Data from: Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analyzing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north, and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.

植物驯化通常会导致驯化作物与其野生祖先之间产生高度的遗传分化。这一过程会被野生与驯化植物间的基因流（gene flow）所抵消，因为二者通常能够杂交并发生基因交流。本研究以以色列境内的896份野生大麦种质（Barley1K）以及以色列基因库中所有可获取的栽培大麦（Hordeum vulgare）种质为研究材料，分析了野生大麦（Hordeum spontaneum）与栽培大麦间的基因流程度，及其对野生大麦种群结构的影响。本研究还比较了基于核心种质集分型的简单序列重复（simple sequence repeats, SSR）与单核苷酸多态性（single nucleotide polymorphisms, SNP）标记数据在种群参数估计中的表现。基于SSR标记的基因流速率估计结果显示，栽培大麦向野生大麦存在高水平的基因渐渗（introgression）。在剔除野生大麦样本中近期与栽培大麦发生遗传混杂的种质后，种群结构的推断结果显著优化。SSR与SNP标记均显示，以色列境内野生大麦的遗传种群结构对应三大主要生态地理区域：沿海地区、地中海北部地区，以及约旦河谷与南部的沙漠地带。基因流速率估计表明，从北向南的基因流动速率高于反向流动。正如其他作物物种中已观测到的那样，野生大麦与栽培品种间存在显著的等位基因交流，这一现象在驯化相关的种群遗传分析中必须予以考量。