MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways

RsWRKY49 promotes cold tolerance via activating the expression of RsCBF2 and RsNR2 in radish (Raphanus sativus L.)

Cold stress adversely affects crop growth and development. WRKY transcription factors play the critical role in regulating abiotic stress response and balancing plant growth and cold stress defense. However, the roles of WRKY in the trade-off between root growth and cold stress response are still rarely known in radish. Herein, RsWRKY49 was specifically expressed in the radish root and the expression was highly induced by low temperature in the root of cold-tolerant radish genotype 'NAU-RG' compared to the cold-sensitive radish genotype 'NAU-XBC'. Overexpression of RsWRKY49 in 'NAU-XBC' enhanced cold tolerance, while interference of its expression in 'NAU-RG' increased cold sensitivity. The increase in cell division activity and root meristem size was observed in the radish hairy root overexpressing RsWRKY49 under both normal and low-temperature conditions, demonstrating its ability to regulate cold stress response and root growth. Natural variation in the RsWRKY49 promoter affects the differences in its expression level in different cold-tolerant radish genotypes, thereby modulating cold tolerance. Comparative promoter analysis identified additional cis-acting regulatory elements (ten TATA boxes, two ABRE elements, and one DRE element) in the RsWRKY49 promoter of 'NAU-RG', which showed enhanced promoter activity compared to that of 'NAU-XBC' under cold stress. In addition, RsWRKY49 could transactivate RsCBF2 and RsNR2 expression to regulate cold stress response. These results provide insights into the molecular mechanism underlying WRKY TFs balancing root growth and defense to cold stress in radish and would facilitate achieving genetic improvement of cold-tolerant cultivars in radish breeding programs.

Genome-wide identification and expression profiles of NAC transcription factors in Poncirus trifoliata reveal their potential roles in cold tolerance

BACKGROUND

Citrus, a globally vital economic crop, faces severe challenges due to extreme climatic conditions and diseases/pests attack. Poncirus trifoliata is closely related to citrus and shows unique cold tolerance, making it a crucial material for unraveling genes involved in cold tolerance. NAC (NAM, ATAF1/2, CUC2) transcription factors play important roles in plant growth, development, and stress responses. However, their evolution patterns and gene functions in citrus remain poorly studied. This study aims to elucidate the genomic characteristics and evolution of the NAC genes in P. trifoliata, and to analyze their expression patterns and conduct functional validation under cold stress.

RESULTS

Genome-wide analysis identified 135 PtrNAC genes in P. trifoliata with non-random chromosomal distribution, including 20 gene clusters. 57.78% of the NAC genes are located in the chromosomes 3, 4 and 5. Gene duplication analysis revealed that proximal and tandem duplications as primary expansion mechanisms, with tandem repeats specifically driving gene expansion in citrus lineages (subfamilies IV, V, and VII). Collinearity analysis showed that 24.44% of the PtrNAC genes were retained in homologous regions, and Ka/Ks ratio analysis further confirmed that purifying selection dominated their evolutionary process. Transcriptome landscapes revealed that Pt5g024390 (PtrNAC2) was induced to the greatest degree under the cold stress. Meanwhile, expression level of PtrNAC2 in tetraploid was more than two folds higher compared to diploid counterpart in the presence of cold stress. Virus-induced gene silencing of PtrNAC2 led to significantly enhanced cold tolerance, implying that it plays a negative role in regulation of cold tolerance.

CONCLUSION

This study systematically elucidated the global distribution and evolutionary patterns of NAC genes in P. trifoliata. In addition, the NAC gene exhibit adaptive expansion driven by tandem duplications. The identification of PtrNAC2, a negative regulator of cold tolerance in P. trifoliata, provides valuable insights into unravelling potential candidates for engineering cold tolerance in citrus.

The MdHB7L-MdICE1L-MdHOS1 Module Fine-Tunes Apple Cold Response via CBF-Dependent and CBF-Independent Pathways

