Genome-Wide Association Study (GWAS) in Cowpea.

Cowpea (Vigna unguiculata L. Walp.) (2n=2x=22) is an important annual legume grown worldwide, especially in Africa. The purpose of this research is to build a molecular breeding platform integrated into a classical breeding approach in cowpea through whole-genome sequencing (WGS), whole-genome resequencing (WGR), and genotyping by sequencing (GBS) platform. So far, WGS is conducted in one cowpea genotype AR08-393 using HiSeq X Ten, 10X Genomics Chromium System and PacBio Sequel System; WGR in 300 cowpea genotypes using the Illumina HiSeq X Ten with 5X sequencing coverage; and GBS using Illumina HiSeq series sequencing platform with 0.1-0.3X depth in 768 cowpea genotypes. Genome-wide association studies (GWAS) are conducted in cowpea using the SNPs discovered from DNA sequencing by WGS, WGR, and GBS. GWAS was conducted for cowpea mosaic virus (CPMV) resistance, bacterial blight (Xanthomonas axonopodis pv. vignicola) resistance, cowpea aphid tolerance, iron deficiency chlorosis (IDC) tolerance, low phosphorus efficiency, salt tolerance, seed protein content, seed antioxidant content, and morphological traits such as seed color, seedcoat color, seed size, and plant habit. Meanwhile, the SNP markers associated with these traits were identified. The research will provide a tool to use these SNP markers in cowpea molecular breeding through marker-assisted selection (MAS) and genomic selection (GS).