水稻籼粳亚种间新合成四倍体早期世代基因组范围内的表观遗传变异

Polyploidy, or whole genome duplication (WGD), as a pervasive driving force in the evolution and speciation of all flowering plants, is often accompanied by emergent genetic and epigenetic instabilities. This study is designed to assess genome-scale epigenetic variations in synthetic tetraploid rice plants between the two subspecies of rice (Oryza sativa L.), i.e., japonica and indica. We used 1st, 5th and10th selfed generation of artificially made tetraploids (designated as NN99 and 99NN), which produced by colchicine-induced WGD of reciprocal F1 hybrids between Nipponbare and 9311..Our previous studies on these newly synthesize tetraploids have shown that large scale of recombinations occurred between chromosomes of Nipponbare and 9311 subgenomes after polyploidizaiton and subsequent selfing, which led to five types of japonica-indica homolog/homeolog constitution in the tetraploids (0N49, 1N39, 2N29, 3N19 and 4N09). Massive genes were differentially expressed after polyploidization. Unlike hybrids, parental expression differences were greatly elaborated at the polyploid level in polyploids. Some of the genes landing on homozygous segments (0N49 or 4N09) also showed altered expression compared to genes in corresponding parents, indicating inheritance of altered gene expression. Interestingly, TE-genes and repeat-sequence contained genes were more likely to be expressed differentially after polyploidization and subsequent selfing. Taking consider of the large amounts of epigenetic variations between the two subspecies (japponica and indica), we suggest that there must be epigenetic regulation mechanism underlying to the gene expression variations. .In this proposal, by taking advantages of the next generation sequencing (NGS) platform, data for genome, methylome and transcriptome of tetraploids, hybrids, and their diploid parental plants can be obtained and used to analyze genome-wide genetic and epigenetic instabilities, as well as gene expression. These genetic and epigenetic variations, coupled with original parental differences, will render the tetraploid plant to show phenotypic novelties which might be useful for rice genetic improvements. By analogy, under natural settings, the novelties rapidly generated by hybridization and WGD may serve as raw material for evolutionary selection. We anticipate those findings will further our understanding of how whole genome doubling promote plant speciation and genome evolution.

多倍化是植物进化和物种形成的重要驱动力，几乎所有被子植物在其进化的过程中都发生过多倍化事件。多倍化事件发生早期，植物体会受到来自基因组融合和基因组加倍带来的双重基因组冲击(genome shock)，而发生广泛的基因组结构变异和表观遗传修饰的变化。这是被子植物在进化上都曾面临过的问题，也是作物改良所需遗传变异的重要来源。本研究通过采用水稻粳、籼亚种代表性基因型日本晴和9311为亲本，通过新一代测序(NGS)技术对水稻亚种间新合成正反交四倍体早期世代(S1，S5和S10)进行基因组重测序、DNA甲基化组、小RNA和转录组测序分析，进而精确解析杂交和多倍化导致的基因组、表观基因组变异的类型、程度和规律，以及受其影响导致的基因表达调控的变化，探讨其对基因(组)功能和表型的影响。研究结果一方面可以丰富我们对多倍化事件促进物种形成和进化机制的认识，另一方面可以为水稻遗传育种实践提供新的启示。

杂交和多倍化是植物物种形成和进化的重要动力（driving force）。杂交和基因组加倍（whole genome duplication）导致的基因组冲击（genome shock），常引发基因组内产生大量的遗传和表观遗传变异。如何应对这种冲击，是被子植物在进化上都曾面临过的问题，也是作物改良所需遗传变异的重要来源。针对这些问题，本研究利用全基因组DNA重测序、DNA甲基化组测序和转录组测序等技术，使用水稻 杂交种和多倍体为研究对象，探究在植物发育的不同阶段，杂交和多倍化背景下的DNA甲基化变异，及其对基因表达的影响。通过对测序结果中亚基因组进行区分，探究杂交、多倍化背景下的亚基因组间互作的可能分子机理及表型后果。.以水稻粳稻亚种的日本晴和籼稻亚种的9311为亲本人工合成双方向的多倍体（NN99和99NN）为实验材料，发现多倍体水稻在自交过程中发生了大量部分同源染色体交换(Homoeologous Exchange, HE)，致使部分同源染色体构成在多倍体单株间具有较强的多态性；基因组融合和加倍导致均对多倍体的DNA甲基化产生影响，而部分同源染色体交换(HE)又将DNA甲基化变异复杂化；相比于杂交种，多倍体中有更多的基因发生了非加性表达，结合多倍体中的DNA甲基化变异，发现基因区CG和CHG甲基化变化与表达相关；重组后已经纯合的染色体区段，其DNA甲基化并没有完全恢复到亲本的水平；与此相应，位于此区域内的基因的表达水平也未恢复到亲本的水平。.综上，杂交和多倍化事件会引发植物基因组范围内大量的DNA甲基化变异，并因此导致基因表达发生改变。基因组杂合的物种一定程度上既可以继承亲本间的遗传结构、表观遗传修饰以及基因表达的模式，又能够通过亚基因组间相互作用，尤其是部分同源染色体交换，快速产生新的变异，并传递给后代。研究结果丰富了我们对杂交、多倍化事件通过影响基因组、表观基因组稳定性促进物种形成和进化机制的认识，同时为水稻遗传育种实践提供一定的理论支持。