Cold stress is a major environmental factor limiting crop yield, quality, and geographical distribution worldwide. The homeodomain-leucine zipper (HD-Zip) transcription factor (TF) family plays a role in regulating plant abiotic stress responses, but the underlying mechanisms remain unclear. A HD-Zip TF, MdHB7L, is identified as promoting cold tolerance in apple. MdHB7L interacts with MdICE1L, enhancing its transcriptional activation of MdCBFs, and directly binds to MdCBF promoters to activate their expression. Conversely, MdICE1L inhibits the direct binding of MdHB7L on MdCBF promoters, revealing that MdHB7L acts as a cofactor rather than a TF when interacting with MdICE1L. Using ChIP-seq and RNA-seq, MdHB7L is found to directly regulate the expression of several key genes involved in ROS scavenging and biosynthesis of anthocyanins, soluble sugars, and proline, thereby enhancing apple cold tolerance. The E3 ubiquitin ligase MdHOS1 negatively regulates cold tolerance by interacting with and mediating the degradation of MdHB7L and MdICE1L, with a preference for MdICE1L over MdHB7L. This preference inhibits the MdHOS1-MdHB7L interaction and stabilizes MdHB7L, allowing it to sustain the plant's cold response as a TF after MdICE1L degradation. These findings provide new insights into the dynamic plant response to cold stress mediated by the MdHB7L-MdICE1-MdHOS1 module.

Comprehensive analysis of the NAC transcription factor gene family in Sophora tonkinensis Gagnep

BACKGROUND

Sophora tonkinensis Gagnep. has long been utilized in the treatment of anti-inflammatory and pain-relieving, with its principal active compounds being alkaloids and flavonoids. NAC transcription factors, a large family of plant-specific regulators, play pivotal roles in growth, development, stress responses, and secondary metabolism. However, comprehensive genome-wide characterization of S. tonkinensis NAC gene family (StNAC) remains unexplored.

RESULTS

This study identified 85 NAC proteins from the S. tonkinensis genome database. Phylogenetic analysis revealed that StNAC proteins were categorized into 15 subgroups based on their homology with Arabidopsis thaliana NAC proteins. Gene structure analysis demonstrated a variation in intron numbers ranging from 1 to 7, with a majority of StNAC genes containing 2-3 introns. Chromosomal distribution analysis indicated an uneven spread of StNAC genes across 9 chromosomes, with the highest number of StNAC genes on Chr3. Detection of 4 tandem duplicates and 32 segmental duplicates revealed that segmental duplication primarily drive StNAC genes amplification. Prediction of cis-regulatory elements suggested the involvement of StNAC genes in growth, stress responses, and hormone regulation. Gene expression analysis showed substantial variability expression of StNAC genes across different tissues. Notably, eight StNAC genes were identified as significantly associated alkaloid and flavonoid levels. qRT-PCR validation indicated that five genes were highly expressed in tissues, corroborating transcriptome data.

CONCLUSION

These findings offer valuable insights for further functional characterization of NAC genes and their potential roles in alkaloid and flavonoid biosynthesis in S. tonkinensis.

Integrative physiological and transcriptomic analysis provides insights on the molecular basis of ABA-enhanced drought tolerance in pear (Pyrus betulaefolia)

BACKGROUND

Drought stress could suppress the carbon assimilation and limit nutrient uptake of pear plants, thus affecting their growth and severely impacting the quality and yield of pear fruit. ABA is a stress hormone and is reported to alleviate drought stress in numerous plants. However, whether and how ABA functions in the drought responses of pear plants is yet explored.

RESULTS

Here, to address this gap, pear seedlings (Pyrus betulaefolia) were used and subjected to PEG-induced drought conditions with or without additional ABA in various doses. The results showed that while drought caused severe leaf water loss and damage, applying ABA at 50 µM and 100 µM dramatically amended the phenomenon, as indicated by the markedly increased relative water content, and notably decreased relative electrolyte leakage and malondialdehyde content. Based on the results of RNA sequencing and related physiological indices, it was found that drought grossly disrupted chlorophyll synthesis and photosynthesis. It induced the over-production of reactive oxygen species (ROS) and broke the ROS homeostasis, despite the pronounced increases in ABA biosynthesis/content and signaling, flavonoid synthesis, and antioxidant enzyme activities, as well as sugar metabolism. However, ABA applications significantly elevated the expressions of genes in chlorophyll synthesis and photosynthesis, partially boosting the SPAD and Fv/Fm values. In addition, ABA treatments further prominently accelerate the synthesis processes of ABA, flavonoids, and antioxidant enzymes by up-regulating the corresponding genes, resulting in endogenous ABA accumulation and enzymatic activity improvement, thereby expediting the ROS scavenging. Of course, the sugar metabolism pathway was also outstandingly enhanced to balance the growth and stress response of pear seedlings. Moreover, through WGCNA analysis, the core turquoise module associated with ABA-attenuated drought stress was identified, and a portion of key transcription factors (TFs) and some hub genes were characterized, particularly for ERF, WRKY, MYB, bHLH, NAC in TFs, and CSP, COR, and DHN in hub genes. Overall, our study reveals that exogenous ABA could help pear plants to efficiently scavenge drought-induced ROS by improving their photosynthesis capacity, ABA accumulation, sugar catabolism, enzymatic antioxidant system, etc. These results will provide a scientific basis and practical direction for utilizing ABA to mitigate the adverse effects of water starvation resulting from the persistent high temperature on pear plants in summer.

