Chapman Mark A, Pashley Catherine H, Wenzler Jessica, Hvala John, Tang Shunxue, Knapp Steven J, Burke John M
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
Plant Cell. 2008 Nov;20(11):2931-45. doi: 10.1105/tpc.108.059808. Epub 2008 Nov 18.
Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution.
基因组选择扫描是识别表型转变潜在基因的有用工具。在本文中，我们描述了一项基因组扫描的结果，该扫描旨在识别栽培向日葵进化过程中受选择作用的目标基因的候选基因。这项工作涉及在大量野生、原始（即地方品种）和改良向日葵（向日葵）品系中筛选492个源自EST的位点。这种抽样策略使我们能够识别具有选择性重要性的基因的候选基因，并研究选择的可能时间。基于多种标准，36个基因在驯化或改良过程中显示出选择的证据，对这些位点的一个子集进行的基于序列的选择测试证实了这一结果。鉴于对向日葵基因组连锁不平衡结构的了解，这些基因本身可能就是选择的目标，而不仅仅是与实际目标连锁。虽然选择候选基因显示出广泛的推定功能，但它们在参与氨基酸合成和蛋白质分解代谢的基因中富集。鉴于在玉米（玉米）中也检测到了类似的模式，这一发现表明对氨基酸组成的选择可能是作物植物进化的一个普遍特征。就基因组位置而言，选择候选基因在导致野生和栽培向日葵表型差异的数量性状位点（QTL）附近显著聚集，QTL共定位的具体实例为这些基因在向日葵进化过程中可能发挥的作用提供了一些线索。
