Whole Genome Sequencing and Resequencing for Genome-Wide Study in Cowpea

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) platform. 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 collaborated with Novogene.com: (1) WGS using 10X Genomics Chromium System powered by 10X GemCode Technology combined 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 each in 230 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 each in 720 cowpea genotypes. Right now, genetic diversity was analyzed in world-wide cowpea germplasm and association analysis was conducted for resistance to cowpea bacterial blight, cowpea aphid, and cowpea mosaic virus, and the seed antioxidant content, and SNP markers were identified to be associated with these traits. It is expected that a de novo genome assembly will be created; whole genome variation and gene call will be analyzed; and genome-wide association study will be conducted for seed protein and sugar contents, salt tolerance, and morphological traits such as seed color, seedcoat color, seed size, and plant habit.