CONCLUSION

50 µM and 100 µM ABA application ameliorated the drought damage in pear seedlings, and the working routes are associated with reinforcement in the photosystem, ABA biosynthesis and signaling, flavonoid accumulation, and sugar metabolism, as well as enzymatic activities in ROS scavenging. The relevant regulatory network is complex, primarily concerned with ERF, WRKY, MYB, bHLH, and NAC TFs, with a focus on the potential target genes named CSP, COR, and DHN.

Genome-Wide Analysis of NAC Transcription Factor Gene Family in Morus atropurpurea

The NAC (NAM/ATAF1/2/CUC2) transcription factors are pivotal regulators in plant development and stress responses. Despite the extensive studies on the NAC gene family across various plant species, the characterization of this gene family in mulberry (Morus atropurpurea) remains unexplored. Here, we conducted a genome-wide identification and characterization of the NAC gene family in M. atropurpurea. A total of 79 MaNAC genes were identified and classified into 20 subgroups, displaying an uneven distribution across the 14 chromosomes. The structural analysis found that most MaNAC genes possess at least three exons and contain the conserved NAC domain and characteristic motifs at the N-terminus. Eleven collinear gene pairs were identified in M. atropurpurea genome. Interspecies collinearity analysis demonstrated a closer evolutionary relationship between M. atropurpurea and Populus trichocarpa, supported by the identification of 116 collinear gene pairs. Expression profiling revealed dynamic changes in the transcript levels of most MaNAC genes during mulberry fruit maturation. Notably, the eight MaNAC members from the OsNAC7 subfamily exhibited tissue-specific expression patterns. A significant proportion of MaNAC genes displayed varying degrees of responsiveness to drought stress and sclerotium disease. MaNAC12, MaNAC32, MaNAC44 and MaNAC67 emerged as the most highly responsive candidates. Overexpression of MaNAC69 enhanced drought tolerance in Arabidopsis. These findings provide a robust foundation for future functional studies and mechanistic investigations into the roles of the NAC gene family in M. atropurpurea, offering insights into their contributions to development and stress adaptation.

PbNAC3 coordinates AsA generation and ABA biosynthesis to improve salt tolerance in pear

In plants, dehydroascorbate reductase (DHAR) is one of the key enzymes in AsA generation during the AsA-GSH cycle, which helps maintain the normal metabolic level of AsA. However, the molecular mechanism of DHAR's response to salt stress is still unknown. Our experiments show a ping-pong mechanism, in which DHA is combined with free reductase DHAR, and free reductase DHAR is combined with GSH in the form of sulfenylation to promote AsA generation in response to salt stress. This mechanism is inhibited by H2O2-mediated sulfenylation modification. The overexpression of PbDHAR3 in pear callus and Arabidopsis plants alleviated salt-induced damage, while its silencing decreased salt tolerance in Pyrus betulaefolia. PbNAC3 can activate the expression of PbDHAR3 by directly binding to the promoter. The overexpression of PbNAC3 in pear callus improved salt tolerance, while silencing it reduced tolerance in P. betulaefolia. Overexpression of PbNAC3 in Arabidopsis plants is able to adjust the trade-off between plant growth and salt stress. Higher expression levels of NCEDs or PYLs, and higher ABA content were observed under salt treatment. Further experiments demonstrate that PbNAC3 activates PbNCED5 through interaction with cis-regulatory elements. Overall, our results show that PbNAC3 plays a critical role in salt stress response by targeting the promoters of PbDHAR3 and PbNCED5, promoting AsA generation and ABA biosynthesis. This study will deepen our understanding of the mechanisms underlying the trade-offs between plant growth and stress tolerance and assist the development of stress-resistant, high-yield crops.

