Search

Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ∼82% were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs.

Summary: MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA‐seq analysis, combined with in situ hybridization assay revealed that up‐regulation of two miR528 targets coding for Cu/Zn‐SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528‐SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528‐SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation‐mediated crop improvement. [ABSTRACT FROM AUTHOR]

SUMMARY: In rice (Oryza sativa), the lemma and palea protect the internal organs of the floret，provide nutrients for seed development, and determine grain size. We previously revealed that a trans‐acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR‐ARF) regulates lemma polarity establishment via post‐transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR‐ARF formation requires RNA‐DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR‐ARF–ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6‐1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping‐by‐sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6‐1 lemma defect but not the defect in tasiR‐ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1‐associated sites, most of which contain the SPBP‐box binding motif (RGAATAWW) and are located in the promoter, protein‐coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR‐ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR‐ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development. Significance Statement: The lemma and palea are unique and important organs for rice, providing nutrients and protection for floret and seed development, and directly affecting grain size. Our findings show that the expression of OsARF3a was controlled by both OsKANADI1 and via RDR6 at the transcription and post‐transcription levels, thus ensuring the normal development of glumes in rice. [ABSTRACT FROM AUTHOR]

Epigenetic gene variants, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Here, we identify a natural epiallele of OsAK1, which encodes a rice adenylate kinase. The Epi-ak1 plants show albino in young leaf and panicle with abnormal chloroplast structures. We found that no nucleotide sequence variation but hypermethylation at promoter region caused silencing of OsAK1 ( Os08g01770) in Epi-ak1 plants. OsAK1 localizes to chloroplast and many genes associated with photosynthesis processes were downregulated in Epi-ak1. Thus, the work identified a novel rice epiallele caused by DNA methylation changes, shedding light on significant roles of DNA methylation on rice development. [ABSTRACT FROM AUTHOR]