Genetic Relationships and Their Effects on the Linkage Disequilibrium in Soybean Germplasm

Soybean is the Brazilian crop which has presented the highest increase in the last decades. This increase is a result of the enhancing of the crop yield, provided by technology progress associated with breeding. Recently, with association mapping strategy, the process of genes identification has become more accessible and it is one of the most promising tools for plant breeding. Thus, linkage disequilibrium studies and population structure are extremely important to obtain the best results in the association mapping, due to their effects in false - positive numbers in the analysis. In this study, the genetic relationships and linkage disequilibrium (LD) were evaluated in a set of 95 worldwide soybean accessions using Axiom Soybean Genotyping Array. The population structure was analyzed bases on DAPC approach implemented in adegenet R package. For the linkage disequilibrium analysis, we used the LDcorSV R package and the usual measure (r2) was used, and compared with others that correct for population structure and relatedness (r2, r2s, r2k, and r2ks). DL analysis considering r2 has revealed mediums and lows LD (0.2-0.5). However, when r2s e r2k e r2ks were used, we verified that pairs of markers with low DL were eliminated. Besides, considering r2ks LD decayed to 0.1 at an average distance of 255Kb. Therefore, these results have highlighted the influence of the structure of the population and kinship about the DL patterns. Also, it has provided us a better understanding of the structure genome of the species and phenomena which took place in each chromosome.