The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis

Involvement of epigenetic factors in flavonoid accumulation during plant cold adaptation

Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation.

INDUCER OF CBF EXPRESSION 1 promotes cold-enhanced immunity by directly activating salicylic acid signaling

Cold stress affects plant immune responses, and this process may involve the salicylic acid (SA) signaling pathway. However, the underlying mechanism by which low-temperature signals coordinate with SA signaling to regulate plant immunity remains unclear. Here, we found that low temperatures enhanced the disease resistance of Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000. This process required INDUCER OF CBF EXPRESSION 1 (ICE1), the core transcription factor in cold-signal cascades. ICE1 physically interacted with NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1), the master regulator of the SA signaling pathway. Enrichment of ICE1 on the PATHOGENESIS-RELATED GENE 1 (PR1) promoter and its ability to transcriptionally activate PR1 were enhanced by NPR1. Further analyses revealed that cold stress signals cooperate with SA signals to facilitate plant immunity against pathogen attack in an ICE1-dependent manner. Cold treatment promoted interactions of NPR1 and TGACG-BINDING FACTOR 3 (TGA3) with ICE1 and increased the ability of the ICE1-TGA3 complex to transcriptionally activate PR1. Together, our results characterize a critical role of ICE1 as an indispensable regulatory node linking low-temperature-activated and SA-regulated immunity. Understanding this crucial role of ICE1 in coordinating multiple signals associated with immunity broadens our understanding of plant-pathogen interactions.

Evolution of PIN gene family between monocotyledons and dicotyledons and VvPIN1 negatively regulates freezing tolerance in transgenic Arabidopsis

The PIN-FORMED (PIN) proteins mediate the auxin flow throughout the plant and have been identified in many species. However, evolution differences in the PIN gene families have not been systematically analyzed, and their functions under abiotic stresses in grape are largely unexplored. In this study, 373 PIN genes were identified from 25 species and divided into 3 subgroups. Physicochemical properties analysis indicated that most of the PIN proteins were unstable alkaline hydrophobic proteins in nature. The synteny analysis showed that the PINs contained strong gene duplication. Motif composition revealed that PIN gene sequence differences between monocotyledons and dicotyledons were due to evolutionary-induced base loss, and the loss was more common in dicotyledonous. Meanwhile, the codon usage bias showed that the PINs showed stronger codon preference in monocotyledons, monocotyledons biased towards C3s and G3s, and dicotyledons biased towards A3s and T3s. In addition, the VvPIN1 can interact with VvCSN5. Significantly, under freezing treatment, the ion leakage,O 2 · - $$ \left({O}_2^{\cdotp -}\right) $$ , H2O2, and malondialdehyde (MDA) were obviously increased, while the proline (Pro) content, peroxidase (POD) activity, and glutathione (GSH) content were decreased in VvPIN1-overexpressing Arabidopsis compared to the wild type (WT). And quantitative real-time PCR (qRT-PCR) showed that AtICE1, AtICE2, AtCBF1, AtCBF2, and AtCBF3 were down-regulated in overexpression lines. These results demonstrated that VvPIN1 negatively regulated the freezing tolerance in transgenic Arabidopsis. Collectively, this study provides a novel insight into the evolution and a basis for further studies on the biological functions of PIN genes in monocotyledons and dicotyledons.

Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants

Stem cell homeostasis is pivotal for continuous and programmed formation of organs in plants. The precise control of meristem proliferation is mediated by the evolutionarily conserved signaling that encompasses complex interactions among multiple peptide ligands and their receptor-like kinases. Here, we identified compensation mechanisms involving the CLAVATA1 (CLV1) receptor and its paralogs, BARELY ANY MERISTEMs (BAMs), for stem cell proliferation in two Solanaceae species, tomato and groundcherry. Genetic analyses of higher-order mutants deficient in multiple receptor genes, generated via CRISPR-Cas9 genome editing, reveal that tomato SlBAM1 and SlBAM2 compensate for slclv1 mutations. Unlike the compensatory responses between orthologous receptors observed in Arabidopsis, tomato slclv1 mutations do not trigger transcriptional upregulation of four SlBAM genes. The compensation mechanisms within receptors are also conserved in groundcherry, and critical amino acid residues of the receptors associated with the physical interaction with peptide ligands are highly conserved in Solanaceae plants. Our findings demonstrate that the evolutionary conservation of both compensation mechanisms and critical coding sequences between receptor-like kinases provides a strong buffering capacity during stem cell homeostasis in tomato and groundcherry.

Discovery of gene regulation mechanisms associated with uniconazole-induced cold tolerance in banana using integrated transcriptome and metabolome analysis

BACKGROUND

The gibberellic acid (GA) inhibitor, uniconazole, is a plant growth regulator commonly used in banana cultivation to promote dwarfing but also enhances the cold resistance in plants. However, the mechanism of this induced cold resistance remains unclear.

RESULTS

We confirmed that uniconazole induced cold tolerance in bananas and that the activities of Superoxide dismutase and Peroxidase were increased in the uniconazole-treated bananas under cold stress when compared with the control groups. The transcriptome and metabolome of bananas treated with or without uniconazole were analyzed at different time points under cold stress. Compared to the control group, differentially expressed genes (DEGs) between adjacent time points in each uniconazole-treated group were enriched in plant-pathogen interactions, MAPK signaling pathway, and plant hormone signal transduction, which were closely related to stimulus-functional responses. Furthermore, the differentially abundant metabolites (DAMs) between adjacent time points were enriched in flavone and flavonol biosynthesis and linoleic acid metabolism pathways in the uniconazole-treated group than those in the control group. Temporal analysis of DEGs and DAMs in uniconazole-treated and control groups during cold stress showed that the different expression patterns in the two groups were enriched in the linoleic acid metabolism pathway. In addition to strengthening the antioxidant system and complex hormonal changes caused by GA inhibition, an enhanced linoleic acid metabolism can protect cell membrane stability, which may also be an important part of the cold resistance mechanism of uniconazole treatment in banana plants.

CONCLUSIONS

This study provides information for understanding the mechanisms underlying inducible cold resistance in banana, which will benefit the production of this economically important crop.

Effects of exogenous glycine betaine on growth and development of tomato seedlings under cold stress

Low temperature is a type of abiotic stress affecting the tomato (Solanum lycopersicum) growth. Understanding the mechanisms and utilization of exogenous substances underlying plant tolerance to cold stress would lay the foundation for improving temperature resilience in this important crop. Our study is aiming to investigate the effect of exogenous glycine betaine (GB) on tomato seedlings to increase tolerance to low temperatures. By treating tomato seedlings with exogenous GB under low temperature stress, we found that 30 mmol/L exogenous GB can significantly improve the cold tolerance of tomato seedlings. Exogenous GB can influence the enzyme activity of antioxidant defense system and ROS levels in tomato leaves. The seedlings with GB treatment presented higher Fv/Fm value and photochemical activity under cold stress compared with the control. Moreover, analysis of high-throughput plant phenotyping of tomato seedlings also supported that exogenous GB can protect the photosynthetic system of tomato seedlings under cold stress. In addition, we proved that exogenous GB significantly increased the content of endogenous abscisic acid (ABA) and decreased endogenous gibberellin (GA) levels, which protected tomatoes from low temperatures. Meanwhile, transcriptional analysis showed that GB regulated the expression of genes involved in antioxidant capacity, calcium signaling, photosynthesis activity, energy metabolism-related and low temperature pathway-related genes in tomato plants. In conclusion, our findings indicated that exogenous GB, as a cryoprotectant, can enhance plant tolerance to low temperature by improving the antioxidant system, photosynthetic system, hormone signaling, and cold response pathway and so on.