Flavonoids as key players in cold tolerance: molecular insights and applications in horticultural crops

Cold stress profoundly affects the growth, development, and productivity of horticultural crops. Among the diverse strategies plants employ to mitigate the adverse effects of cold stress, flavonoids have emerged as pivotal components in enhancing plant resilience. This review was written to systematically highlight the critical role of flavonoids in plant cold tolerance, aiming to address the increasing need for sustainable horticultural practices under climate stress. We provide a comprehensive overview of the role of flavonoids in the cold tolerance of horticultural crops, emphasizing their biosynthesis pathways, molecular mechanisms, and regulatory aspects under cold stress conditions. We discuss how flavonoids act as antioxidants, scavenging reactive oxygen species (ROS) generated during cold stress, and how they regulate gene expression by modulating stress-responsive genes and pathways. Additionally, we explore the application of flavonoids in enhancing cold tolerance through genetic engineering and breeding strategies, offering insights into practical interventions for improving crop resilience. Despite significant advances, a research gap remains in understanding the precise molecular mechanisms by which specific flavonoids confer cold resistance, especially across different crop species. By addressing current knowledge gaps, proposing future research directions and highlighting implications for sustainable horticulture, we aim to advance strategies to enhance cold tolerance in horticultural crops.

An integrative overview of cold response and regulatory pathways in horticultural crops

Global climate change challenges agricultural production, as extreme temperature fluctuations negatively affect crop growth and yield. Low temperature (LT) stress impedes photosynthesis, disrupts metabolic processes, and compromises the integrity of cell membranes, ultimately resulting in diminished yield and quality. Notably, many tropical or subtropical horticultural plants are particularly susceptible to LT stress. To address these challenges, it is imperative to understand the mechanisms underlying cold tolerance in horticultural crops. This review summarizes recent advances in the physiological and molecular mechanisms that enable horticultural crops to withstand LT stress, emphasizing discrepancies between horticultural crops and model systems. These mechanisms include C-repeat binding factor-dependent transcriptional regulation, post-translational modifications, epigenetic control, and metabolic regulation. Reactive oxygen species, plant hormones, and light signaling pathways are integrated into the cold response network. Furthermore, technical advances for improving cold tolerance are highlighted, including genetic improvement, the application of light-emitting diodes, the utility of novel plant growth regulators, and grafting. Finally, prospective directions for fundamental research and practical applications to boost cold tolerance are discussed.

RsWRKY40 coordinates the cold stress response by integrating RsSPS1-mediated sucrose accumulation and the CBF-dependent pathway in radish (Raphanus sativus L.)

Cold stress adversely affects crop growth and development. Radish is an important root vegetable crop, and its taproot formation is susceptible to low temperatures. However, the molecular basis of the cold stress response has not yet been fully dissected in radish. Here, a sucrose phosphate synthase gene (RsSPS1) was identified through a genome-wide association study and transcriptome analysis. RsSPS1 was responsible for sucrose synthesis, and sucrose was shown to be involved in taproot growth, cambium activity, and cold tolerance in radish. RsSPS1 regulated cambium activity and cold stress response by modulating sucrose content. Moreover, RsWRKY40 was identified as the upstream transcription activator of RsSPS1 by binding to its promoter. RsWRKY40 functioned in cambium activity and cold tolerance by modulating RsSPS1-mediated sucrose accumulation. Furthermore, RsWRKY40 promoted the RsCBF1 and RsCBF2 expression levels, resulting in elevated cold resilience. RsWRKY40 also enhanced its own transcription, forming a positive auto-regulatory loop to regulate cold stress response in radish. Together, a transcription module of RsWRKY40 orchestrated cold stress response by integrating sucrose accumulation and the CBF-dependent pathway was uncovered. These findings would provide novel insight into the molecular mechanism underlying cold-responsive sucrose accumulation and cambium activity and facilitate the genetic improvement of cold tolerance in radish breeding programs.

EIL (ethylene-insensitive 3-like) transcription factors in apple affect both ethylene- and cold response-dependent fruit ripening

EIN3/EIL (ethylene-insensitive 3/EIN3-like) transcription factors are positive downstream transcriptional regulators of ethylene signalling. In apple (Malus × domestica), a small family of MdEIL genes was identified, with four expressed in fruit. Transgenic lines were generated to manipulate MdEIL1 expression, and fruits were sampled at harvest maturity and after cold treatment. Their fruit ripening behaviour was compared with control lines and contrasted to a ACC OXIDASE 1 antisense line (ACO1as) which produced no ripening associated ethylene. Two transgenic lines showed strong co-suppression of MdEIL1-4 expression as well as reduced ethylene production, softening and aroma production, while one overexpressing line showed enhanced ripening. Key genes involved in ethylene biosynthesis and ethylene-dependent genes involved in cell wall modification (MdXTH1, MdβGAL) and aroma biosynthesis (MdAFS1, MdoOMT1) were downregulated in the co-suppressed lines. Co-suppressed lines showed reduced softening/volatile production after cold treatment and in contrast to the ACO1as line, expression of cold response-dependent genes (MdCBF2, dehydrins MdDHN2, -14, -16 and MdNAC29a) remained cold-repressed. The action of MdEILs was shown using dual-luciferase reporter assays to occur through direct activation of MdAFS1, MdXTH1 and MdβGAL promoters. Exogenous ethylene was unable to further stimulate ripening promoter activation, but cold treatment could. Promoter deletion analysis identified potential EIL binding sites in the MdAFS1 and MdβGAL promoters and electrophoretic mobility shift assays showed that MdEIL1-3 could all bind to a 32 bp fragment in the MdAFS1 promoter. Together these results indicate that MdEILs contribute to a suite of apple fruit ripening attributes via activation of genes in an ethylene-dependent manner, but also in response to cold.

