生态式物种形成是新物种产生的重要方式。尽管已有大量研究探索其遗传机理，但对表观遗传调控在生态式物种形成中的作用仍知之甚少。Oryza rufipogon 和 O. nivara 在形态、生活史和生境偏好上存在显著差异，但二者遗传差异却很小，被认为是处于物种形成初期的一对姊妹类群，因此是研究生态式物种形成的一个很好的自然体系。本项目拟采用全基因组Bisulfite测序构建两野生稻高精度的DNA甲基化图谱, 并同时进行RNA-Seq转录组测序。通过对两个野生种进行系统比较，检测DNA甲基化在两个野生稻分化过程中的基本变异式样，探索DNA甲基化分化与DNA序列变异和基因表达分化间的关系，寻找控制两个野生稻适应性表型分化特征的关键甲基化位点以及关联基因。上述研究不仅有助于揭示表观遗传变异在两个野生稻分化中的作用，也为理解植物适应性进化和生态式物种形成的分子遗传机理提供了有益的资料。

Ecological speciation, in which divergent selection arising from habitat heterogeneity play a dominant role in driving population divergence and reproductive isolation, has been supported by many lines of evidence in recent decades. Despite substantial studies, however, the role of epigenetic regulation in the ecological speciation remains unclear. With distinct differences in morphology, life history traits and habitat preference, Oryza rufipogon and O. nivara are two incipient species at the early stage of speciation and provide a unique model for studying ecological speciation. In this study, we construct the high-resolution DNA methylation maps of the two wild species by using the technology of whole genome bisulfite sequencing, and perform transcriptome profiling of the same samples by RNA-Seq. On these basis, we study the divergence patterns of DNA methylation during the process of ecological speciation, explore the relationships of the differentiation of DNA methylation with the genetic variation and expression divergence, and finally attempt to find the putative genes responsible for the key traits of phenotypic divergence of the two species. These studies not only help reveal the role of epigenetic regulation in the divergence of two Oryza species, but also provide further insights into genetics mechanisms underlying adaptive evolution and ecological speciation in plants.