Department of Biology, Washington University, St Louis, Missouri, USA.
Mol Biol Evol. 2011 Jan;28(1):659-71. doi: 10.1093/molbev/msq243. Epub 2010 Sep 9.
The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.
代谢途径的进化是进化变化中一个基本但尚未被充分理解的方面。理解途径进化复杂性的一种方法是研究共同构成一个综合代谢途径的基因的分子进化。水稻胚乳淀粉生物合成途径是植物中最全面描述的代谢途径之一，淀粉是一个在水稻驯化过程中受到强烈选择而进化的特征。在这项研究中，我们研究了水稻胚乳淀粉生物合成途径中的六个关键基因（AGPL2、AGPS2b、SSIIa、SBEIIb、GBSSI、ISA1），以研究这些基因在水稻驯化前后的进化情况。全基因组序列标记位点数据被用作中性参考，以克服在像水稻这样具有复杂人口历史的物种中检测选择的问题。我们采集了 Oryza sativa（aus、indica、热带粳稻、温带粳稻、芳香稻）及其野生祖先（O. rufipogon）的五个品种群。我们的结果表明，在 O. rufipogon 中，AGPL2 存在纯化选择的证据，在温带粳稻和热带粳稻品种以及芳香稻品种中，GBSSI 和 SBEIIb 存在强烈的正选择证据。所有其他基因在栽培稻及其野生祖先中都表现出与中性进化一致的模式。这些结果表明，在水稻驯化过程中，正选择在淀粉基因进化中起着重要作用。我们讨论了 SBEIIb 和 GBSSI 在水稻驯化过程中淀粉质量进化中的作用，以及使用全基因组数据作为中性参考检测选择的力量和局限性。
