Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies
Abstract
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 바카라 사이트˜standard vegetable바카라 사이트™ type (subgroup SV) and the 바카라 사이트˜non-standard vegetable바카라 사이트™ 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 (0바카라 사이트“2바카라 사이트‰cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈5바카라 사이트‰cM) five times longer than the shortest (≈1바카라 사이트‰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.
Citation
Xu, P.; Wu, X.; Wang, B.; Luo, J.; Liu, Y.; Ehlers, J.D.; Close, T.J.; Roberts, P.A.; Lu, Z.; Wang, S.; Li, G. Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity (2012) 109 (1) 34-40. [DOI: 10.1038/hdy.2012.8]