Transcriptome and Epigenome analysis in Polyploidy Wheat and its progenitors

We analyzed sequence features of intergenic spacer (IGS) in the progenitors of common wheat Triticum aestivum (AABBDD), which revealed nucleolar organizing region (NOR) dominance hierarchy (BB > DD > AA). The hierarchy is based on the length, transcript start site, number and sequence variation of Rep1 (promoter-like repeat) unit. Transcriptome and epigenome in the synthetic tetraploid wheat (AADD / DDAA) and their progenitors T. urartu (AA) and Ae. tauschii (DD) were further investigated to explore the mechanism for NOR silencing. We found that long non-coding RNAs and 24-nt small interfering RNAs were highly abundant in the IGS regions of the DD, and scarcity in AA. After polyploidy formation, NORs of AA subgenome were silenced and associated with increased levels of 24-nt siRNAs derived from active NOR of the DD subgenome. These DD-subgenome 24-nt siRNAs may trans-act on AA-genome IGS to induce DNA methylation via RNA directed DNA methylation (RdDM). Furthermore, BS-Seq and MeDIP-Seq assay show siRNA-targeted regions in AA-subgenome IGS were hypermethylated. Additionally, the increased H3K27me3 and decreased H4K12ac were found in AA-subgenome IGS after polyploidization. This similar phenomenon of BB 24-nt siRNAs trans-act on DD was detected in hexaploid wheat.