Recombination and linkage disequilibrium in Arabidopsis thaliana
Recombination and linkage disequilibrium in Arabidopsis thaliana
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DOI：
10.1038/ng2115
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发表时间：
2007-09-01
期刊：
影响因子：
30.8
通讯作者：
Nordborg, Magnus
中科院分区：
文献类型：
--
作者：
Kim, Sung;Plagnol, Vincent;Nordborg, Magnus
连锁不平衡（LD）是自然群体遗传变异组织的一个重要方面。在这里，我们使用341，602个非单基因SNPs描述了19个拟南芥种质中LD的全基因组模式. LD平均在10 kb内衰减，比以前估计的要快得多。标签SNP选择算法和“隐藏SNP”模拟表明，全基因组关联作图将只需要观察到的SNP的40% - 50%，这一减少与非洲裔美国人样本中的估计相似.基于这些结果，设计了包含250，000个SNP的Affymbox基因分型阵列;我们证明它应该具有足够的覆盖范围用于全基因组关联作图。LD的程度是高度可变的，我们发现重组热点，这似乎优先发生在基因间区域的明确证据。LD也反映了选择的作用，并且非同义多态性之间的LD比同义多态性之间的LD更广泛。
Linkage disequilibrium ( LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome- wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non- singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and ' hide- the- SNP' simulations suggest that genome- wide association mapping will require only 40% - 50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome- wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms.