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）是源自中美洲的豆科物种，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，以采收其干种子与可食用的幼嫩豆荚。与普通菜豆不同，红花菜豆（P. coccineus）在遗传学领域受到的关注相对较少。本研究旨在达成以下三个目标：（1）阐明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种群的遗传多样性分布特征与水平；（3）鉴定受自然选择与人工选择的候选基因座。为此，我们通过测序分型（genotyping by sequencing）技术获取了包含42548个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的数据集，样本涵盖242份红花菜豆个体，以及亲缘关系密切的普通菜豆驯化型（20份）和多花菜豆（P. dumosus，35份）的驯化型。我们共检测到8个遗传聚类群，其中一半对应野生种群，另一半对应栽培植株。栽培种群构成一个单系支系，这表明墨西哥境内仅发生过一次驯化事件，且该事件起源于跨墨西哥火山带（Trans-Mexican Volcanic Belt）的种群周边。未检测到野生与栽培种群间遗传多样性水平的显著差异，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效应。多数种群存在杂合子过剩现象，推测其原因为近交衰退。其中红花菜豆条纹亚种（P. coccineus subsp. striatus）的一个种群杂合子过剩程度最高，尽管其地理分布与其他野生种群较为接近，但遗传上却处于隔离状态。与以往研究不同，我们未发现野生与栽培种群间存在近期基因流的证据。基于异常位点检测方法，我们共鉴定出24个与驯化相关的SNP位点、13个与品种分化相关的SNP位点以及8个受自然选择的SNP位点。这些SNP位点中仅有少数落在已注释的基因座内，但已注释的驯化相关SNP位点在花与豆荚组织中呈现高表达水平。本研究结果有助于加深对红花菜豆驯化历史的认知，并凸显了亲缘关系密切的物种间，驯化的遗传特征可能存在显著差异。