Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites

Understanding the population structure and linkage disequilibrium (LD) is a prerequisite for association mapping of complex traits in a target population. In this study, we assessed the genetic diversity, population structure and the extent of LD in a panel of 192 inbred lines of Brassica napus from all over the world using 451 single-locus microsatellite markers. The inbred lines could be divided into P1 and P2 groups by a model-based population structure analysis. Out of the 142 inbred lines in the P1 group, 126 lines were from China and Japan, and the remaining 16 lines were from Europe, Canada and Australia. In the P2 group, 33 out of the 50 lines were from Europe, Canada, and Australia, and the remaining 17 lines were from China. Structure analysis further divided each group into two subgroups. AMOVA, pairwise F (ST) and neutrality analyses confirmed the differentiation between groups and subgroups. More than 80 % of the pairwise kinship estimates between inbred lines were <0.05, indicating that relative kinship is weak in our panel. Only 6 % linked marker pairs showed LD, suggesting the low level of LD in this association panel. The LD decayed within 0.5-1 cM at the genome level, and varied considerably across each group and subgroup, due to the population size, genetic background and genetic drift. The characterization of the population structure and LD patterns would be useful for performing association studies for complex agronomic traits in rapeseed.