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Introduction

Peanut (Arachis hypogaea L.), also called groundnut is an important oil and cash crop grown widely in the world. The annual global production of groundnuts has increased to approximately 50 million tons, which provides a rich source of vegetable oils and proteins for humans. Low temperature (non-freezing) is one of the major factors restricting peanut growth, yield, and geographic distribution. Since the complexity of cold-resistance trait, the molecular mechanism of cold tolerance and related gene networks were largely unknown in peanut.

Methods

In this study, comparative transcriptomic analysis of two peanut cultivars (SLH vs. ZH12) with differential cold tolerance under low temperature (10°C) was performed using Oxford Nanopore Technology (ONT) platform.

Results and discussion

As a result, we identified 8,949 novel gene loci and 95,291 new/novel isoforms compared with the reference database. More differentially expressed genes (DEGs) were discovered in cold-sensitive cultivar (ZH12) than cold-tolerant cultivar (SLH), while more alternative splicing events were found in SLH compared to ZH12. Gene Ontology (GO) analyses of the common DEGs showed that the "response to stress", "chloroplast part", and "transcription factor activity" were the most enriched GO terms, indicating that photosynthesis process and transcription factors play crucial roles in cold stress response in peanut. We also detected a total of 708 differential alternative splicing genes (DASGs) under cold stress compared to normal condition. Intron retention (IR) and exon skipping (ES) were the most prevalent alternative splicing (AS) events. In total, 4,993 transcription factors and 292 splicing factors were detected, many of them had differential expression levels and/or underwent AS events in response to cold stress. Overexpression of two candidate genes (encoding trehalose-6-phosphatephosphatases, AhTPPs) in yeast improves cold tolerance. This study not only provides valuable resources for the study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.

Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29

C-repeat binding factors (CBFs) are well-known transcription factors (TFs) that regulate plant cold acclimation. RNA sequencing (RNA-seq) data from diverse plant species provide opportunities to identify other TFs involved in the cold response. However, this task is challenging because gene gain and loss has led to an intertwined community of co-orthologs and in-paralogs between and within species. Using orthogroup (closely related homologs) analysis, we identified 10,549 orthogroups in five representative eudicots. A phylotranscriptomic analysis of cold-treated seedlings from eudicots identified 35 high-confidence conserved cold-responsive transcription factor orthogroups (CoCoFos). These 35 CoCoFos included the well-known cold-responsive regulators CBFs, HSFC1, ZAT6/10, and CZF1 among others. We used Arabidopsis BBX29 for experimental validation. Expression and genetic analyses showed that cold-induction of BBX29 is CBF- and abscisic acid-independent, and BBX29 is a negative regulator of cold tolerance. Integrative RNA-seq and Cleavage Under Targets and Tagmentation followed by sequencing analyses revealed that BBX29 represses a set of cold-induced TFs (ZAT12, PRR9, RVE1, MYB96, etc.). Altogether, our analysis yielded a library of eudicot CoCoFos and demonstrated that BBX29 is a negative regulator of cold tolerance in Arabidopsis.

Integrated Transcriptomic and Metabolomics Analyses Reveal Molecular Responses to Cold Stress in Coconut (Cocos nucifera L.) Seedlings

Coconut is an important tropical and subtropical fruit and oil crop severely affected by cold temperature, limiting its distribution and application. Thus, studying its low-temperature reaction mechanism is required to expand its cultivation range. We used growth morphology and physiological analyses to characterize the response of coconuts to 10, 20, and 30 d of low temperatures, combined with transcriptome and metabolome analysis. Low-temperature treatment significantly reduced the plant height and dry weight of coconut seedlings. The contents of soil and plant analyzer development (SPAD), soluble sugar (SS), soluble protein (SP), proline (Pro), and malondialdehyde (MDA) in leaves were significantly increased, along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the endogenous hormones abscisic acid (ABA), auxin (IAA), zeatin (ZR), and gibberellin (GA) contents. A large number of differentially expressed genes (DEGs) (9968) were detected under low-temperature conditions. Most DEGs were involved in mitogen-activated protein kinase (MAPK) signaling pathway-plant, plant hormone signal transduction, plant-pathogen interaction, biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism, carbon metabolism, starch and sucrose metabolism, purine metabolism, and phenylpropanoid biosynthesis pathways. Transcription factors (TFs), including WRKY, AP2/ERF, HSF, bZIP, MYB, and bHLH families, were induced to significantly differentially express under cold stress. In addition, most genes associated with major cold-tolerance pathways, such as the ICE-CBF-COR, MAPK signaling, and endogenous hormones and their signaling pathways, were significantly up-regulated. Under low temperatures, a total of 205 differentially accumulated metabolites (DAMs) were enriched; 206 DAMs were in positive-ion mode and 97 in negative-ion mode, mainly including phenylpropanoids and polyketides, lipids and lipid-like molecules, benzenoids, organoheterocyclic compounds, organic oxygen compounds, organic acids and derivatives, nucleosides, nucleotides, and analogues. Comprehensive metabolome and transcriptome analysis revealed that the related genes and metabolites were mainly enriched in amino acid, flavonoid, carbohydrate, lipid, and nucleotide metabolism pathways under cold stress. Together, the results of this study provide important insights into the response of coconuts to cold stress, which will reveal the underlying molecular mechanisms and help in coconut screening and breeding.

AP2/EREBP Pathway Plays an Important Role in Chaling Wild Rice Tolerance to Cold Stress

Cold stress is the main factor limiting rice production and distribution. Chaling wild rice can survive in cold winters. AP2/EREBP is a known transcription factor family associated with abiotic stress. We identified the members of the AP2/EREBP transcription factor family in rice, maize, and Arabidopsis, and conducted collinearity analysis and gene family analysis. We used Affymetrix array technology to analyze the expression of AP2/EREBP family genes in Chaling wild rice and cultivated rice cultivar Pei'ai64S, which is sensitive to cold. According to the GeneChip results, the expression levels of AP2/EREBP genes in Chaling wild rice were different from those in Pei'ai64S; and the increase rate of 36 AP2/EREBP genes in Chaling wild rice was higher than that in Pei'ai64S. Meanwhile, the MYC elements in cultivated rice and Chaling wild rice for the Os01g49830, Os03g08470, and Os03g64260 genes had different promoter sequences, resulting in the high expression of these genes in Chaling wild rice under low-temperature conditions. Furthermore, we analyzed the upstream and downstream genes of the AP2/EREBP transcription factor family and studied the conservation of these genes. We found that the upstream transcription factors were more conserved, indicating that these upstream transcription factors may be more important in regulating cold stress. Meanwhile, we found the expression of AP2/EREBP pathway genes was significantly increased in recombinant inbred lines from Nipponbare crossing with Chaling wild rice, These results suggest that the AP2/EREBP signaling pathway plays an important role in Chaling wild rice tolerance to cold stress.

Brassinosteroid signaling regulator BIM1 integrates brassinolide and jasmonic acid signaling during cold tolerance in apple

Although brassinolide (BR) and jasmonic acid (JA) play essential roles in the regulation of cold stress responses, the molecular basis of their crosstalk remains elusive. Here, we show a key component of BR signaling in apple (Malus × domestica), BR INSENSITIVE1 (BRI1)-EMS-SUPPRESSOR1 (BES1)-INTERACTING MYC-LIKE PROTEIN1 (MdBIM1), increases cold tolerance by directly activating expression of C-REPEAT BINDING FACTOR1 (MdCBF1) and forming a complex with C-REPEAT BINDING FACTOR2 (MdCBF2) to enhance MdCBF2-activated transcription of cold-responsive genes. Two repressors of JA signaling, JAZMONATE ZIM-DOMAIN1 (MdJAZ1) and JAZMONATE ZIM-DOMAIN2 (MdJAZ2), interact with MdBIM1 to integrate BR and JA signaling under cold stress. MdJAZ1 and MdJAZ2 reduce MdBIM1-promoted cold stress tolerance by attenuating transcriptional activation of MdCBF1 expression by MdBIM1 and interfering with the formation of the MdBIM1-MdCBF2 complex. Furthermore, the E3 ubiquitin ligase ARABIDOPSIS TÓXICOS en LEVADURA73 (MdATL73) decreases MdBIM1-promoted cold tolerance by targeting MdBIM1 for ubiquitination and degradation. Our results not only reveal crosstalk between BR and JA signaling mediated by a JAZ-BIM1-CBF module but also provide insights into the posttranslational regulatory mechanism of BR signaling.

Genome-Wide Identification of GmSPS Gene Family in Soybean and Expression Analysis in Response to Cold Stress

Sucrose metabolism plays a critical role in development, stress response, and yield formation of plants. Sucrose phosphate synthase (SPS) is the key rate-limiting enzyme in the sucrose synthesis pathway. To date, genome-wide survey and comprehensive analysis of the SPS gene family in soybean (Glycine max) have yet to be performed. In this study, seven genes encoding SPS were identified in soybean genome. The structural characteristics, phylogenetics, tissue expression patterns, and cold stress response of these GmSPSs were investigated. A comparative phylogenetic analysis of SPS proteins in soybean, Medicago truncatula, Medicago sativa, Lotus japonicus, Arabidopsis, and rice revealed four families. GmSPSs were clustered into three families from A to C, and have undergone five segmental duplication events under purifying selection. All GmSPS genes had various expression patterns in different tissues, and family A members GmSPS13/17 were highly expressed in nodules. Remarkably, all GmSPS promoters contain multiple low-temperature-responsive elements such as potential binding sites of inducer of CBF expression 1 (ICE1), the central regulator in cold response. qRT-PCR proved that these GmSPS genes, especially GmSPS8/18, were induced by cold treatment in soybean leaves, and the expression pattern of GmICE1 under cold treatment was similar to that of GmSPS8/18. Further transient expression analysis in Nicotiana benthamiana and electrophoretic mobility shift assay (EMSA) indicated that GmSPS8 and GmSPS18 transcriptions were directly activated by GmICE1. Taken together, our findings may aid in future efforts to clarify the potential roles of GmSPS genes in response to cold stress in soybean.

Comprehensive analysis of transcriptional data on seed germination of two maize inbred lines under low-temperature conditions

Seed germination directly affect maize yield and grain quality. Low-temperature reduces maize yield by affecting seed germination and seedling growth. However, the molecular mechanism of maize seed germination under low-temperature remains unclear. In this study, the transcriptome data of two maize inbred lines SCL127 (chilling-sensitive) and SCL326 (chilling-tolerant) were analyzed at five time points (0 H, 4 H, 12 H, 24 H, and 48 H) under low-temperature conditions. Through the comparison of SCL127-0 H-vs-SCL326-0 H (Group I), SCL127-4 H-vs-SCL326-4 H (Group Ⅱ), SCL127-12 H-vs-SCL326-12 H (Group Ⅲ), SCL127-24 H-vs-SCL326-24 H (Group Ⅳ), and SCL127-48 H-vs SCL326-48 H (Group Ⅴ), a total of 8,526 differentially expressed genes (DEGs) were obtained. Weighted correlation network analysis revealed that Zm00001d010445 was the hub gene involved in seed germination under low-temperature conditions. Zm00001d010445-based association analysis showed that Hap Ⅱ (G) was the excellent haplotype for seed germination under low-temperature conditions. These findings provide a new perspective for the study of the genetic architecture of maize tolerance to low-temperature and contribute to the cultivation of maize varieties with low-temperature tolerance.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

Characterization of sandalwood (E,E)-α-farnesene synthase whose overexpression enhances cold tolerance through jasmonic acid biosynthesis and signaling in Arabidopsis

MAIN CONCLUSION

Santalum album (E,E)-α-farnesene synthase catalyzes FPP into (E,E)-α-farnesene. Overexpression of the SaAFS gene positively improved cold stress tolerance through JA biosynthesis and signaling pathways in Arabidopsis. Volatile terpenoids are released from plants that suffer negative effects following exposure to various biotic and abiotic stresses. Recent studies revealed that (E,E)-α-farnesene synthase (AFS) plays a significant role in a plant's defence against biotic attack. However, little is known about whether AFS contributes to plant resistance to cold stress. In this study, a SaAFS gene was isolated from Indian sandalwood (Santalum album L.) and functionally characterized. The SaAFS protein mainly converts farnesyl diphosphate to (E,E)-α-farnesene. SaAFS was clustered into the AFS clade from angiosperms, suggesting a highly conserved enzyme. SaAFS displayed a significant response to cold stress and methyl jasmonate. SaAFS overexpression (OE) in Arabidopsis enhanced cold tolerance by increasing proline content, reducing malondialdehyde content, electrolyte leakage, and accumulating reactive oxygen species. Transcriptomic analysis revealed that upregulated genes related to stress response and JA biosynthesis and signaling were detected in SaAFS-OE lines compared with wild type plants that were exposed to cold stress. Endogenous JA and jasmonoyl-isoleucine content increased significantly in SaAFS-OE lines exposed to cold stress. Collectively considered, these results suggest that the SaAFS gene is a positive regulator during cold stress tolerance via JA biosynthesis and signaling pathways.

