Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic

California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species’ geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.

加州季节性池（vernal pool, VP）生态系统支撑着多样的特有植物群落，这些植物正受到多重人为活动的威胁，因此亟需开发分子工具以量化原生种群的遗传变异程度与分布格局。本研究针对一种广泛分布的VP特有植物——弗雷蒙特金菲草（Lasthenia fremontii），利用限制性位点相关DNA测序（RADseq）技术开发单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记。研究团队选用限制性内切酶SbfI，对采自不同VP复合体的12份个体构建RAD标签文库，以此开发核基因组来源的SNPs；该酶不会在金菲草属（Lasthenia）植物的叶绿体基因组中产生切割位点。该文库覆盖的12份个体中共获得316106个聚类位点，其中713个位点具有多态性，共得到3918个候选SNPs。随后，研究人员对额外采集的285份植株样本进行基因分型，以验证并解析其中71个候选SNPs的特征。其中44个位点在不同VP复合体间表现出多态性。利用这些位点开展的遗传变异分布初步分析显示，该物种的地理分布范围内存在显著的距离隔离效应；而在单个VP复合体内部不同池体的亚种群间，虽遗传分化程度较弱，但部分亚种群组仍存在显著的遗传分化。综上，本研究通过RADseq技术成功开发出可用于解析弗雷蒙特金菲草多空间尺度下遗传变异格局的SNPs标记，可为VP种群的保护与人为干扰缓解工作提供科学指导。