Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites
Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites
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微卫星揭示油菜（Brassica napus L.）关联图谱的遗传结构和连锁不平衡模式
DOI：
10.1007/s00122-012-1843-5
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发表时间：
2012-08-01
影响因子：
5.4
通讯作者：
Liu, Kede
中科院分区：
文献类型：
--
作者：
Xiao, Yingjie;Cai, Dongfang;Liu, Kede
了解群体结构和连锁不平衡（LD）是在目标群体中进行复杂性状关联定位的前提。本研究利用451个单位点微卫星标记对来自世界各地的192个甘蓝型油菜自交系的遗传多样性、群体结构和LD程度进行了分析。通过模型分析，可将自交系分为P1和P2类群。在P1群的142个自交系中，126个系来自中国和日本，其余16个系来自欧洲、加拿大和澳大利亚。在P2组中，50条线路中有33条来自欧洲、加拿大和澳大利亚，其余17条线路来自中国。结构分析进一步将每组分为两个亚组。AMOVA、配对F（ST）和中性分析证实了组和亚组之间的差异。超过80%的近交系之间的成对亲缘关系估计值<0.05，表明在我们的面板中相对亲缘关系较弱。只有6%的连锁标记对显示LD，表明LD在该关联组中的水平较低。在基因组水平上，LD在0.5- 1cM内衰减，并且由于群体大小、遗传背景和遗传漂变，在每个组和亚组之间差异很大。群体结构和LD模式的表征将有助于对油菜复杂农艺性状进行关联研究。
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.