The DREB transcription factor, a biomacromolecule, responds to abiotic stress by regulating the expression of stress-related genes

Abiotic stress is a crucial factor that affects plant survival and growth and even leads to plant death in severe cases. Transcription factors can enhance the ability of plants to fight against various stresses by controlling the expression of downstream genes. The dehydration response element binding protein (DREB) is the most extensive subfamily of AP2/ERF transcription factors involved in abiotic stress. However, insufficient research on the signal network of DREB transcription factors has limited plant growth and reproduction. Furthermore, field planting of DREB transcription factors and their roles under multiple stress also require extensive research. Previous reports on DREB transcription factors have focused on the regulation of DREB expression and its roles in plant abiotic stress. In recent years, there has been new progress in DREB transcription factors. Here, the structure and classification, evolution and regulation, role in abiotic stress, and application in crops of DREB transcription factors were reviewed. And this paper highlighted the evolution of DREB1/CBF, as well as the regulation of DREB transcription factors under the participation of plant hormone signals and the roles of subgroups in abiotic stress. In the future, it will lay a solid foundation for further study of DREB transcription factors and pave the way for the cultivation of resistant plants.

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

Arabidopsis LFR, a SWI/SNF complex component, interacts with ICE1 and activates ICE1 and CBF3 expression in cold acclimation

Low temperatures restrict the growth and geographic distribution of plants, as well as crop yields. Appropriate transcriptional regulation is critical for cold acclimation in plants. In this study, we found that the mutation of Leaf and flower related (LFR), a component of SWI/SNF chromatin remodeling complex (CRC) important for transcriptional regulation in Arabidopsis (Arabidopsis thaliana), resulted in hypersensitivity to freezing stress in plants with or without cold acclimation, and this defect was successfully complemented by LFR. The expression levels of CBFs and COR genes in cold-treated lfr-1 mutant plants were lower than those in wild-type plants. Furthermore, LFR was found to interact directly with ICE1 in yeast and plants. Consistent with this, LFR was able to directly bind to the promoter region of CBF3, a direct target of ICE1. LFR was also able to bind to ICE1 chromatin and was required for ICE1 transcription. Together, these results demonstrate that LFR interacts directly with ICE1 and activates ICE1 and CBF3 gene expression in response to cold stress. Our work enhances our understanding of the epigenetic regulation of cold responses in plants.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Suppression of the HOS1 Gene Affects the Level of ROS Depending on Light and Cold

The E3 ubiquitin-protein ligase HOS1 is an important integrator of temperature information and developmental processes. HOS1 is a negative regulator of plant cold tolerance, and silencing HOS1 leads to increased cold tolerance. In the present work, we studied ROS levels in hos1^Cas9Arabidopsis thaliana plants, in which the HOS1 gene was silenced by disruption of the open reading frame via CRISPR/Cas9 technology. Confocal imaging of intracellular reactive oxygen species (ROS) showed that the hos1 mutation moderately increased levels of ROS under both low and high light (HL) conditions, but wild-type (WT) and hos1^Cas9 plants exhibited similar ROS levels in the dark. Visualization of single cells did not reveal differences in the intracellular distribution of ROS between WT and hos1^Cas9 plants. The hos1^Cas9 plants contained a high basal level of ascorbic acid, maintained a normal balance between reduced and oxidized glutathione (GSH and GSSG), and generated a strong antioxidant defense response against paraquat under HL conditions. Under cold exposure, the hos1 mutation decreased the ROS level and substantially increased the expression of the ascorbate peroxidase genes Apx1 and Apx2. When plants were pre-exposed to cold and further exposed to HL, the expression of the NADPH oxidase genes RbohD and RbohF was increased in the hos1^Cas9 plants but not in WT plants. hos1-mediated changes in the level of ROS are cold-dependent and cold-independent, which implies different levels of regulation. Our data indicate that HOS1 is required to maintain ROS homeostasis not only under cold conditions, but also under conditions of both low and high light intensity. It is likely that HOS1 prevents the overinduction of defense mechanisms to balance growth.

Recent progress and perspectives on physiological and molecular mechanisms underlying cold tolerance of tea plants

Tea is one of the most consumed and widely planted beverage plant worldwide, which contains many important economic, healthy, and cultural values. Low temperature inflicts serious damage to tea yields and quality. To cope with cold stress, tea plants have evolved a cascade of physiological and molecular mechanisms to rescue the metabolic disorders in plant cells caused by the cold stress; this includes physiological, biochemical changes and molecular regulation of genes and associated pathways. Understanding the physiological and molecular mechanisms underlying how tea plants perceive and respond to cold stress is of great significance to breed new varieties with improved quality and stress resistance. In this review, we summarized the putative cold signal sensors and molecular regulation of the CBF cascade pathway in cold acclimation. We also broadly reviewed the functions and potential regulation networks of 128 cold-responsive gene families of tea plants reported in the literature, including those particularly regulated by light, phytohormone, and glycometabolism. We discussed exogenous treatments, including ABA, MeJA, melatonin, GABA, spermidine and airborne nerolidol that have been reported as effective ways to improve cold resistance in tea plants. We also present perspectives and possible challenges for functional genomic studies on cold tolerance of tea plants in the future.

Thioredoxin h2 inhibits the MPKK5-MPK3 cascade to regulate the CBF-COR signaling pathway in Citrullus lanatus suffering chilling stress

Thioredoxins (TRXs) are ubiquitous oxidoreductases and present as a multigenic family. TRXs determine the thiol redox balance, which is crucial for plants in the response to cold stress. However, limited knowledge is available about the role of TRXs in watermelon (Citrullus lanatus), which is highly sensitive to chilling stress in agricultural practice. Here, we identified 18 genes encoding 14 typical and 4 atypical TRXs from the watermelon genome, and found that ClTRX h2 localized at the plasma membrane was largely induced by chilling. Virus-induced gene silencing of ClTRX h2 resulted in watermelon plants that were more sensitive to chilling stress. We further found that ClTRX h2 physically interacted with mitogen-activated protein kinase kinase 5 (ClMPKK5), which was confirmed to phosphorylate and activate ClMPK3 in vitro, and the activation of ClMPK3 by ClMPKK5 was blocked by a point mutation of the Cys-229 residue to Ser in ClMPKK5. Additionally, ClTRX h2 inhibited the chilling-induced activation of ClMPK3, suggesting that the ClMPKK5-ClMPK3 cascade is regulated in a redox-dependent manner. We showed that ClMPK3-silenced plants had increased tolerance to chilling, as well as enhanced transcript abundances of the C-repeat/DREB binding factor (ClCBF) and cold-responsive (ClCOR) genes. Taken together, our results indicate that redox status mediated by ClTRX h2 inhibits ClMPK3 phosphorylation through the interaction between ClTRX h2 and ClMPKK5, which subsequently regulates the CBF-COR signaling pathway when submitted to chilling stress. Hence, our results provide a link between thiol redox balance and MAPK cascade signaling, revealing a conceptual framework to understand how TRX regulates chilling stress tolerance in watermelon.

