum* L.）是北美本土多年生草本植物，存在两种生态型：旱生型（upland）主要分布于柳枝稷栖息地的北部区域，湿生型（lowland）则多集中在其南部分布区。既往研究多以北方柳枝稷种群为主的多样性研究群体为对象，为拓宽我们对北美更广范围柳枝稷遗传多样性的认知，本研究为632份新增的、以湿生型为主的个体生成了外显子组捕获测序数据（exome capture sequence data）。本研究共鉴定出超过3700万个单核苷酸多态性（single nucleotide polymorphisms, SNPs），并从来自140个种群（其中67个为旱生型种群、65个为湿生型种群、8个为混合种群）的1169份个体中筛选得到190万个高置信度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个独立的种群组，且湿生型与旱生型种群间存在中等程度的遗传分化[平均固定指数（fixation index, Fst）估值为0.06]。本研究还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.]及蒺藜苜蓿（Medicago truncatula Gaertn.），本研究对核苷酸多样性的分析显示，所有个体的平均核苷酸多样性达0.0135，这与柳枝稷的异交繁殖方式及多倍体特性相符。本研究支持下述假说：反复发生的冰川作用、倍性障碍以及由开花时间差异导致的基因流限制，共同造就了不同生态型与地理区域间独特的基因库。本研究产生的数据可为柳枝稷饲用、生态修复及生物燃料原料相关研究中的等位基因-目标性状关联分析提供资源支撑。