Data from: Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies
Xu, Pei, ZheJiang Academy of Agricultural Sciences
Wang, Baogen, ZheJiang Academy of Agricultural Sciences
Luo, Jie, ZheJiang Academy of Agricultural Sciences
Ehlers, Jeffrey D., University of California, Riverside
Close, Timothy J., University of California, Riverside
Roberts, Philip A., University of California, Riverside
Wang, Sha, ZheJiang Academy of Agricultural Sciences
Li, Guojing, ZheJiang Academy of Agricultural Sciences
Published Jan 30, 2012 on Dryad.
Cite this dataset
Xu, Pei et al. (2012). Data from: Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies [Dataset]. Dryad. https://doi.org/10.5061/dryad.6tv35cc2
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.
Xu et al raw SNP genotyping data_Heredity
This file contains the raw genotyping data of the 1102 EST-derived SNPs loci with successful calls in the sample set used in this study. Column A: IDs of the plant materials; Line1: names of the SNP markers. Question marks indicate unsuccessful or ambiguous calls.