The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice.

Recurrent heat stress and pathogen invasion seriously threaten crop production, and abiotic stress often antagonizes biotic stress response against pathogens. However, the molecular mechanisms of trade-offs between thermotolerance and defense remain obscure. Here, we identify a rice thermo-sensitive mutant that displays a defect in floret development under high temperature with a mutation in SUPPRESSOR OF GENE SILENCING 3a (OsSGS3a). OsSGS3a interacts with its homolog OsSGS3b and modulates the biogenesis of trans-acting small interfering RNA (tasiRNA) targeting AUXIN RESPONSE FACTORS (ARFs). We find that OsSGS3a/b positively, while OsARF3a/b and OsARF3la/lb negatively modulate thermotolerance. Moreover, OsSGS3a negatively, while OsARF3a/b and OsARF3la/lb positively regulate disease resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae (M. oryzae). Taken together, our study uncovers a previously unknown trade-off mechanism that regulates distinct immunity and thermotolerance through the OsSGS3-tasiRNA-OsARF3 module, highlighting the regulation of abiotic-biotic stress response trade-off in plants.

Mobile ARGONAUTE 1d binds 22-nt miRNAs to generate phasiRNAs important for low-temperature male fertility in rice.

Phased small interfering RNAs (phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice (Oryza sativa) low temperature-induced Argonaute (AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis; it also binds 21-nt phasiRNAs with a 5' terminal U. In total, phasiRNAs from 972 loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.

Control of OsARF3a by OsKANADI1 contributes to lemma development in rice.

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.

Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line.

Translational regulation, especially tissue- or cell type-specific gene regulation, plays essential roles in plant growth and development. Thermo-sensitive genic male sterile (TGMS) lines have been widely used for hybrid breeding in rice (Oryza sativa). However, little is known about translational regulation during reproductive stage in TGMS rice. Here, we use translating ribosome affinity purification (TRAP) combined with RNA sequencing to investigate the reproductive tissue-specific translatome of TGMS rice expressing FLAG-tagged ribosomal protein L18 (RPL18) from the germline-specific promoter MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1). Differentially expressed genes at the transcriptional and translational levels are enriched in pollen and anther-related formation and development processes. These contain a number of genes reported to be involved in tapetum programmed cell death (PCD) and lipid metabolism during pollen development and anther dehiscence in rice, including several encoding transcription factors and key enzymes, as well as several long non-coding RNAs (lncRNAs) that potentially affect tapetum and pollen-related genes in male sterility. This study represents the comprehensive reproductive tissue-specific characterization of the translatome in TGMS rice. These results contribute to our understanding of the molecular basis of sterility in TGMS rice and will facilitate further genetic manipulation of TGMS rice in two-line breeding systems.

Processing of coding and non-coding RNAs in plant development and environmental responses.

Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5' capping, 3'-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant-environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.

PRMdb: A Repository of Predicted RNA Modifications in Plants.

Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.

Comparison of the effects of symmetric and asymmetric temperature elevation and CO2 enrichment on yield and evapotranspiration of winter wheat (Triticum aestivum L.).

Under the changing climate, asymmetric warming pattern would be more likely during day and night time, instead of symmetric one. Concurrently, the growth responses and water use of plants may be different compared with those estimated based on symmetric warming. In this work, it was compared with the effects of symmetric (ETs) and asymmetric (ETa) elevation of temperature alone, and in interaction with elevated carbon dioxide concentration (EC), on the grain yield (GY) and evapotranspiration in winter wheat (Triticum aestivum L.) based on pot experiment in the North China Plain (NCP). The experiment was carried out in six enclosed-top chambers with following climate treatments: (1) ambient temperature and ambient CO2 (CON), (2) ambient temperature and elevated CO2 (EC), (3) elevated temperature and ambient CO2 (ETs; ETa), and (4) elevated temperature and elevated CO2 (ECETs, ECETa). In symmetric warming, temperature was increased by 3°C and in asymmetric one by 3.5°C during night and 2.5°C during daytime, respectively. As a result, GY was in ETa and ETs 15.6 (P < 0.05) and 10.3% (P < 0.05) lower than that in CON. In ECETs and ECETa treatments, GY was 14.9 (P < 0.05) and 9.1% (P < 0.05) higher than that in CON. Opposite to GY, evapotranspiration was 7.8 (P < 0.05) and 17.9% (P < 0.05) higher in ETa and ETs treatments and 7.2 (P < 0.05) and 2.1% (P > 0.05) lower in ECETs and ECETa treatments compared with CON. Thus, GY of wheat could be expected to increase under the changing climate with concurrent elevation of CO2 and temperature as a result of increased WUE under the elevated CO2. However, the gain would be lower under ETa than that estimated based on ETs due to higher evapotranspiration.

[Effects of drought stress, high temperature and elevated CO2 concentration on the growth of winter wheat].

The impacts of climate change on the grain yield, photosynthesis, and water conditions of winter wheat were assessed based on an experiment, in which wheat plants were subjected to ambient and elevated CO2 concentrations, ambient and elevated temperatures, and low and high water conditions independently and in combination. The CO2 enrichment alone had no effect on the photosynthesis of winter wheat, whereas higher temperature and drought significantly decreased the photosynthetic rate. Water conditions in flag leaves were not significantly changed at the elevated CO2 concentration or elevated temperature. However, drought stress decreased the relative water content in flag leaves, and the combination of elevated temperature and drought reduced the water potential in flag leaves. The combination of elevated CO2 concentration, elevated temperature, and drought significantly reduced the photosynthetic rate and water conditions, and led to a 41.4% decrease in grain yield. The elevated CO2 concentration alone increased the grain yield by 21.2%, whereas the elevated temperature decreased the grain yield by 12.3%. The grain yield was not affected by the combination of elevated CO2 concentration and temperature, but the grain yield was significantly decreased by the drought stress if combined with any of the climate scenarios applied in this study. These findings suggested that maintaining high soil water content might be a vital means of reducing the potential harm caused by the climate change.