Abstract
Understanding the population structure and linkage disequilibrium (LD) is a prerequisite for association map** 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.
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Acknowledgments
We thank Prof. Jianbing Yan at Huazhong Agricultural University for his critical review of this manuscript, and sincerely thank Mayank Gautam for his critical reading of the manuscript. The research was supported by the National Natural Science Foundation of China (No. 31071452) and the Doctoral Fund of Ministry of Education of China (No. 20100146110019).
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122_2012_1843_MOESM1_ESM.ppt
Supplemental Fig. 1 Estimation of LnP(D) and Δk in the total panel and inferred groups. a) the total panel; b) the P1 group; c) the P2 group. The blue and red curves represent LnP(D) and Δk, respectively. The bar indicates standard deviation. Supplementary material 1 (PPT 161 kb)
122_2012_1843_MOESM2_ESM.ppt
Supplemental Fig. 2 The PCA analysis on the different populations. a) the total panel; b) the P1 group; c) the P2 group. Colored points represent inbred lines belonging to different groups and subgroups. Supplementary material 2 (PPT 172 kb)
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Supplemental Fig. 3 Unrooted Neigbour-Joining tree of 192 inbred lines. Colored lines correspond to assignments to different model-based subgroups. Supplementary material 3 (PPT 219 kb)
122_2012_1843_MOESM4_ESM.ppt
Supplemental Fig. 4 LD decays (r 2) in the inferred groups and subgroups. The r 2 value for markers with genetic distance of 0 cM is defined as 1. The dots are mean r 2 values for marker genetic intervals of 0 cM, 0-0.5 cM, 0.5-1 cM, 1-2 cM, 2-5 cM, 5-10 cM, 10-50 cM, 50-100 cM and 100-200 cM, respectively. The curves were drawn using the nonlinear regression model. G4 subgroup was not included in the analysis due to its small population size. Supplementary material 4 (PPT 147 kb)
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DOI: https://doi.org/10.1007/s00122-012-1843-5