杂交和多倍化是植物中的一种普遍现象并在进化中扮演着重要角色。异源多倍体中重复基因（部分同源等位基因）的进化式样一直都是多倍体研究的核心内容。近年来的研究发现，种间杂交和基因组加倍可能对全基因组范围内的基因表达产生冲击作用，极大程度上改变其原有表达模式。然而，纵观不同的植物类群，重复基因的表达式样错综复杂，尚未达成共识，尤其是表达分化形成的分子机制还一直成谜。本项目拟以稻属中具有独特研究优势的BBCC异源四倍体物种体系为研究对象，充分利用大规模测序技术和进化基因组的分析方法，开展基因组重测序、转录组测序、全基因组DNA甲基化和小RNA分析的整合研究，以期从全基因组水平分析部分同源等位基因的基因表达分化式样，并探寻其可能的遗传和表观遗传机理。本研究的预期结果将有助于揭示异源多倍化过程所诱导产生的亚基因组之间基因表达分化的式样及其潜在分子机制，同时，也将对植物遗传育种提供新的启示。

Hybridization and polyploidization have long been recognized as a common phenomenon and played important roles in the evolution of plants. The expression patterns of duplicated genes in allopolyploids (i.e., homoeologs) are always a hot topic in evolutionary biology. Recent studies show that allopolyploidization, which involves the interspecies hybridization and genome doubling, is usually accompanied by extensive changes to patterns of parental gene expression ("transcriptome shock"). However, the expression patterns of homoeologs varied in a complicated way, and in particular, the mechanism involved is poorly understood. In this study, we select the BBCC tetraploid and its diploid progenitors in Oryza, which is an excellent system for allopolyploid research, and take full advantage of the Next-generation Sequencing technology. Through Whole-genome Resequencing, RNA-seq, Whole-genome Bisulfite Sequencing, as well as small RNA-Seq, we aim to detect the expression divergence of homoeologous genes at the genomic level and explore the genetic and epigenetic consequences of allopolyploidization in BBCC tetraploid. The proposed investigation will not only enhance our knowledge on gene expression divergence between subgenomes of allopolyploids and its underlying mechanism, but also facilitate molecular breeding in crop improvement.