落粒基因序列和微卫星指纹揭示的杂草稻起源及分子进化

Weedy rice is one of the most noxious weeds in rice fields and has severely affected sustainable rice production. The effective control of weedy rice is important for rice production. The abundant genetic diversity of weedy rice promotes its successful invasion to a rice field, causing significant yield losses of cultivated rice. The formation and maintenance of such diversity are intimately associated with the origin and evolution of weedy rice. Our previous research indicated that the complicated pathway of weedy rice origin can be divided as: the "wild origin" that involves wild rice species; and the "cultivar origin" that only involves cultivated rice. The project will focus on the DNA sequence polymorphisms of the genes encoding seed shattering traits (Sh4 and qsh1), as well as microsatellite polymorphisms to conduct the following researches: 1) to compare the sequence polymorphisms of the Sh4 and qsh1 genes and their flanking regions in a large sample set including weedy rice, wild rice and cultivated rice from wide sources to reveal the origin of weedy rice; 2) to determine genetic structure and affinity of weedy rice in comparison with wild rice and cultivated rice based on microsatellite fingerprints; and 3) to determine the origin and evolutionary process of weedy rice based on the DNA sequence and microsatellite data. The resolution of the origin and genetic diversity in weedy rice will provide a strong scientific basis for understanding the reason of weedy rice persistence in rice fields, which causes serious losses of rice grain yield, and consequently design a method for effective weedy rice control.

杂草稻是全球最严重稻田恶性杂草之一，严重影响了水稻可持续生产。揭示杂草稻危害的生物学机制并对其有效防治非常必要。杂草稻成功入侵和危害的重要原因是其具有丰富的遗传多样性，而多样性的形成和维持与杂草稻起源和进化密切相关。本项目通过前期研究，将杂草稻复杂起源方式归纳为与野生稻相关的"野生起源"和仅与栽培稻相关的"作物起源"，锁定上述关键科学问题，利用编码落粒性状基因sh4和qsh1 DNA序列以及微卫星分子指纹多态性，开展如下研究：1）比较广泛来源杂草稻、野生稻和栽培稻sh4和qsh1及旁侧序列的多态性，揭示杂草稻起源方式；2）利用微卫星分子指纹分析杂草稻与野生稻、栽培稻的遗传结构和微进化关系；3）综合DNA序列和微卫星指纹多态性结果，确定杂草稻的起源方式及分子进化过程。上述研究将揭示杂草稻遗传多样性形成和维持机制，为阐明杂草稻危害规律及制定有效控制策略提供科学依据。

揭示杂草稻的起源和进化动力对制定其防治措施尤为重要。利用落粒基因（sh4和qsh1）及旁侧DNA序列多态性，结合多种分子标记（微卫星、InDel、SNP和叶绿体基因组等）研究了杂草稻的起源方式以及适应性进化。开展了以下研究内容：1）检测杂草稻、栽培稻及普通野生稻落粒基因及旁侧序列多态性，通过单倍型多态和network分析揭示了杂草稻的起源方式；2）利用微卫星和InDel标记分析全球杂草稻的遗传结构以及与野生稻、栽培稻的遗传关系，确定其“野生起源（exo-feral origin）”和“作物起源（endo-feral origin）”；3）利用叶绿体的全基因组多态性，分析杂草稻的起源和进化途径；4）利用SNPs和转基因，研究人类活动以及转基因水稻种植对杂草稻的适应性进化影响。上述研究获得了系列结果，包括：1）证实了杂草稻分别起源于野生稻和栽培稻，而且栽培稻的去驯化（de-domestication）是杂草稻的主要起源方式，起源于栽培稻的杂草稻又进一步分化为“籼型”和“粳型”；2）发现杂草稻的遗传分化与其地理分布和栽培稻籼-粳分化密切相关，长距离基因流受限以及与当地栽培稻频繁基因渐渗影响了杂草稻进化，在水稻生产较为落后地区，种子介导的基因流是杂草稻群体内遗传多样性的来源；3）水稻生产方式的改变以及栽培稻物品更换等人类活动导致的环境变化，对杂草稻群体的适应性突变（adaptive mutation）的产生以及进化均有重要影响；4）现代生物技术应用于水稻生产（如抗虫和抗除草剂转基因水稻的环境释放），以及转基因渐渗到杂草稻群体的不可避免性，均会在很大程度上影响杂草稻的进化。上述以杂草稻为例获得的研究结果，不仅从理论上揭示了植物遗传多样性的形成和维持机制，同时也阐明了杂草稻的进化动力及其在稻田生态系统中的危害基础，为制定有效的杂草稻控制策略提供了重要科学依据。