水稻赤霉素代谢途径的适应性进化

Adaptive evolution of metabolic pathways is very important to understanding the molecular mechanism of phenotypic differentiation between species, which is a key to the fundamental problem of biological evolution on phenotypic diversification and adaptation. Nowadays, the background of Gibberellin metabolic pathway in rice is very clear in that all 18 genes of the pathway have been mapped to the rice genome. Therefore, in this project, we plan to study the adaptive evolution of Gibberellin metabolic pathway with two different systems in rice. One is a domestication system under artificial selection, comprising Asian cultivated rice subspecies Oryza sativa L. ssp. japonica and its wild progenitor species O. rufipogon occurring in China. The other one is a differentiation system between plant species under natural selection, consisting of the wild rice O. nivara and O. rufipogon that have sympatric distributions in Southeast and South Asian.160 individual samples are collected to represent the two systems. All the 18 genes' sequences of Gibberellin metabolic pathway for all samples are obtained by either assembling with the Next-generation sequencing data or directly Sanger sequencing. Using these genes' sequences, we plan to analyze the pattern of population genetic variation, including nucleotide diversity, genetic differentiation, neutral test, gene flow and simulation of population evolution history, for detecting the signals of adaptive variation in the pathway. To verify the signals, we intend to conduct the RT-PCR experiment and measure the production of bioactive Gibberellin for determining the distribution of adaptive variation in the pathway. Finally, we plan to compare the distributional patterns of adaptive variation in Gibberellin metabolic pathway between the domestication system and the differentiation system for understanding the mechanism of adaptive evolution in plant metabolic pathway.

研究植物代谢途径的适应性进化,对理解植物物种的适应分化这一基本的进化生物学问题具有重要的理论意义。本项目选择亚洲栽培水稻亚种Oryza sativa L. ssp. japonica和中国分布的野生祖先种O. rufipogon，以及在东南亚和南亚同域物种分化的野生水稻O. nivara和O. rufipogon为研究材料, 通过分析赤霉素代谢途径基因的群体遗传变异，检测适应性变异发生的信号，并从基因表达水平和活性赤霉素产量方面，揭示适应性变异的功能意义，阐明适应性变异在代谢途径上的分布。并通过对比自然选择和人工选择两种体系下赤霉素代谢途径适应性变异的分布式样，揭示水稻代谢途径适应性进化的分子机制。

理解代谢途径的进化机制，对解释进化生物学基本的表型分化与适应的问题具有重要意义。本研究以水稻粳稻亚种Oryza sativa L. ssp. japonica与产自中国的野生祖先种O. rufipogon和东南亚南亚的野生稻O. nivara与O.rufipogon 为研究材料，以赤霉素代谢途径为研究对象，从代谢途径基因的序列变异、表达式样和活性赤霉素含量三个方面入手，开展赤霉素代谢途径的适应性进化研究。.首先，本研究利用重测序数据，获得所有21个赤霉素代谢途径基因的序列，进行群体遗传分析。结果表明，相比野生祖先种，粳稻中有9个基因的遗传多样性降低的比例显著偏离瓶颈效应，表明这9个基因在驯化过程中受到了强烈的人工选择作用。在这些基因编码的酶中，1个作用于代谢途径第一步，1个直接催化核心产物，其余7个作用于代谢途径下游重要分支点上，并且作用于下游分支点的基因在粳稻与野生祖先种之间遗传分化程度更高，表明分支点的基因受到了更强的选择。中性检测表明，在O. nivara与O.rufipogon群体中，偏离中性的3个基因也位于下游分支点上。其次，我们利用qPCR检测参与赤霉素代谢途径的基因在幼苗、拔节和孕穗期的表达量，发现在幼苗和拔节期，在序列上检测到人工选择信号的基因在粳稻中表达量显著下调，且绝大部分基因在粳稻中的表达量低于野生种；但在孕穗期，在粳稻中表达量高于野生种。最后，通过测定活性赤霉素GA1、GA3、GA4和GA7的含量，发现无论在拔节期还是孕穗期，野生祖先种中GA1含量占比较高，而粳稻中GA4含量占比较高。由于GA1与GA4分别是不同分支途径的产物，该结果支持选择作用于代谢通量的分配，这与影响植物体内GA1和GA4含量分配的分支点基因在序列和表达水平的变异相一致。.综上所述，水稻进化过程中，选择主要作用于赤霉素代谢途径中代谢通量的分配，即对代谢通量分配影响最大的下游分支点上基因是选择的主要目标，其次作用在代谢途径的第一步和产生核心产物的环节。本项目的研究结果对不仅对理解代谢途径的进化机制，进而解释物种表型和功能的适应性分化具有重要的理论意义，而且对作物的遗传改良也有一定的理论指导意义。