Search

Summary: Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown.Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss‐function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature.We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre‐rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre‐rRNAs are observed in ospus1‐1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1‐1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress‐responsive state, preventing excess reactive oxygen species accumulation.Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in 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]

Transposable elements (TEs) have long been regarded as ‘selfish DNA’, and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice ( Oryza sativa ) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions. [ABSTRACT FROM AUTHOR]

Higher plants have evolved multiple RNA-dependent RNA polymerases (RDRs), which work with Dicer-like (DCL) proteins to produce different classes of small RNAs with specialized molecular functions. Here we report that OsRDR6, the rice ( Oryza sativa L.) homolog of Arabidopsis RDR6, acts in the biogenesis of various types and sizes of small RNAs. We isolated a rice osrdr6-1 mutant, which was temperature sensitive and showed spikelet defects. This mutant displays reduced accumulation of tasiR-ARFs, the conserved trans-acting siRNAs (tasiRNAs) derived from the TAS3 locus, and ectopic expression of tasiR-ARF target genes, the Auxin Response Factors (including ARF2 and ARF3/ETTIN). The loss of tasiR-mediated repression of ARFs in osrdr6- 1 can explain its morphological defects, as expression of two non-targeted ARF3 gene constructs ( ARF3muts) in a wild-type background mimics the osrdr6 and osdcl4- 1 mutant phenotypes. Small RNA high-throughput sequencing also reveals that besides tasiRNAs, 21-nucleotide (nt) phased small RNAs are also largely dependent on OsRDR6. Unexpectedly, we found that osrdr6- 1 has a strong impact on the accumulation of 24-nt phased small RNAs, but not on unphased ones. Our work uncovers the key roles of OsRDR6 in small RNA biogenesis and directly illustrates the crucial functions of tasiR-ARFs in rice development. [ABSTRACT FROM AUTHOR]

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties. [ABSTRACT FROM AUTHOR]