Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes.
Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes.
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拟南芥中全基因组的关联映射确定了先前已知的开花时间和病原体抗性基因。
DOI：
10.1371/journal.pgen.0010060
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发表时间：
2005-11
期刊：
影响因子：
4.5
通讯作者：
Nordborg M
中科院分区：
文献类型：
--
作者：
Aranzana MJ;Kim S;Zhao K;Bakker E;Horton M;Jakob K;Lister C;Molitor J;Shindo C;Tang C;Toomajian C;Traw B;Zheng H;Bergelson J;Dean C;Marjoram P;Nordborg M
目前，人们对利用全基因组关联作图来鉴定自然变异基因，特别是人类疾病易感性基因的可能性产生了极大的兴趣。模式植物拟南芥在许多方面是此类研究的理想候选者，因为它是高度自交的雌雄同体。因此，该物种在很大程度上是作为自然发生的近交系或加入物的集合而存在的，其可以被一次基因分型并重复表型。此外，在这样的物种中的连锁不平衡将比可比的异交物种广泛得多。我们在A.通过在95份全基因组多态性数据可用的样本中搜索与开花时间和病原体抗性的关联，对拟南芥进行了研究。尽管由于群体结构导致的假阳性率极高，但我们能够鉴定出所有测试表型的已知主基因，从而证明了A. thaliana和其他物种具有相似的变异模式。假阳性率在性状之间差异很大，更多的临床性状显示出最高的比率。然而，无论性状如何，假阳性率总是很大的，这突出了在关联研究中适当的基因组控制的必要性。目前有巨大的兴趣，使用关联映射来找到负责自然变异的基因，特别是人类疾病。在关联图谱中，研究人员试图确定基因组中表型相似的个体（例如，他们都患有相同的疾病）也异常密切相关的区域。一个潜在的严重问题是，如果群体的结构使得一个子组的成员往往更密切相关，则可能出现虚假相关。由于很少进行全基因组关联研究，因此尚不清楚这个问题在实践中有多重要。在迄今为止的第一个全基因组关联研究中，本文考虑了模式植物拟南芥。大量的虚假基因型-表型相关被发现，特别是在地理上不同的性状。例如，来自北方纬度的植物开花较晚;然而，除了共享使其开花较晚的遗传变异外，它们还倾向于在整个基因组中共享变异，因此难以确定哪些基因负责开花。尽管如此，在这项研究中成功鉴定了几个先前已知的基因，研究人员对该物种的关联图谱前景持乐观态度。
There is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. The model plant Arabidopsis thaliana is in many ways an ideal candidate for such studies, because it is a highly selfing hermaphrodite. As a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. Furthermore, linkage disequilibrium in such a species will be much more extensive than in a comparable outcrossing species. We tested the feasibility of genome-wide association mapping in A. thaliana by searching for associations with flowering time and pathogen resistance in a sample of 95 accessions for which genome-wide polymorphism data were available. In spite of an extremely high rate of false positives due to population structure, we were able to identify known major genes for all phenotypes tested, thus demonstrating the potential of genome-wide association mapping in A. thaliana and other species with similar patterns of variation. The rate of false positives differed strongly between traits, with more clinal traits showing the highest rate. However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies. There is currently tremendous interest in using association mapping to find the genes responsible for natural variation, particularly for human disease. In association mapping, researchers seek to identify regions of the genome where individuals that are phenotypically similar (for example, they all have the same disease) are also unusually closely related. A potentially serious problem is that spurious correlations may arise if the population is structured so that members of a subgroup tend to be much more closely related. Because few genome-wide association studies have been carried out, it is not yet known how important this problem will be in practice. In one of the first genome-wide association studies to date, this paper considers the model plant Arabidopsis thaliana. A very large number of spurious genotype–phenotype correlations are found, especially for traits that vary geographically. For example, plants from northern latitudes flower later; however, in addition to sharing genetic variants that make them flower late, they also tend to share variants across the genome, making it difficult to determine which genes are responsible for flowering. This notwithstanding, several previously known genes were successfully identified in this study, and the researchers are optimistic about the prospects for association mapping in this species.
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影响因子：
1.8
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Chapman, JM;Cooper, JD;Clayton, DG
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Clayton, DG
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