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.）是一种原产于北美的多年生草本植物，存在两种生态型：旱地生态型主要分布于柳枝稷栖息地的北部范围，低地生态型则多分布于其南部区域。此前的研究多聚焦于以北方柳枝稷为主的多样性群体，为了更全面地解析北美柳枝稷的遗传多样性，本研究对额外632份（主要为低地生态型）个体开展了外显子组捕获测序，生成了外显子组捕获测序数据（exome capture sequence data）。共计鉴定出超过3700万个单核苷酸多态性（single nucleotide polymorphisms，简称SNPs），并从覆盖140个种群（其中旱地生态型种群67个、低地生态型种群65个、混合种群8个）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，低地与旱地生态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。与水稻（*Oryza sativa* L.）、玉米（*Zea mays* L.）、大豆[*Glycine max* (L.) Merr.]以及蒺藜苜蓿（*Medicago truncatula* Gaertn.）相比，全群体核苷酸多样性分析显示，所有个体的平均核苷酸多样性为0.0135，遗传多样性水平较高，这与柳枝稷的异交繁殖方式及多倍体特性相符。本研究验证了如下假说：反复发生的冰川事件、多倍体障碍以及由开花时间差异导致的基因流受限，共同造成了不同生态型与地理区域间基因库的分化。本数据集可为柳枝稷在饲草、生态修复以及生物燃料原料相关的目标性状关联等位基因研究提供数据支持。