Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections - a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

中文翻译：

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合并来自两个异位收集的基因分型测序数据提供了对豌豆进化历史的见解。


豌豆（Pisum sativum L. subsp. sativum）是最古老的驯化物种之一，也是广泛种植的豆科植物。在这项研究中，我们结合了两个测序基因分型 (GBS) 文库的下一代测序 (NGS) 数据，每个文库均由不同的豌豆种质资源库制备。在两个种质保藏中调用的单核苷酸多态性（SNP）位点的选择导致了一些信息的丢失；然而，这并没有妨碍获得有史以来用于探索豌豆生物多样性的最大数据集之一，其中包括 652 个种质和 22 127 个标记。对种群结构的分析反映了基于地理模式的遗传变异，并允许定义豌豆种植从驯化中心扩展到世界其他地区的模型。在遗传上不同的群体中，连锁不平衡（LD）的平均衰减范围从几个碱基到数百个碱基，从而表明不同的进化历史导致了它们的多样化。全基因组扫描鉴定了与驯化和育种相关的假定选择性扫描，包括已知调节枝条分枝、子叶颜色和抗倒伏的基因，以及两个孟德尔基因的正确定位。除了为豌豆基础和应用研究提供重要信息外，我们的工作还描述了从异地收集生成的不同 GBS 数据集整合的第一个成功示例 - 这是一个对多种目的具有潜在兴趣的过程，包括保护遗传学、全基因组关联研究和育种。