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Background Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12–4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12–4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12–4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

Switching from repressed to active status in chromatin regulation is part of the critical responses that plants deploy to survive in an ever-changing environment. We previously reported that HOS15, a WD40-repeat protein, is involved in histone deacetylation and cold tolerance in Arabidopsis. However, it remained unknown how HOS15 regulates cold responsive genes to affect cold tolerance. Here, we show that HOS15 interacts with histone deacetylase 2C (HD2C) and both proteins together associate with the promoters of cold-responsive COR genes, COR15A and COR47. Cold induced HD2C degradation is mediated by the CULLIN4 (CUL4)-based E3 ubiquitin ligase complex in which HOS15 acts as a substrate receptor. Interference with the association of HD2C and the COR gene promoters by HOS15 correlates with increased acetylation levels of histone H3. HOS15 also interacts with CBF transcription factors to modulate cold-induced binding to the COR gene promoters. Our results here demonstrate that cold induces HOS15-mediated chromatin modifications by degrading HD2C. This switches the chromatin structure status and facilitates recruitment of CBFs to the COR gene promoters. This is an apparent requirement to acquire cold tolerance.

DELLA proteins are repressors of the gibberellin (GA) hormone signaling pathway that act mainly by regulating transcription factor activities in plants. GAs induce DELLA repressor protein degradation and thereby control a number of critical developmental processes as well as responses to stresses such as cold. The strong effect of cold temperatures on many physiological processes has rendered it difficult to assess, based on phenotypic criteria, the role of GA and DELLAs in plant growth during cold stress. Here, we uncover substantial differences in the GA transcriptomes between plants grown at ambient temperature (21°C) and plants exposed to cold stress (4°C) in Arabidopsis (Arabidopsis thaliana). We further identify over 250, to the largest extent previously unknown, DELLA-transcription factor interactions using the yeast two-hybrid system. By integrating both data sets, we reveal that most members of the nine-member GRF (GROWTH REGULATORY FACTOR) transcription factor family are DELLA interactors and, at the same time, that several GRF genes are targets of DELLA-modulated transcription after exposure to cold stress. We find that plants with altered GRF dosage are differentially sensitive to the manipulation of GA and hence DELLA levels, also after cold stress, and identify a subset of cold stressresponsive genes that qualify as targets of this DELLA-GRF regulatory module.

In plants, cold temperatures0 trigger stress responses and long-term responses that result in cold tolerance. In Arabidopsis thaliana, three dehydration-responsive element (DRE) binding protein 1/C-repeat binding factors (DREB1/CBFs) act as master switches in cold-responsive gene expression. Induction of DREB1 genes triggers the cold stress-inducible transcriptional cascade, followed by the induction of numerous genes that function in the cold stress response and cold tolerance. Many regulatory factors involved in DREB1 induction have been identified, but how these factors orchestrate the cold stressspecific expression of DREB1s has not yet been clarified. Here, we revealed that plants recognize cold stress as two different signals, rapid and gradual temperature decreases, and induce expression of the DREB1 genes. CALMODULIN BINDING TRANSCRIPTION ACTIVATOR3 (CAMTA3) and CAMTA5 respond to a rapid decrease in temperature and induce the expression of DREB1s, but these proteins do not respond to a gradual decrease in temperature. Moreover, they function during the day and night, in contrast to some key circadian components, including CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL, which regulate cold-responsive DREB1 expression as transcriptional activators only during the day. Thus, plants efficiently control the acquisition of freezing tolerance using two different signaling pathways in response to a gradual temperature decrease during seasonal changes and a sudden temperature drop during the night.

Summary Cold stress significantly affects the growth and productivity of tomatoes. Despite the known involvement of jasmonate (JA) in cold stress responses, the underlying mechanism remains to be elucidated. Here, we observed that JA peaked 24 h after cold treatment. The expression of the SlLOXD gene, a key player in JA biosynthesis, also peaked at 24 h of cold exposure, and mutation in SlLOXD reduced JA content and cold tolerance. Downstream of JA signalling, the transcription factor SlMYC2 was implicated in enhancing cold resistance by directly binding to the SlCBF1/2 promoters. Furthermore, the SlMYC2‐silenced plants and mutants exhibited increased sensitivity to cold damage. Additionally, SlMYB15 directly bound to the SlLOXD and SlMYC2 promoters. Within 6 h of cold stress, SlMYB15 activated SlLOXD expression while repressing SlMYC2 expression. Between 6 and 24 h, the expression level of SlMYB15 decreased, thereby alleviating the repression of SlMYC2 expression. SlMYC2 further enhanced JA signalling through the transcriptional activation of SlLOXD, thus improving cold tolerance in tomato plants. These findings provide valuable insights into the dynamic regulation of the SlLOXD–SlMYC2 –CBF1/2 module by SlMYB15 and its critical role in tomato cold stress responses.

