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.

加利福尼亚季节性池（California vernal pool, VP）生态系统孕育着多样的特有植物群落，这类植物正受到多种人为活动的威胁，因此亟需开发分子工具以量化本地种群遗传变异的范围与分布。本研究利用限制性位点相关DNA测序（RADseq），针对一种广泛分布的VP特有植物——弗氏扁果菊（Lasthenia fremontii）开发单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记。我们使用限制性内切酶（restriction enzyme）SbfI，构建了来自不同VP复合体的12份个体的RAD标签文库（RAD-tag library）；该酶不会在扁果菊属的叶绿体基因组（chloroplast genome）中产生酶切位点。在全部12份个体的文库中共获得316,106个catalog位点，其中713个位点为多态性位点，共得到3918个候选SNPs。随后，我们对额外的285株植株进行基因分型（genotyping），以验证并表征其中71个候选SNPs。结果显示，44个位点在不同VP复合体间呈现多态性。利用这些位点开展的遗传变异分布初步分析表明，该物种的整个地理分布范围内存在显著的距离隔离（isolation-by-distance）效应。在单个VP复合体内部，不同水池对应的亚种群间虽遗传分化（genetic differentiation）较弱，但部分亚种群间仍存在显著的遗传分化。综上，本研究通过RADseq成功开发了可表征弗氏扁果菊在多个空间尺度上遗传变异模式的SNP标记，可为VP种群的保护与影响缓解工作提供科学参考。