Development of SNP-based high-density genetic map and gene mapping of pod colour trait in Cowpea (Vigna unguiculata L. Walp.)

Abstract

ABSTRACT The colour of fresh pods is one of the most important traits that affects the commercial value of cowpea (Vigna unguiculata) beans. To investigate the genetic architecture, we firstly scored the fresh pod colour of cowpea for six generations in field trials. Afterwards, an F2 population of 150 recombinant individuals was derived from crosses between two high-generation inbred cowpea lines, ‘Baojia’ (green pod colour, P1) and ‘Qilong’ (purple pod colour, P2). Ahigh-density genetic map based on 9,493 single nucleotide polymorphisms was constructed through SLAF sequencing and used for gene/s mapping of pod colour trait. We observed 59 single nucleotide polymorphism markers in one candidate gene region that may be associated with fresh pod colour trait located on LG6. The locus of pc was confirmed on chromosome 5 of the cowpea genome, which was corresponded to the genes encoding anthocyanin 5-aromatic acyltransferase and MYB-90 and MYB-114 domain proteins, that play important roles in the anthocyanin biosynthesis. Lastly, dCAPS markers were developed that explained the high rate of identification for the phenotypes of the F2 population. This study provides new knowledge of the genomic regions and will accelerate the genetic improvements, regarding the fresh pod colour (pc) trait in cowpea and marker-assisted selection.