The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators of plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA (miR) in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4 °C revealed that the auxin signaling mutant, solitary root 1 (slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRs in the wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26–31 nt small RNA population in slr1 compared with wild type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRs in slr1 at 4 °C compared with wild type. Target gene expression analysis of the members from one potential candidate miR, miR169, revealed the possible involvement of miR169/NF-YA module in the Aux/IAA14-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRs in auxin and cold responses.

Cold stress is a major factor limiting rice (Oryza sativa) production worldwide, especially at the seedling and booting stages. The identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed-setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2G, at position 343 in LOC_Os10g34840 is responsible for conferring CT at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC₄F₃ near-isogenic lines possessing the cold-tolerant allele SNP2G. When subjected to cold stress, plants carrying SNP2G survived better as seedlings and showed higher grain weight than plants carrying the SNP2A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of CT in rice.

Low temperature is an important environmental stress that adversely affects rice (Oryza sativa) growth and productivity. Splicing of pre-mRNA is a crucial posttranscriptional regulatory step in gene expression in plants and is sensitive to temperature. DEAD-box RNA helicases belong to an RNA helicase family involved in the rearrangement of ribonucleoprotein complexes and the modification of RNA structure and are therefore involved in all aspects of RNA metabolism. In this study, we demonstrate that the rate of pre-mRNA splicing is reduced in rice at low temperatures and that the DEAD-box RNA Helicase42 (OsRH42) is necessary to support effective splicing of pre-mRNA during mRNA maturation at low temperatures. OsRH42 expression is tightly coupled to temperature fluctuation, and OsRH42 is localized in the splicing speckles and interacts directly with U2 small nuclear RNA. Retarded pre-mRNA splicing and plant growth defects were exhibited by OsRH42-knockdown transgenic lines at low temperatures, thus indicating that OsRH42 performs an essential role in ensuring accurate pre-mRNA splicing and normal plant growth under low ambient temperature. Unexpectedly, our results show that OsRH42 overexpression significantly disrupts the pre-mRNA splicing pathway, causing retarded plant growth and reducing plant cold tolerance. Combined, these results indicate that accurate control of OsRH42 homeostasis is essential for rice plants to respond to changes in ambient temperature. In addition, our study presents the molecular mechanism of DEAD-box RNA helicase function in pre-mRNA splicing, which is required for adaptation to cold stress in rice.

Natural evolution has resulted in reduced cold tolerance in cultivated tomato ( Solanum lycopersicum ). Herein, we perform a combined analysis of ATAC-Seq and RNA-Seq in cold-sensitive cultivated tomato and cold-tolerant wild tomato ( S. habrochaites ). We identify that WRKY34 has the most significant association with differential chromatin accessibility and expression patterns under cold stress. We find that a 60 bp InDel in the WRKY34 promoter causes differences in its transcription and cold tolerance among 376 tomato accessions. This 60 bp fragment contains a GATA cis -regulatory element that binds to SWIBs and GATA29, which synergistically suppress WRKY34 expression under cold stress. Moreover, WRKY34 interferes with the CBF cold response pathway through regulating transcription and protein levels. Our findings emphasize the importance of polymorphisms in cis -regulatory regions and their effects on chromatin structure and gene expression during crop evolution. Cold tolerance has lost during tomato natural evolution. Here, the authors report that absence of a 60 bp promoter fragment in the WRKY34 gene results in loss of cold tolerance in domesticated tomato varieties, and reveal how this natural variation can affect cold tolerance.

Background Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. Results To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 °C) and COLD stress groups (13 °C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein ( HSP70 ) and cold-induced RNA-binding protein ( CIRBP ) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. Conclusions This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress .