Linkage disequilibrium in wild and cultured populations of Pacific oyster (Crassostrea gigas)
Linkage disequilibrium in wild and cultured populations of Pacific oyster (Crassostrea gigas)
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DOI：
10.1007/s11802-016-2832-0
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发表时间：
2016-02
影响因子：
1.6
通讯作者：
Xiang Guo;Qi Li;L. Kong;Hong Yu
中科院分区：
文献类型：
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作者：
Xiang Guo;Qi Li;L. Kong;Hong Yu
连锁不平衡（LD）可以通过关联作图来定位经济重要性状变异的实际基因。关联研究的可行性和有效性在很大程度上取决于LD的程度，LD决定了研究人群中标记的数量和密度，以及关联分析的实验设计。在这项研究中，我们首先描述了野生种群和养殖的大量选择的太平洋牡蛎（长牡蛎）的LD程度。利用53颗微卫星分别对88个野生个体和96个培养个体的全基因组LD水平进行了测定。对于同型标记对，在野生种群中未观察到显著的相关性；然而，在培养群体中出现了3个显著关联，且显著LD延伸至12.7 cM，表明强人工选择是培养群体全基因组LD大幅增加的关键力量。野生种群与养殖种群的遗传密度差异表明，通过选择关联作图种群，可以在合理的标记密度下以较低的成本完成太平洋牡蛎的关联研究。此外，非同型位点和稀有等位基因之间频繁发生的遗传变异，也鼓励了在牡蛎基因定位时联合应用连锁分析和遗传变异定位。研究结果对今后牡蛎群体连锁不平衡的定位有重要意义。
Linkage disequilibrium (LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping. The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population, as well as the experimental design for an association analysis. In this study, we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster (Crassostrea gigas). A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites, respectively. For syntenic marker pairs, no significant association was observed in the wild population; however, three significant associations occurred in the cultured population, and the significant LD extended up to 12.7 cM, indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population. The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population. Furthermore, the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster. The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.