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 'standard vegetable' type (subgroup SV) and the 'nonstandard 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 (E5 cM) five times longer than the shortest (E1 cM). Partitioning of LD variance into withinand between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 11 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.

QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits

“…These include a denser consensus genetic map of cowpea [6,7], a unigene data reservoir consisting of tens of thousands of transcript assemblies [6], and a genome wide association study (GWAS) panel for asparagus bean [5]. At present, a work toward verification/more precisely mapping of QTLs for pod related traits by GWAS is now underway in our lab.…”

“…unguiculata ), forms the two main divisions of cultivated cowpea [3]. Due to selection towards traits favorable for vegetable use, the present day asparagus bean differs a lot from African cowpea in many aspects including plant architecture (climbing versus erect), growth habit (indeterminate versus determinate), pod length and pod fiber content [4,5]. …”

Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp)

“…sesquipedialis (Fang et al ., ; Timko et al ., ). This theory has been partially validated by the lower genetic diversity in Chinese asparagus bean germplasm compared to African common cowpea through SSR and SNP marker analyses (Xu et al ., , ). However, evidence that selection for pod characteristics, particularly pod length, has contributed essentially to the formation of present‐day asparagus bean is lacking.…”

Association Mapping for Fusarium Wilt Resistance in Chinese Asparagus Bean Germplasm

“…No reports on genetic mapping of FW resistance are publically available for asparagus bean thus far, primarily due to the lack of genomic resources for this subspecies. Recently, an AM panel comprising 95 asparagus bean and four common cowpea accessions each genotyped with 1127 SNP markers were available (Xu et al, 2012), providing the first opportunity to pinpoint genetic loci related to FW resistance based on marker–trait associations. The marker–trait AM or linkage disequilibrium (LD) mapping is a method of mapping QTLs through the detection of LD between marker loci and targeted genes.…”