Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, PR China.
Heredity (Edinb). 2012 Jul;109(1):34-40. doi: 10.1038/hdy.2012.8. Epub 2012 Feb 29.
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 (r(2)) 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分析依赖于首先了解特定种质资源中连锁不平衡（LD）的程度和模式。我们在这里描述了一组来自中国的芦笋豆（Vigna.unguiculata ssp. sesquipedialis）种质的遗传多样性、群体结构和全基因组 LD 模式。用 1127 个表达序列标签衍生的单核苷酸多态性标记（SNP）对 99 份芦笋豆和正常豇豆进行了基因型分析。整个集合中多态 SNP 的比例相对较低（39%），每个位点的 SNP 数量平均为 1.33。贝叶斯群体结构分析表明，在所采样的集合中存在两个细分，分别代表“标准蔬菜”型（SV 亚组）和“非标准蔬菜”型（NSV 亚组）。在 SV 亚组中，LD（r(2)）水平较高，LD 持续时间较长，而在 NSV 亚组中，LD 衰减较快（0-2 cM）。LD 衰减距离在染色体之间存在差异，最长的（约 5 cM）是最短的（约 1 cM）的五倍。将 LD 方差分为亚组内和亚组间成分，并结合比较 LD 衰减分析表明，连锁群 5、7 和 10 可能经历了最密集的上位性选择，有利于蔬菜利用的性状。这项工作首次提供了对芦笋豆驯化历史的群体遗传见解，并证明了使用当前可用的豇豆 SNP 标记平台通过全基因组关联研究对芦笋豆复杂性状进行作图的可行性。
