National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
BMC Evol Biol. 2010 Apr 23;10:108. doi: 10.1186/1471-2148-10-108.
Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection.
Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process.
How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.
各种进化模型被提出以解释同源基因的命运，这些模型为进化选择提供了作用的底物。特别是驯化作为一种特殊的选择，在作物栽培中发挥了重要作用，导致许多控制重要农艺性状的基因发生分歧。最近的研究表明，一对同源基因通常会从其祖先功能中发生亚功能化。我们之前证明，在籽粒灌浆过程中起重要作用的水稻细胞壁转化酶（CWI）基因 GIF1 很可能在启动子区域受到了驯化选择。在这里，我们报告说，GIF1 和另一个 CWI 基因 OsCIN1 通过独立选择构成一对具有分化表达和功能的同源基因对。
通过共线性分析，我们表明 GIF1 和另一个细胞壁转化酶基因 OsCIN1 是源自禾本科基因组加倍过程中发生的片段重复的同源基因。基于对 25 个栽培品种和 25 个野生稻序列的群体遗传学和基因系统发育树分析的结果表明，与在启动子区域受到选择的 GIF1 不同，OsCIN1 在水稻驯化过程中也受到了人工选择，其编码区发生了固定突变。GIF1 和 OsCIN1 已经进化出不同的表达模式和可能不同的酶动力学参数，后者表现出较低的酶活性。过表达 GIF1 和 OsCIN1 也导致了不同的表型，表明 OsCIN1 可能调节其他未被识别的生物学过程。
基因复制和分歧如何导致遗传新颖性和形态适应性一直是遗传学家和生物学家感兴趣的问题。我们发现，复制对 GIF1 和 OsCIN1 经历了亚功能化，这意味着选择可以独立作用于每个副本，使其朝着不同的功能特异性进化，这为模型作物中遗传新颖性的进化提供了一个生动的例子。我们的结果也进一步支持了已建立的假设，即基因复制和亚功能化可能是遗传适应冲突的一种解决方案。
