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，学名*Panicum virgatum L.*）是一种原产于北美的多年生草本禾草，分为两种生态型：高地型（upland）与低地型（lowland）。高地型主要分布于柳枝稷生境的北部区域，低地型则多集中于其南部分布范围。既往研究多聚焦于北部柳枝稷的多样性群体，为拓展我们对北美更广范围柳枝稷遗传多样性的认知，本研究针对额外的632份（主要为低地型）个体生成了外显子组捕获测序数据（exome capture sequence data）。总计共鉴定出超过3700万个单核苷酸多态性（single nucleotide polymorphisms，简称SNPs），并从来自140个群体（其中高地型67个、低地型65个、混合类型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群体结构分析。研究共鉴定出7个独立的群体分组，低地型与高地型群体间存在中等程度的遗传分化[平均固定指数（fixation index，简称Fst）估值为0.06]。本研究还鉴定得到生态型特异性与群体特异性SNPs，可用于种质资源（germplasm）评价。相较于水稻（*Oryza sativa L.*）、玉米（*Zea mays L.*）、大豆[*Glycine max (L.) Merr.*]与蒺藜苜蓿（*Medicago truncatula Gaertn.*），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模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的柳枝稷形成了分化的基因库。本数据集可为柳枝稷在饲草、生态修复及生物燃料原料相关研究中，实现等位基因与目标性状的关联分析提供宝贵资源。