Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.

分iller是决定水稻植株结构和谷物产量的主要因素。在这里，我们报道说，水稻矮化OsNRPD1a和OsNRPD1b是RNA聚合酶IV的最大亚基的两个直系同源基因，除了矮化和较小的穗外，还导致了高分iller的表型。OsNRPD1a和OsNRPD1b是生产24 nt小干扰RNA所必需的，这些小RNA指导DNA甲基化到包括微型反向重复TEs（MITEs）在内的转座因子（TEs）上。有趣的是，许多基因受到TE甲基化的正调控或负调控。其中，促进水稻分till的OsMIR156d和OsMIR156j被启动子中两个MITE处的CHH甲基化所抑制。相比之下，D14CHH甲基化在其下游的MITE处激活，从而抑制水稻分till。我们的发现揭示了MITE处RNA定向DNA甲基化对水稻分till的调控，并为通过表观基因组编辑提高农艺性状提供了潜在的靶标。