StICE1 enhances plant cold tolerance by directly upregulating StLTI6A expression

Under cold conditions, StICE1 enhances plant cold tolerance by upregulating StLTI6A expression to maintain the cell membrane stability. Cold stress affects potato plants growth and development, crop productivity and quality. The ICE-CBF-COR regulatory cascade is the well-known pathway in response to cold stress in plants. ICE1, as a MYC-like bHLH transcription factor, can regulate the expressions of CBFs. However, whether ICE1 could regulate other genes still need to be explored. Our results showed that overexpressing ICE1 from potato in Arabidopsis thaliana could enhance plant cold tolerance. Under cold stress, overexpressed StICE1 in plants improved the stability of cell membrane, enhanced scavenging capacity of reactive oxygen species and increased expression levels of CBFs and COR genes. Furthermore, StICE1 could bind to the promoter of StLTI6A gene, which could maintain the stability of the cell membrane, to upregulate StLTI6A expression under cold conditions. Our findings revealed that StICE1 could directly regulate StLTI6A, CBF and COR genes expression to response to cold stress.

Research progress on plant noncoding RNAs in response to low-temperature stress

Low temperature (LT) is an important factor limiting plant growth and distribution. Plants have evolved sophisticated adaptive mechanisms to cope with hypothermia. RNA silencing is the orchestrator of these cellular responses. RNA silencing, which modifies gene expression through noncoding RNAs (ncRNAs), is a strategy used by plants to combat environmental stress. ncRNAs, which have very little protein-coding capacity, work by binding reverse complementary endogenous transcripts. In plants, ncRNAs include small non-coding RNAs (sncRNAs), medium-sized non-coding RNAs (mncRNAs), and long non-coding RNAs (lncRNAs). Apart from describing the biogenesis of different ncRNAs (miRNAs, siRNAs, and lncRNAs), we thoroughly discuss the functions of these ncRNAs during cold acclimation. Two major classes of sncRNAs, microRNAs and siRNAs, play essential regulatory roles in cold response processes through the posttranscriptional gene silencing (PTGS) pathway or transcriptional gene silencing (TGS) pathway. Microarray or transcriptome sequencing analysis can reveal a large number of cold-responsive miRNAs in plants. In this review, the cold-response patterns of miRNAs verified by Northern blotting or quantitative PCR in Arabidopsis thaliana, rice, and many other important crops are discussed. The detailed molecular mechanisms of several miRNAs in Arabidopsis (miR397, miR408, miR402, and miR394) and rice (Osa-miR156, Osa-miR319, and Osa-miR528) that regulate plant cold resistance are elucidated. In addition, the regulatory mechanism of the lncRNA SVALKA in the cold signaling pathway is explained in detail. Finally, we present the challenges for understanding the roles of small ncRNAs in cold signal transduction.

Overexpression of CfICE1 from Cryptomeria fortunei Enhances Cold, Drought and Salt Stress in Poplar

ICE1, a regulator of the cold-inducible transcriptome and freezing tolerance, is currently widely believed to be involved in plant resistance to cold stress. In this study, CfICE1 from Cryptomeria fortunei was transformed into poplar. Physiological indicators of transgenic, empty vector and wild-type poplar after abiotic stress (cold, drought and salt) were determined. Transgenic lines had a higher chlorophyll content, antioxidant enzyme activity and soluble protein content, as well as a lower malondialdehyde and hydrogen peroxide content. The ultrastructure of the plant was observed by transmission electron microscopy, and after stress, the cell structure of the transgenic line was more complete than that of the wild type. CfICE1 was upregulated in transgenic poplar trees after abiotic stress (cold, drought and salt). The CfICE1 transgenic plants improved plant resistance by regulating the CBF gene of poplar under cold and salt stress. In terms of plant responses to abiotic stress, this study showed that overexpression of CfICE1 improved the cold, drought and salt tolerance of poplars.

Antagonistic control of seed dormancy in rice by two bHLH transcription factors

Preharvest sprouting (PHS) due to lack of seed dormancy seriously threatens crop production worldwide. As a complex quantitative trait, breeding of crop cultivars with suitable seed dormancy is hindered by limited useful regulatory genes. Here by repeatable phenotypic characterization of fixed recombinant individuals, we report a quantitative genetic locus, Seed Dormancy 6 (SD6), from aus-type rice, encoding a basic helix-loop-helix (bHLH) transcription factor, which underlies the natural variation of seed dormancy. SD6 and another bHLH factor inducer of C-repeat binding factors expression 2 (ICE2) function antagonistically in controlling seed dormancy by directly regulating the ABA catabolism gene ABA8OX3, and indirectly regulating the ABA biosynthesis gene NCED2 via OsbHLH048, in a temperature-dependent manner. The weak-dormancy allele of SD6 is common in cultivated rice but undergoes negative selection in wild rice. Notably, by genome editing SD6 and its wheat homologs, we demonstrated that SD6 is a useful breeding target for alleviating PHS in cereals under field conditions.

Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes

Whole-genome duplication (WGD or polyploidization) has been suggested as a genetic contributor to angiosperm adaptation to environmental changes. However, many eudicot lineages did not undergo recent WGD (R-WGD) around and/or after the Cretaceous-Paleogene (K-Pg) boundary, times of severe environmental changes; how those plants survived has been largely ignored. Here, we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD: 12 R-WGD-containing plants (R-WGD-Y) and 10 R-WGD-lacking plants (R-WGD-N). Subsequently, we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation. The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF III and IX subfamilies through recurrent independent WGDs and tandem duplications (TDs) after the radiation of the plants. The expansions showed coincident enrichments in- times around and/or after the K-Pg boundary, when global cooling was a major environmental stressor. Consequently, convergent expansions and co-retentions of AP2/ERF III C-repeat binding factor (CBF) duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks. Moreover, promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code (G-box: CACGTG). We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes, and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.

Cold Tolerance of ScCBL6 Is Associated with Tonoplast Transporters and Photosynthesis in Arabidopsis

Plants that are adapted to harsh environments offer enormous opportunity to understand stress responses in ecological systems. Stipa capillacea is widely distributed in the frigid and arid region of the Tibetan Plateau, but its signal transduction system under cold stress has not been characterized. In this study, we isolated a cDNA encoding the signal transduction protein, ScCBL6, from S. capillacea, and evaluated its role in cold tolerance by ectopically expressing it in Arabidopsis. Full-length ScCBL6 encode 227 amino acids, and are clustered with CBL6 in Stipa purpurea and Oryza sativa in a phylogenetic analysis. Compared with tolerance in wild-type (WT) plants, ScCBL6-overexpressing plants (ScCBL6-OXP) were more tolerant to cold stress but not to drought stress, as confirmed by their high photosynthetic capacity (Fv/Fm) and survival rate under cold stress. We further compared their cold-responsive transcriptome profiles by RNA sequencing. In total, 3931 genes were differentially expressed by the introduction of ScCBL6. These gene products were involved in multiple processes such as the immune system, lipid catabolism, and secondary metabolism. A KEGG pathway analysis revealed that they were mainly enriched in plant hormone signal transduction and biomacromolecule metabolism. Proteins encoded by differentially expressed genes were predicted to be localized in chloroplasts, mitochondria, and vacuoles, suggesting that ScCBL6 exerts a wide range of functions. Based on its tonoplast subcellular location combined with integrated transcriptome and physiological analyses of ScCBL6-OXP, we inferred that ScCBL6 improves plant cold stress tolerance in Arabidopsis via the regulation of photosynthesis, redox status, and tonoplast metabolite transporters.

