Development of SSR and SNP Markers and Association Mapping of Morphological Traits in Cowpea [Vigna unguiculata (L.) Walp.]

Cowpea [Vigna unguiculata (L.) Walp.] (2n=2x=22) is a major crop cultivated in the tropics and sub-tropics areas including Asia, Southern Europe, Africa, southern USA, and Central and South America. It is used for human food, animal fodder, or as a cover crop. Molecular marker development is an essential part of quantitative trait loci (QTL) identification, map-based cloning, genetic diversity assessment, association mapping, and applied breeding in marker-assisted selection (MAS) schemes. Molecular markers such as EST-SSR and EST-SNP markers have advantages because they are a component of expressed genes. In this study, 187,487 expressed sequence tag (EST) sequences were downloaded from GenBank; 4,572 contigs and 2,697 singlets were created by CAP3. A total of 7,878 EST-SSRs were identified with di-, tri-, tetra-, penta-, and hexa-nucleotide repeats of 6 to 35, 4 to 29, 3 to 7, 3 to 7, and 3 to 6, respectively, using SSRLoator. Also, 7,588 SNPs were postulated among the 3,389 contigs by DNASTAR Lasergene Genomics Suite. Genome-wide SNPs were discovered through genotyping by sequencing (GBS) in 800 cowpea genotypes. SNP markers associated with morphological traits including dry pod color, pod placement, mature seed pattern and color, seed coat color, flower color, and leaf shape were identified through association mapping approaches and will be used in cowpea breeding to select morphological traits through MAS.