Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

Abstract

Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

QTL Analysis of Domestication Syndrome in Zombi Pea (Vigna vexillata), an Underutilized Legume Crop

“…In addition, Dachapak et al [4] reported that only 21.2% of 1,024 SSR markers screened in 6 accessions of V. vexillata from Asia, Africa, Australia and America were polymorphic. However, the percentage of amplifiable SSR markers in Marubodee et al [33] and Dachapak et al [4] (65.4% and 58.1%, respectively) was higher than in our study (36.6%). It is worth noting that almost all of the markers used by Marubodee et al [33] and Dachapak et al [4] were used in our study.…”

“…However, the percentage of amplifiable SSR markers in Marubodee et al [33] and Dachapak et al [4] (65.4% and 58.1%, respectively) was higher than in our study (36.6%). It is worth noting that almost all of the markers used by Marubodee et al [33] and Dachapak et al [4] were used in our study. Nonetheless, these results indicate moderate transferability but low polymorphism of SSR markers from other Vigna species in V. vexillata .…”

“…Although as high as 1,876 SSR primers pairs from various Vigna species were screened for polymorphism between the cultivated and wild parents, only 36.6% of them were amplifiable and only 10.7% of them were polymorphic. The low polymorphism of SSR markers was also observed in the mapping parents of V. vexillata used by Marubodee et al [33] in which only 6.2% of 1,336 SSR markers were polymorphic. In addition, Dachapak et al [4] reported that only 21.2% of 1,024 SSR markers screened in 6 accessions of V. vexillata from Asia, Africa, Australia and America were polymorphic.…”

“…RAD-tag sequences were extracted and bi-allelic RAD-markers were detected using Stacks ver. 1.30 [36] following the procedures described by Marubodee et al [33]. With the Stacks pipeline, the low quality sequences were filtered to obtain 51bp RAD-tag sequence reads, and classified the RAD-tags sequences into the parental accessions and F 2 individuals.…”

A rapid quantification method for tissue Na+ and K+ concentrations in salt-tolerant and susceptible accessions in Vigna vexillata (L.) A. Rich.

“…macrosperma Maréchal, Mascherpa & Stainier (JP235905: macro) were used in this study. V1 and V5 are known as salt-tolerant and susceptible accessions, respectively (Marubodee et al, 2015). All of the accessions were provided by the Genebank, National Agriculture and Food Research Organization, Tsukuba, Japan.…”