Data from: Domestication genomics of the open-pollinated scarlet runner bean (Phaseolus coccineus L.)

The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.红花菜豆（runner bean）是起源于中美洲的豆科物种，与普通菜豆（Phaseolus vulgaris）亲缘关系密切。该物种为多年生植物，但在小规模农业生产中通常作为一年生作物栽培，以收获其干种子和可食用的幼嫩豆荚。与普通菜豆不同，红花菜豆（P. coccineus）在遗传学层面受到的关注相对较少。本研究旨在达成以下三个目标：（1）解析红花菜豆的驯化历史与驯化事件；（2）探究该物种野生与栽培墨西哥居群的遗传多样性分布与水平；（3）筛选受自然选择与人工选择的候选基因座。为此，我们对242份红花菜豆个体、近缘物种普通菜豆的驯化型个体（20份）以及杜莫萨菜豆（P. dumosus，35份个体）进行了测序分型（genotyping by sequencing），共获得42548个单核苷酸多态性位点（Single Nucleotide Polymorphism，SNPs）。研究共检测到8个遗传聚类群，其中一半对应野生居群，另一半对应栽培植株。栽培居群构成一个单系进化枝，表明红花菜豆仅在墨西哥发生过一次驯化事件，且驯化发生于跨墨西哥火山带（Trans-Mexican Volcanic Belt）周边的居群中。未检测到野生与栽培居群间的遗传多样性水平存在显著差异，且有效种群规模相对较高，这支持了其驯化过程中仅存在较弱的遗传瓶颈。多数居群表现出杂合子过剩现象，这可能由近交衰退所致。其中红花菜豆条纹亚种（P. coccineus subsp. striatus）的一个居群杂合子过剩程度最高，尽管其地理分布与其他野生居群较为接近，但遗传上呈现明显的隔离状态。与既往研究结果不同，我们未发现野生与栽培居群间存在近期基因交流的证据。基于异常值检测方法，我们共筛选得到24个与驯化相关的SNPs、13个与品种分化相关的SNPs以及8个受自然选择的SNPs。其中仅有少量SNPs位于已注释的基因座内，但已注释的驯化相关SNPs在花与豆荚中呈现高表达水平。本研究结果有助于我们理解红花菜豆的驯化历史，并凸显了亲缘关系密切的物种之间，驯化的遗传特征可能存在显著差异。