Construction of a genetic linkage map and QTL analysis using a recombinant inbred population derived from an intersubspecific cross of cowpea (Vigna unguiculata (L.) Walp.)

Cowpea (Vigna unguiculata (L.) Walp,) is an important grain legume crop commonly grown and consumed in many parts of the tropics and subtropics. A genetic linkage map of cowpea was constructed using randomly amplified polymorphic DNA (RAPD) markers and a recombinant inbred (RI) population derived from the intersubspecific cross between IT84S-2246-4, an improved cowpea line, and TVNu 110-3A (Vigna unguiculata spp, dekindtiana var. pubescens), The map spanned 669.8 centiMorgans (cM) of the genome and comprised 80 mapped loci (77 RAPD and 3 morphological loci) assembled into 12 linkage groups. The 12 linkage groups ranged in size from 14.0 to 175.4 cM, The distribution of interval sizes between adjacent markers on the cowpea map ranged from 0.7 to 26.7 cM with an average distance of 9.9 cM, Random amplified polymorphic DNA marker loci exhibiting distorted segregation ratios were detected. The linkage map was used to locate quantitative trait loci (QTLs) for days to flowering, days to maturity, pod length, seed/pod weight percent, leaf length, leaf width, primary leaf length, primary leaf width, and the derived traits: leaf area and primary leaf area in the RI population, Significant (p<0.01) quantitative trait locus (QTL) associations of marker loci were identified for each trait. A total of 88 significant marker locus-trait associations were identified in all the linkage groups. Six markers with effects on these traits are yet unlinked. Both parental types contributed alleles with positive effects on these traits. The percentage of phenotypic variation associated with individual markers ranged from 6.6 to 16.9 %, Several regions of the genome affected more than one trait. The coincident map locations of many QTLs for more than one trait corroborate the strong correlations observed between these traits.