Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.)

Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.作物野生种质资源与地方品种是植物育种以及在植株体内保存等位基因与基因组合的珍贵遗传资源。栽培普通菜豆的初级基因库包含普通菜豆（Phaseolus vulgaris）的野生种质资源。这类野生种质与驯化栽培种同属一个物种，因此可与栽培种质轻松进行杂交。对野生菜豆与地方品种开展分子标记评价，对于合理利用与保护这类重要遗传资源具有重要意义。本研究的目标为：利用荧光微卫星（microsatellite）或简单序列重复（simple sequence repeat，SSR）标记对一批野生菜豆种质进行评价，并结合所有已知品系群的栽培菜豆材料，解析其群体结构。针对36个标记与104份野生基因型材料的组合分析显示，以每个标记的平均等位基因数计的标记多样性较高（为13），与针对606份栽培基因型材料测得的每个标记平均14个等位基因的水平相近。从每份基因型材料的角度来看，野生菜豆的多样性略高于栽培菜豆。对野生菜豆开展群体结构分析后，共鉴定出5个种群/基因库，它们对应着不同地理分布区域，分别为中美洲（墨西哥）、危地马拉、哥伦比亚、厄瓜多尔-北秘鲁以及安第斯（阿根廷、玻利维亚与秘鲁南部）种群/基因库。对野生与栽培种质的联合分析结果显示，上述基因库中的第一个与最后一个分别与同名的栽培基因库具有亲缘关系，而倒数第二个基因库则表现出独特性，但并非其他基因库的祖先类群。危地马拉基因库是极为独特的新类群，可能与危地马拉品系群的栽培品种存在亲缘关系，而哥伦比亚种群同样具有独特性。研究结果表明，地理隔离、奠基者效应或自然选择可能造就了野生菜豆的多个半离散种群，而栽培菜豆的多样性则是由多次驯化事件与基因渐渗共同塑造的。