Sprayed biodegradable liquid film improved the freezing tolerance of cv. Cabernet Sauvignon by up-regulating soluble protein and carbohydrate levels and alleviating oxidative damage

Most cultivars of Vitis vinifera L. are very sensitive to cold. As an exogenous protectant, Biodegradable Liquid Film (BLF) is considered to protect winegrapes from low temperatures and dry winds for safe overwintering. This study aimed to reveal the physiological and biochemical mechanisms of BLF regulating the freezing tolerance of wine grapes. Groups of ten-year-old vines (Cabernet Sauvignon) were sprayed with BLF in November 2020 and 2021, or left untreated as a control treatment, and field plant mortality after overwintering were investigated. Branch samples were collected monthly for determination of biochemical indicators. Dormant two-year-old cuttings (Cabernet Sauvignon) were also used for the determination of relative expression levels of key genes. The results showed that the application of BLF reduced the branch semi-lethal temperature in January and February samples compared with control, and reduced the mortality of above-ground parts, branches and buds. The physiological status of shoots was greatly affected by the climatic conditions of the year, but BLF treatment increased the levels of soluble protein and soluble sugar, and also decreased the content of superoxide anion and malondialdehyde at most sampling times. Correlation analysis showed that the differences in freezing tolerance between BLF and no treated overwintering(CK) vines were mainly related to peroxidase activity, soluble sugar, reducing sugar and starch content. Low temperature stress activated the over expression of ICE1, CBF1, and CBF3, especially for 12h. BLF treatment significantly increased the expression levels of CBF1 and CBF3 under low temperature stress. Overall, these results demonstrate that BLF treatment protects vines from freezing damage by upregulating osmo-regulatory substances and alleviating oxidative damage.

Overexpression of PgCBF3 and PgCBF7 Transcription Factors from Pomegranate Enhances Freezing Tolerance in Arabidopsis under the Promoter Activity Positively Regulated by PgICE1

Cold stress limits plant growth, development and yields, and the C-repeat binding factors (CBFs) function in the cold resistance in plants. However, how pomegranate CBF transcription factors respond to cold signal remains unclear. Considering the significantly up-regulated expression of PgCBF3 and PgCBF7 in cold-tolerant Punica granatum ‘Yudazi’ in comparison with cold-sensitive ‘Tunisia’ under 4 °C, the present study focused on the two CBF genes. PgCBF3 was localized in the nucleus, while PgCBF7 was localized in the cell membrane, cytoplasm, and nucleus, both owning transcriptional activation activity in yeast. Yeast one-hybrid and dual-luciferase reporter assay further confirmed that PgICE1 could specifically bind to and significantly enhance the activation activity of the promoters of PgCBF3 and PgCBF7. Compared with the wild-type plants, the PgCBF3 and PgCBF7 transgenic Arabidopsis thaliana lines had the higher survival rate after cold treatment; exhibited increased the contents of soluble sugar and proline, while lower electrolyte leakage, malondialdehyde content, and reactive oxygen species production, accompanying with elevated enzyme activity of catalase, peroxidase, and superoxide dismutase; and upregulated the expression of AtCOR15A, AtCOR47, AtRD29A, and AtKIN1. Collectively, PgCBFs were positively regulated by the upstream PgICE1 and mediated the downstream COR genes expression, thereby enhancing freezing tolerance.

Cloning and function analysis of a Saussurea involucrata LEA4 gene

Late embryogenesis abundant proteins (LEA) help adapt to adverse low-temperature environments. The Saussurea involucrate SiLEA4, which encodes a membrane protein, was significantly up-regulated in response to low temperature stress. Escherichia coli expressing SiLEA4 showed enhanced low-temperature tolerance, as evident from the significantly higher survival numbers and growth rates at low temperatures. Moreover, tomato strains expressing SiLEA4 had significantly greater freezing resistance, due to a significant increase in the antioxidase activities and proline content. Furthermore, they had higher yields due to higher water utilization and photosynthetic efficiency under the same water and fertilizer conditions. Thus, expressing SiLEA4 has multiple advantages: (1) mitigating chilling injury, (2) increasing yields, and (3) water-saving, which also indicates the great potential of the SiLEA4 for breeding applications.

Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops

The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.

Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress

The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.

Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption

BACKGROUND

The citrus genus comprises a number of sensitive tropical and subtropical species to cold stress, which limits global citrus distribution to certain latitudes and causes major economic loss. We used RNA-Seq technology to analyze changes in the transcriptome of Valencia delta seedless orange in response to long-term cold stress grafted on two frequently used citrus rootstocks: Carrizo citrange (CAR), considered one of the most cold-tolerant accessions; C. macrophylla (MAC), a very sensitive one. Our objectives were to identify the genetic mechanism that produce the tolerant or sensitive phenotypes in citrus, as well as to gain insights of the rootstock-scion interactions that induce the cold tolerance or sensitivity in the scion.

RESULTS

Plants were kept at 1 ºC for 30 days. Samples were taken at 0, 15 and 30 days. The metabolomic analysis showed a significant increase in the concentration of free sugars and proline, which was higher for the CAR plants. Hormone quantification in roots showed a substantially increased ABA concentration during cold exposure in the CAR roots, which was not observed in MAC. Different approaches were followed to analyze gene expression. During the stress treatment, the 0-15-day comparison yielded the most DEGs. The functional characterization of DEGs showed enrichment in GO terms and KEGG pathways related to abiotic stress responses previously described in plant cold adaption. The DEGs analysis revealed that several key genes promoting cold adaption were up-regulated in the CAR plants, and those repressing it had higher expression levels in the MAC samples.

CONCLUSIONS

The metabolomic and transcriptomic study herein performed indicates that the mechanisms activated in plants shortly after cold exposure remain active in the long term. Both the hormone quantification and differential expression analysis suggest that ABA signaling might play a relevant role in promoting the cold hardiness or sensitiveness of Valencia sweet orange grafted onto Carrizo citrange or Macrophylla rootstocks, respectively. Our work provides new insights into the mechanisms by which rootstocks modulate resistance to abiotic stress in the production variety grafted onto them.

Genomic Survey and Cold-Induced Expression Patterns of bHLH Transcription Factors in Liriodendron chinense (Hemsl) Sarg

bHLH transcription factors play an animated role in the plant kingdom during growth and development, and responses to various abiotic stress. In this current study, we conducted, the genome-wide survey of bHLH transcription factors in Liriodendron chinense (Hemsl) Sarg., 91 LcbHLH family members were identified. Identified LcbHLH gene family members were grouped into 19 different subfamilies based on the conserved motifs and phylogenetic analysis. Our results showed that LcbHLH genes clustered in the same subfamily exhibited a similar conservative exon-intron pattern. Hydrophilicity value analysis showed that all LcbHLH proteins were hydrophilic. The Molecular weight (Mw) of LcbHLH proteins ranged from 10.19 kD (LcbHLH15) to 88.40 kD (LcbHLH50). A greater proportion, ~63%, of LcbHLH proteins had a theoretical isoelectric point (pI) less than seven. Additional analysis on the collinear relationships within species and among dissimilar species illustrated that tandem and fragment duplication are the foremost factors of amplification of this family in the evolution process, and they are all purified and selected. RNA-seq and real-time quantitative PCR analysis of LcbHLH members showed that the expression of LcbHLH35, 55, and 86 are up-regulated, and the expression of LcbHLH9, 20, 39, 54, 56, and 69 is down-regulated during cold stress treatments while the expression of LcbHLH24 was up-regulated in the short term and then later down-regulated. From our results, we concluded that LcbHLH genes might participate in cold-responsive processes of L. chinense. These findings provide the basic information of bHLH gene in L. chinense and their regulatory roles in plant development and cold stress response.

