2017 ASHS Annual Conference

This purpose of this research is to build a molecular breeding platform integrated into a classical breeding approach in cowpea through whole-genome sequencing (WGS) and whole-genome resequencing (WGR) technology. With improved next generation sequencing (NGS) and the decreasing cost of sequencing, it is becoming feasible to discover millions of SNPs for any plant and to connect these markers to desirable phenotypic traits. So far, three levels of genome sequencing have been conducting in cowpea: (1) WGS using 10X Genomics Chromium System powered by 10X GemCode Technology combined with the Illumina HiSeq X Ten sequencing platform with 100X sequencing depth and 200X sequencing data in one cowpea genotype AR08-393; (2) WGR using the Illumina HiSeq X Ten sequencing platform with 5X sequencing depth and 3.5 Gb sequencing data in 300 cowpea genotypes; and (3) genotyping by sequencing (GBS) using Illumina HiSeq series sequencing platform with 0.1-0.3X depth and 100 – 200 Mb data in 720 cowpea genotypes. The de novo genome assembly of cowpea AR08-393 was created; whole genome variations were analyzed; and genome-wide association study (GWAS) was conducted for cowpea bacterial blight resistance, cowpea aphid tolerance, cowpea mosaic virus resistance, 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).