Whole Genome Sequencing and Resequencing for Genome-Wide Study in Common Bean (Phaseolus vulgaris L.).

Common bean (Phaseolus vulgaris L.), also known as green bean or snap bean, is a herbaceous annual plant grown worldwide for its edible dry seed and green beans. The purpose of this research is to build a molecular breeding platform integrated into a classical breeding approach in common bean through whole-genome resequencing (WGR) platform. The objective of this study is to conduct genome-wide association study (GWAS) and identify SNP markers associated with important traits in common bean. 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. A total of 355 USDA common bean core germplasm accessions are used in the study. WGR is conducted using the Illumina HiSeq X Ten sequencing platform to create 6X sequencing depth of the genome coverage and 4 Gb sequencing data in each accession. The de novo genome assembly of common bean germplasm BAT93 is created; whole genome variations are analyzed; and GWAS are conducted for soybean cyst nematode (SCN) resistance, salt tolerance, drought tolerance, and morphological traits such as seed color, seedcoat color, seed size, and plant habit. Meanwhile, the SNP markers associated with these traits are identified. The research will provide a tool to use these SNP markers in common bean molecular breeding through marker-assisted selection (MAS) and genomic selection (GS).