Data from: Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies

Association mapping of important traits of crop plants relies on first understanding the extent and patterns of linkage disequilibrium (LD) in the particular germplasm being investigated. We characterize here the genetic diversity, population structure and genome wide LD patterns in a set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm from China. A diverse collection of 99 asparagus bean and normal cowpea accessions were genotyped with 1127 expressed sequence tag-derived single nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs across the collection was relatively low (39%), with an average number of SNPs per locus of 1.33. Bayesian population structure analysis indicated two subdivisions within the collection sampled that generally represented the ‘standard vegetable’ type (subgroup SV) and the ‘non-standard vegetable’ type (subgroup NSV), respectively. Level of LD (r2) was higher and extent of LD persisted longer in subgroup SV than in subgroup NSV, whereas LD decayed rapidly (0–2 cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈5 cM) five times longer than the shortest (≈1 cM). Partitioning of LD variance into within- and between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 10 may have undergone the most intensive epistatic selection toward traits favorable for vegetable use. This work provides a first population genetic insight into domestication history of asparagus bean and demonstrates the feasibility of mapping complex traits by genome wide association study in asparagus bean using a currently available cowpea SNPs marker platform.

作物重要性状的关联定位，首先有赖于明确所研究的特定种质资源中连锁不平衡（linkage disequilibrium, LD）的程度与分布模式。本研究针对一套采自中国的长豇豆（Vigna unguiculata ssp. sesquipedialis）种质资源，解析了其遗传多样性、群体结构及全基因组连锁不平衡模式。研究团队对99份涵盖长豇豆与普通豇豆的种质资源开展了基因分型，所用标记为1127个表达序列标签衍生的单核苷酸多态性（expressed sequence tag-derived single nucleotide polymorphism markers, SNPs）标记。该群体的多态性SNPs占比相对较低（39%），每个位点的平均SNPs数量为1.33。贝叶斯群体结构分析结果显示，所采样的群体可划分为两个亚群，分别对应“标准菜用型”（subgroup SV）与“非标准菜用型”（subgroup NSV）。SV亚群的连锁不平衡水平（r²）更高，且连锁不平衡的有效维持距离更长；而两个亚群的连锁不平衡均在0~2 cM范围内快速衰减。不同染色体的连锁不平衡衰减距离存在显著差异，最长的约为5 cM，是最短的约1 cM的5倍。将连锁不平衡的方差分解为亚群内与亚群间组分，并结合比较连锁不平衡衰减分析，结果表明连锁群5、7与10可能经历了针对菜用优良性状的最强上位选择。本研究首次从群体遗传学角度为长豇豆的驯化历史提供了认知依据，并证实利用现有豇豆SNP标记平台，在长豇豆中开展复杂性状全基因组关联研究（genome wide association study）的可行性。