多倍体中不同亚基因组产生的小RNA可以相互作用于对方基因组，这种小RNA介导的反式调控是多倍体协调不同亚基因组表达和表观遗传变化的关键，对多倍体基因组塑性的产生和成功进化具有重要意义。然而，对于小RNA介导的亚基因组间反式调控如何调节基因表达和表观遗传变化以及反式调控的全基因组模式的研究相当缺乏。本项目拟采用二倍体白菜和甘蓝，四倍体甘蓝型油菜和特殊分离A亚基因组为材料，基于叶和花蕾的多组学数据，通过四倍体和二倍体基因组之间的相互比较，鉴定参与C对A亚基因组反式调控的小RNA和靶标基因/TE的类型，综合分析miRNA—靶标基因表达和TE衍生的siRNA—靶标TE甲基化—临近基因表达这两种反式调控对于多倍化后基因表达变化、TE甲基化变化以及A-C重复基因间表达分化的作用，解析小RNA介导的亚基因组间反式调控的全基因组模式。本项目的开展将有助于阐明多倍体物种形成、演化和基因组塑性形成的分子机理。

Genome-wide subgenomic interaction should be occurred and regulated by small RNAs derived from each other in the polyploid. This trans-regulation of sRNAs is an important way to coordinate the expression of duplicated genes and play a key role in the evolution of polyploid. However, the way and pattern how subgenome interacted to regulate gene expression and epigenetic modification remains unclear. In this project, Brassica rapa, Brassica oleracea, Brassica napus and its extracted AA subgenome will be used as materials. Leaf and flower tissues from these species will be collected for mRNA sequencing, small RNA sequencing and bisulphite sequencing. By comparing the expression difference of miRNA, TE-derived siRNA and genes between tetraploid and diploids, the sRNAs and its targeted gene or TE involved in trans-regulation will be identified. We will investigate and compare the genome-wide pattern of subgenomic trans-regulation by miRNA-mRNA and siRNA-TE-nearby genes, and study their roles in regulating gene expression, TE methylation and expression divergence between duplicated genes in polyploid. These comprehensive analysis will be conducted to reveal the relationship between subgenomic interaction and the gene expression and epigenetic modification in polyploid. The proposed research will improve understanding and knowledge of the speciation, evolution and genomic plasticity of polyploid.