Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS One. 2009 Dec 9;4(12):e8227. doi: 10.1371/journal.pone.0008227.
Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance.
As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes.
Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered.
大规模的玉米基因组筛选鉴定出 48 个基因，这些基因显示了玉米驯化或改良过程中人为选择的潜在特征。这些候选选择基因可能作为控制玉米与其祖先大刍草之间表型差异的数量性状位点（QTL）。候选选择基因似乎比随机预期更接近驯化 QTL 在基因组中的位置。
作为定义这些基因控制的性状的一步，我们对 32 个候选选择基因中的 32 个加上另外三个候选选择基因在大刍草中进行了表型-基因型关联作图。我们的分析检测了 32 个表型性状，其中许多在玉米驯化或改良过程中发生了改变。我们观察到候选选择基因中的 SNP 与大刍草中性状变异之间存在几个显著关联。其中包括两个关联超过了 Bonferroni 校正，五个实例中一个基因与我们两个关联作图面板中相同性状显著相关。尽管存在这些显著关联，但作为一个整体，候选选择基因的表现并不优于随机选择的基因。
我们的结果表明，关联分析有助于识别候选选择基因控制下的性状。事实上，我们为几个候选选择基因提供了新功能的证据。然而，在当前的候选选择基因集和我们的关联作图策略下，我们总体上发现的显著关联非常少，并不比随机选择的基因多。我们讨论了未发现大量显著基因型-表型关联的可能原因。
