Linkage Disequilibrium in a Diverse Panel of Phaseolus vulgaris Considering Population Structure and Kinship Information

Common bean (P. vulgaris) is an important grain legume for direct human consumption. Recently, GWAS have been performed for the species aiming to identify loci related to important quantitative traits. For association genetics, the extent to which measures of linkage disequilibrium (LD) reflect the true association between a marker and QTL is an issue of great interest. In this study, we used r² to estimate LD and r² extensions that correct bias due to population structure (r²s), kinship (r²k) and both (r²ks). A set of 180 genotypes, including inbred lines from different breeding programs, was genotyped by sequencing and 10,362 high quality SNPs were obtained. Intra and inter-chromosomal LD was estimated by an optimized version of 'LD.Measure' in the R package 'LDcorSV'. Considering r², we were able to identify high LD (over 0.7) between SNPs localized at opposite ends of the chromosomes. Considering r²ks, LD decayed to 0.1 at an average distance of 155 kb. Different LD patterns were observed for each chromosome, illustrating their particularities. Interestingly, some inter-chromosomal LD was found, possibly due to selection of epistatic loci during the breeding process. This is the first r²ks SNP-based LD analysis performed for P. vulgaris and it can lead to better understanding of the genomic structure of the species.