SSR and GBS based GWAS study for identification of QTLs associated with nutritional elemental in common bean (Phaseolus vulgaris L.)

Common bean is one of the important staple food legumes, and is a potential source of minerals with high content of P, K, B and S and is being targeted for nutritional improvement to overcome mineral malnutrition and hidden hunger problem globally. In the present study, we used Genome Wide Association approach (GWAS) for P, K, B and S using a core set of 96 genotypes of common bean representing landrace diversity of Western Himalayas. Significant variation in mineral content among the genotypes was observed and an inventory of nutrients for the available germplasm was established. Four genotypes (R9, WB1680, WB923 and N13) were found with highest content of P, K, B and S respectively. Moreover, we also categorized germplasm in 10 highest and lowest genotypes for utilization in breeding program. Further, the germplasm was genotyped using SSR's and SNP's (genotyping by sequencing; GBS) for studying genetic diversity and population structure. 22 SSRs selected from the linkage map that were distributed on 11 chromosomes of common bean were used. Moreover, GBS approach was also used for dense genome wide marker coverage. Based on SSRs, germplasm was divided into 2 subpopulations whereas SNPs divided the germplasm into 5 subpopulations. GWAS was also done for both the markers systems. Our study concluded with the establishment of nutrient inventory in the available germplasm and identification of 9 significant SSR markers and 35 significant SNP markers associated with these traits, out of which 4 SSR markers were located on chromosome 2 and 7. Most of the SNP markers were located on chromosome 10 which suggest that maximum genes responsible for nutrient accumulation might be present on chromosome 10 of common bean. Further 58 candidate genes near to the vicinity of significant SNPs were identified. The significant markers associated with the traits of interest after validation can prove an asset for plant breeders to enhance the nutrient status (biofortification) of common bean which can help in tackling the malnutrition and can solve the hunger related problems majorly in the developing countries as it forms the cheap but widely used energy source in these countries.