双季稻田内早、晚季杂草稻群体之间的同域遗传分化及分子基础

Weedy rice occurs in rice fields all over the world. It becomes one of the most noxious weeds in rice fields because of its abundant genetic variation and strong competitiveness and invasiveness. Therefore, weedy rice poses severe threats to the sustainable rice production. To reveal the origin and maintenance of genetic diversity in weedy rice is important for understanding the mechanisms of its infestation and damage to cultivated rice. Our previous studies indicated substantial genetic divergence between weedy rice populations that occurred in the same fields with early-season and late-season cultivated rice varieties, promoting the overall genetic diversity of weedy rice. To explore the underlying mechanisms of the sympatric genetic divergence and maintenance of the divergence between the early-season and late-season weedy rice populations, we attempted to undertake the following research activities: (1) to identify the divergence of key phenotypic traits and the ecological influences between the sympatric early-season and late-season weedy rice populations through a common-garden experiment; (2) to determine the molecular bases of sympatric genetic divergence and to identify functional genes related to the sympatric divergence through sequencing and analyses of total genomic DNA sequences between the typical early-season and late-season weedy rice individuals; (3) to confirm the functional genes that are responsible for the sympatric genetic divergence between the early-season and late-season weedy rice populations by gene expression analyses. Results from these studies will not only facilitate the revealing of the underlying mechanisms for the sympatric genetic divergence between the two seasons’ weedy rice populations, and the design of effective strategies for weedy rice control, but also provide a model system for studying the driving forces of divergent evolution adapting to different environments in plants.

杂草稻广布于全球水稻种植区，因其遗传变异丰富、生存竞争和扩散能力强，已成为世界稻田恶性杂草，严重威胁水稻生产。揭示杂草稻遗传变异的形成和维持机制，对掌握其发生规律和有效防治极为重要。本项目组前期研究发现，在同一稻田中，分别伴生于早、晚稻的两季杂草稻群体之间产生了明显遗传分化，导致杂草稻的总体遗传多样性增加。为探索早、晚两季杂草稻群体之间的同域遗传分化及维持机制，拟开展如下研究：1）通过同质园实验，鉴定早、晚两季杂草稻群体之间的表型差异及相关生态因子；2）对典型的早、晚季杂草稻实验群体进行全基因组测序及序列分析，揭示同域遗传分化的分子基础并挖掘相关功能基因；3）对可能影响遗传分化的关键功能基因进行表达分析，确认其在实验群体中的表达差异。上述研究结果不仅有助于阐明不同生长季节杂草稻群体产生同域遗传分化的机制，有益于制定杂草稻防治策略，也为研究植物适应环境产生同域物种趋异进化提供了一种模式体系。

生态物种形成是进化生物学的重要理念和物种形成研究最活跃的领域。在生态物种形成的初期有两个重要过程：异域遗传分化和同域遗传分化。前者实例众多广为接受，后者缺乏足够的实例而饱受争议。利用发生在同一稻田但不同水稻种植季节的杂草稻群体，来研究植物同域遗传分化及维持机制意义重大。本项目通过同质园实验，分析了早、晚季杂草稻群体之间的表型差异及相关生态因子，对早、晚季杂草稻群体进行全基因组DNA测序及序列分析，通过转录组分析挖掘可能影响遗传分化的关键功能基因，获得了以下重要结果：（1）早、晚季稻田中的杂草稻群体之间由于基因流受限，导致在全基因组某些区域产生了显著的遗传分化和群体间不同遗传组成的形成，而且早、晚季稻田中的杂草稻由于受不同生态因子（如温度和光周期变化）的选择，加之基因流受限，最终造成了群体间的同域遗传分化。（2）同质园种植实验表明，来自于早季和晚季的杂草稻群体，分别在不同水稻种植季节进行种植，表现出了明显的表型形状差异，特别是在种子萌发能力、分蘖数、株高、开花时期和结实率等形状方面，早季和晚季的杂草稻群体都表现显著的差异，表明杂草稻分别适应于早季和晚季的生长环境，也产生了形态上的分化，这一结果与基因组测序分析结果一致。（3）早季与晚季稻田中的典型杂草稻群体，不同生长阶段（种子萌发后后35天和70天）的植株，在转录组层面发生了明显的分化，表现出不同数量的差异表达基因，并与早晚季群体的分化相关，特别是控制开花时间和防御响应（如抗病、抗逆）相关基因的差异表达，可能是促进同域杂草稻群体分化的主要原因。（4）发现了早、晚季杂草稻群体的种子可以由于埋土的诱导，产生二次休眠性，而且早、晚季杂草稻种子的二次休眠程度也有一定的分化，并与种子中的激素水平变化和表观遗传修饰有一定的关联。上述结果为阐明植物同域遗传分化及其分子机制提供了强烈的证据，同时也为制定有效的杂草稻防治措施提供了方法。