Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in (Medicago truncatula)

Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.

自下而上的进化研究方法（包括空间显式种群基因组分析）具备揭示适应性演化机制基础的能力。本研究以模式豆科植物蒺藜苜蓿（Medicago truncatula）为研究对象开展种群基因组分析，旨在解析其种群遗传结构，并筛选出呈现空间可变选择信号的共生相关基因。本研究利用RAD-seq技术，从欧洲原生分布区三个区域内的191份材料中开发出超过26000个单核苷酸多态性位点（SNPs）。STRUCTURE软件分析结果显示，样本可被划分为5个清晰的遗传聚类群，聚类边界与地中海盆地东西区域的分界相吻合。绝大多数遗传变异留存于采样点内部，且存在显著的距离隔离效应。本研究检测到广泛的连锁不平衡现象，尤其在种群内部更为显著。我们分别采用基于固定分化指数（FST）的基因组扫描法与贝叶斯建模方法（PCAdapt）开展遗传异常位点分析。两种分析方法共得到70个核心异常位点，其中关联到1个明确的共生相关候选基因DMI1。本研究为后续开展功能实验以解析选择作用靶标的重要表型，以及对根瘤菌种群开展相关补充研究奠定了基础。