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

文献类型： 外文期刊

作者： Xu, P. 1 ; Wu, X. 1 ; Wang, B. 1 ; Luo, J. 2 ; Liu, Y. 1 ; Ehlers, J. D. 3 ; Close, T. J. 3 ; Roberts, P. A. 3 ; Lu, Z. 1 ; Wan 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Vegetables, Hangzhou 310021, Zhejiang, Peoples R China

2.Zhejiang Acad Agr Sci, Inst Digital Agr Res, Hangzhou 310021, Zhejiang, Peoples R China

3.Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

关键词： asparagus bean;association mapping;cowpea;domestication history;linkage disequilibrium;population structure

期刊名称：HEREDITY （ 影响因子：3.821； 五年影响因子：4.553 ）

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收录情况： SCI

摘要： 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.

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