The network centered on ICEs play roles in plant cold tolerance, growth and development

ICEs are key transcription factors in response to cold in plant, they also balance plant growth and stress tolerance. Thus, we systematize the information about ICEs published to date. Low temperature is an important factor affecting plant growth and development. Exposing to cold condition results in a suit of effects on plants including reduction of plant growth and reproduction, and decrease in crop yield and quality. Plants have evolved a series of strategies to deal with cold stress such as reprogramming of the expression of genes and transcription factors. ICEs (Inducer of CBF Expression), as transcription factors regulating CBFs (C-repeat binding factor), play key roles in balancing plant growth and stress tolerance. Studies on ICEs focused on the function of ICEs on cold tolerance, growth and development; post-translational modifications of ICEs and crosstalk between the ICEs and phytohormones. In this review, we focus on systematizing the information published to date. We summarized the main advances of the functions of ICEs on the cold tolerance, growth and development. And we also elaborated the regulation of ICEs protein stability including phosphorylation, ubiquitination and SUMOylation of ICE. Finally, we described the function of ICEs in the crosstalk among different phytohormone signaling pathway and cold stress. This review provides perspectives for ongoing research about cold tolerance, growth and development in plant.

SPL9 mediates freezing tolerance by directly regulating the expression of CBF2 in Arabidopsis thaliana

BACKGROUND

Freezing stress inhibits plant development and causes significant damage to plants. Plants therefore have evolved a large amount of sophisticated mechanisms to counteract freezing stress by adjusting their growth and development correspondingly. Plant ontogenetic defense against drought, high salt, and heat stresses, has been extensively studied. However, whether the freezing tolerance is associated with ontogenetic development and how the freezing signals are delivered remain unclear.

RESULTS

In this study, we found that the freezing tolerance was increased with plant age at the vegetative stage. The expressions of microRNA156 (miR156) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), playing roles in regulation of ontogenetic development, were induced by cold stress. Overexpression of SPL9 (rSPL9) promoted the expression of C-REPEAT BINDING FACTOR 2 (CBF2) and hereafter enhanced the freezing tolerance. Genetic analysis indicated that the effect of rSPL9 on freezing tolerance is partially restored by cbf2 mutant. Further analysis confirmed that SPL9 directly binds to the promoter of CBF2 to activate the expression of CBF2, and thereafter increased the freezing tolerance.

CONCLUSIONS

Therefore, our study uncovers a new role of SPL9 in fine-tuning CBF2 expression and thus mediating freezing tolerance in plants, and implies a role of miR156-SPL pathway in balancing the vegetative development and freezing response in Arabidopsis.

Norway spruce deploys tissue-specific responses during acclimation to cold

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.

Functional Identification of ICE Transcription Factors in Rubber Tree

ICE (inducer of CBF expression) is a positive regulator of cold signaling pathway in plants. Identification of ICE transcription factors is important for the sustainable development of the natural rubber planting industry in nontraditional regions where sudden cold waves often occur. In this study, five ICE genes were isolated from genome of rubber tree (Hevea brasiliensis Muell. Arg.) for analysing tolerance to cold stress. They shared an ICE-specific region in the highly conserved bHLH-ZIP domain and were localized in the nucleus. The HbICEs were different in transcript abundance and expression patterns in response to cold and drought stresses and among different rubber tree clones. Generally, the expression level of HbICEs was significantly higher in the cold-tolerant rubber tree clones than that in the cold-sensitive rubber tree clones. Overexpression of HbICE1, HbICE2, and HbICE4 significantly enhanced the cold tolerance of transgenic Arabidopsis and tobacco, which showed a significant increase in chlorophyll content and decrease in relative water content and conductivity at the early stage of cold stress in comparison with wild-type plants. Furthermore, overexpression of HbICE2 and HbICE4, but also HbICE1 enhanced drought tolerance in transgenic Arabidopsis. The cold tolerance of rubber tree clones is positively controlled by the expression level of HbICE1, HbICE2, and HbICE4.

Poplar PsnICE1 enhances cold tolerance by binding to different cis-acting elements to improve reactive oxygen species-scavenging capability

Low temperature is a major stress that severely affects plant growth and development. Inducer of CBF expression 1 (ICE1) plays a key role in plant cold tolerance by regulating the expression of cold stress-responsive genes. In the present study, we characterized the function and underlying regulatory mechanism of PsnICE1 from Xiaohei poplar (Populus simonii × Populus nigra). PsnICE1 was significantly induced in response to cold stress in the roots, stems and leaves. PsnICE1 proteins were found to localize to the nucleus and exert transactivation activity via their N-terminal transactivation domain. Compared with non-transgenic poplar, transgenic poplar overexpressing PsnICE1 showed substantially enhanced tolerance to cold stress, with higher survival rates and antioxidant enzyme activity levels and reduced reactive oxygen species (ROS) accumulation. In contrast, plants with RNA inhibition-mediated silencing of PsnICE1 showed the opposite phenotype. PsnICE1 can bind to H-box element and abscisic acid-responsive element (ABRE), and more importantly, it mainly binds to IBS1 (a newly discovered cis-acting element) and E-box elements to regulate stress-related genes involved in ROS scavenging. Overall, these results indicated that PsnICE1 functions as a positive regulator of cold tolerance and serves as a potential candidate gene for plant cold tolerance improvement via molecular breeding.

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Prunus mume is an illustrious ornamental woody plant with colorful flowers, delicate fragrances, and graceful tree forms. Low temperature limits its geographical distribution. The basic helix-loop-helix (bHLH) proteins exist in most eukaryotes as a transcription factor superfamily, which play a crucial role in metabolism, physiology, development, and response to various stresses of higher organisms. However, the characteristics of the bHLH gene family and low-temperature response remain unknown in P. mume. In the present study, we distinguished 95 PmbHLH genes in the P. mume whole-genome and analyzed their features. PmbHLHs were divided into 23 subfamilies and one orphan by phylogenetic analysis. Similar gene structures and conserved motifs appeared in the same subfamily. These genes were situated in eight chromosomes and scaffolds. Gene duplication events performed a close relationship to P. mume, P. persica, and P. avium. Tandem duplications probably promoted the expansion of PmbHLHs. According to predicted binding activities, the PmbHLHs were defined as the Non-DNA-binding proteins and DNA-binding proteins. Furthermore, PmbHLHs exhibited tissue-specific and low-temperature induced expression patterns. By analyzing transcriptome data, 10 PmbHLHs which are responsive to low-temperature stress were selected. The qRT-PCR results showed that the ten PmbHLH genes could respond to low-temperature stress at different degrees. There were differences in multiple variations among different varieties. This study provides a basis to research the evolution and low-temperature tolerance of PmbHLHs, and might enhance breeding programs of P. mume by improving low-temperature tolerance.

Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

BACKGROUND

Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 °C, 4 °C and 0 °C, was compared by RNA sequencing.

RESULTS

Over 426 million clean reads were produced from three libraries (22 °C, 4 °C and 0 °C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation.

CONCLUSION

M. denudata exhibits responses to non-freezing cold temperature (4 °C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 °C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.

Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.)

Background

Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this study, wucai seedlings were treated with different temperatures, including low temperature (LT), high temperature (HT), and a control.

Results

According to transcriptomics analysis, the number of differentially expressed genes (DEGs) in HT and LT was 10,702 and 7267, respectively, compared with the control. The key genes associated with the physiological response of wucai to the treatments were analyzed. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations indicated the importance of the photosynthesis and photosynthetic-antenna protein pathways. We found that a high-temperature environment greatly inhibited the expression of important genes in the photosynthetic pathway (BrLhc superfamily members, PsaD, PsaE, PsaD, PsaD, PsbO, PsbP, PsbQ, PsbR, PsbS, PsbW, PsbY, Psb27, and Psb28), whereas low temperature resulted in the expression of certain key genes (BrLhc superfamily members, Psa F, Psa H, Psb S, Psb H, Psb 28). In addition, the wucai seedlings exhibited better photosynthetic performance under low-temperature conditions than high-temperature conditions.

Conclusions

Based on the above results, we speculate that upon exposure to low temperature, the plants developed higher cold tolerance by upregulating the expression of genes related to photosynthesis. Conversely, high-temperature stress inhibited the expression of pivotal genes and weakened the self-regulating ability of the plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07981-9.

Function and Mechanism of Jasmonic Acid in Plant Responses to Abiotic and Biotic Stresses

As sessile organisms, plants must tolerate various environmental stresses. Plant hormones play vital roles in plant responses to biotic and abiotic stresses. Among these hormones, jasmonic acid (JA) and its precursors and derivatives (jasmonates, JAs) play important roles in the mediation of plant responses and defenses to biotic and abiotic stresses and have received extensive research attention. Although some reviews of JAs are available, this review focuses on JAs in the regulation of plant stress responses, as well as JA synthesis, metabolism, and signaling pathways. We summarize recent progress in clarifying the functions and mechanisms of JAs in plant responses to abiotic stresses (drought, cold, salt, heat, and heavy metal toxicity) and biotic stresses (pathogen, insect, and herbivore). Meanwhile, the crosstalk of JA with various other plant hormones regulates the balance between plant growth and defense. Therefore, we review the crosstalk of JAs with other phytohormones, including auxin, gibberellic acid, salicylic acid, brassinosteroid, ethylene, and abscisic acid. Finally, we discuss current issues and future opportunities in research into JAs in plant stress responses.

Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis

Background

Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress.

Results

Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism.

Conclusion

These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07763-3.

Cloning and cold-resistance analyses of CfICE1 gene in Cryptomeria fortunei

Cryptomeria fortunei is a conifer species that can attain a height of ~70 m and is cultivated for its timber as well as its ornamental value. It is a subtropical plant that prefers a warm and humid environment. Therefore, low temperature (LT) affects its growth, development, productivity and ecological distribution. Inducer of C-repeat binding factor (CBF) expression 1 (ICE1) plays an important role in the response to cold/freezing stress in plants through the CBF regulation pathway. To date, there is no research on homologue of ICE1 in C. fortunei. In this study, we first isolated the CfICE1 transcript from C. fortunei. The CfICE1 coding sequence was 1728 nucleotides encoding a 575-aa protein and contained a serine-rich motif, a basic helix-loop-helix-Zipper (bHLH-Zip), an ACT domain and a nuclear localization signal (NLS), which were conserved in ICE1 homologous genes. Phylogenetic analysis showed that CfICE1 and all dicots ICE1 proteins were clustered together. CfICE1 had transcriptional activity in yeast cells, was predominantly located in the nucleus and highly expressed in tender needles and roots. 35S::CfICE1 transgenic Arabidopsis thaliana could increase antioxidant enzyme activities and photosynthesis and reduce the malondialdehyde content compared to the wild-type to better cope with LT. Under LT, CfICE1 expression was higher; the C. fortunei clone with stronger cold resistance (CR) significantly upregulated the expression of CfICE1 compared to the weaker clone. In conclusion, these results suggest that CfICE1 plays an active role in CR, which provides a theoretical basis for breeding for CR in C. fortunei.

Characterization of the key region and putative phosphorylation sites of EcaICE1 in its molecular interaction with the EcaHOS1 protein in Eucalyptus camaldulensis

Inducer of CBF expression 1 (ICE1), a MYC-like bHLH transcriptional activator, plays an important role in plants under cold stress. The ubiquitination-proteasome pathway mediated by high expression of osmotically responsive gene1 (HOS1) can effectively induce the degradation of ICE1 and decrease the expression of CBFs and their downstream genes under cold stress response in Arabidopsis, but knowledge of ubiquitination regulation of ICE1 by HOS1 is still limited in woody plants. In this study, a E3 ubiquitin ligase gene EcaHOS1 were amplified from Eucalyptus camaldulensis and the protein interactions between EcaICE1 and EcaHOS1 were analysed. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assay results showed that EcaICE1 can interact with the EcaHOS1 protein in the nucleus and, further, the Y2H assay demonstrated that the 126-185 amino acid region at the N-terminus of the EcaICE1 protein was indispensable for its interaction with EcaHOS1 protein. Moreover, we found that the amino acids at positions 145, 158 and 184 within the key interaction region were the putative phosphorylation sites of EcaICE1, based on bioinformatics analysis, and only the substitution of serine (Ser) 158 by alanine (Ala) blocked the protein-protein interactions between EcaICE1 and EcaHOS1 based on Y2H and β-galactosidase activity assays using site-directed mutagenesis. We identified Ser 158 of EcaICE1 as the key putative phosphorylation site for its interaction with the EcaHOS1 protein.

Plant Mitogen-Activated Protein Kinase Cascades in Environmental Stresses

Due to global warming and population growth, plants need to rescue themselves, especially in unfavorable environments, to fulfill food requirements because they are sessile organisms. Stress signal sensing is a crucial step that determines the appropriate response which, ultimately, determines the survival of plants. As important signaling modules in eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades play a key role in regulating responses to the following four major environmental stresses: high salinity, drought, extreme temperature and insect and pathogen infections. MAPK cascades are involved in responses to these environmental stresses by regulating the expression of related genes, plant hormone production and crosstalk with other environmental stresses. In this review, we describe recent major studies investigating MAPK-mediated environmental stress responses. We also highlight the diverse function of MAPK cascades in environmental stress. These findings help us understand the regulatory network of MAPKs under environmental stress and provide another strategy to improve stress resistance in crops to ensure food security.