Alleviation of salt stress in strawberries by hydrogen-rich water: Physiological, transcriptomic and metabolomic responses

The increasing impacts of climate change and intensified human activities exacerbate soil salinization, posing significant challenges to agricultural productivity. Therefore, addressing salt stress in crops is a critical area of research. In this study, strawberry seedlings (Fragaria×ananassa Duch. 'Benihoppe') were used to investigate the alleviating effects of hydrogen-rich water (HRW) on salt stress through integrated transcriptomic and metabolomic analyses. HRW treatment was found to significantly enhance plant growth, notably increasing root biomass by 49.50%. Additionally, HRW modulated key parameters, including the levels of soluble sugars, malondialdehyde (MDA), and antioxidant enzyme activities, while promoting K+ uptake and Na+ exclusion. Transcriptomic analysis revealed that HRW induced the expression of genes associated with ion transport, antioxidant defence, and cell wall biosynthesis in roots. Metabolomic profiling identified phenolic acids, flavonoids, and amino acids as critical metabolites in HRW-mediated salt stress mitigation. Integrated multi-omics analysis highlighted two key metabolic pathways, phenylpropanoid biosynthesis and amino and nucleoside sugar metabolism, pivotal to the observed protective effects. This study provides molecular insights into the mechanisms by which HRW alleviates salt stress in strawberry seedlings, underscoring the potential of hydrogen gas applications in sustainable agriculture.

PhNH10 Suppresses Low Temperature Tolerance in Petunia Through the Abscisic Acid-Dependent Pathway

Low-temperature stress limits plant growth, and reduces aesthetics of many ornamental plants. Plants have developed different adaptive mechanisms to cope with low-temperature stress, in which NAC transcription factor family members playing an important role in low-temperature tolerance. However, their roles in petunia in response to low temperature are still largely unknown. Here, we found that a NAC transcription factor, namely, PhNH10, negatively regulates low-temperature response in petunia. PhNH10-silenced and -CRISPR/Cas9 mutant plants displayed higher survival rate, anthocyanin content and abscisic acid concentration than PhNH10-overexpression and wild-type plants under low-temperature condition. PhNH10 can directly bind to the PhABA8ox promoter to active its expression, which further promotes the abscisic acid catabolism, while silencing of PhABA8ox increased the ABA concentration and low-temperature tolerance. In addition, PhNH10 interact with a low-temperature-related E2 ubiquitin-conjugating enzyme, PhUBC2-1, which in turn inhibited the binding capacity of PhNH10 on PhABA8ox promoter. Our research has elucidated an extensive mechanistic network underlying the PhNH10-mediated regulation of low-temperature response in petunia. This finding not only presents a new viewpoint in understanding the low-temperature tolerance mechanisms but also delineates a promising pathway for transgenic petunia with improved low-temperature resistance.

Galactinol synthase gene 5 (MdGolS5) enhances the cold resistance of apples by promoting raffinose family oligosaccharide accumulation

Low-temperature stress is a limiting factor affecting the safe overwintering and stable production of apples. Galactinol, produced by galactinol synthase (GolS), is an important plant cryoprotectant. This study showed for the first time that exogenous spraying of apple saplings with 100 mg mL-1 galactinol could effectively alleviate the damage from low-temperature stress. Further, we found that transgenic apple callus and tobacco overexpressing MdGolS5 showed strong cold tolerance. Specifically, the activities of antioxidant enzymes such as superoxide dismutase and GolS in transgenic tobacco overexpressing MdGolS5 increased under low-temperature treatment at -2 °C, and the contents of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower than those of wild type tobacco. Moreover, large amounts of proline, galactinol, and raffinose were accumulated. In addition, the expression levels of cold-responsive genes MdCBF1, MdCBF2, MdCBF3, and MdCOR47 were significantly up-regulated in transgenic tobacco, further confirming the important role of MdGolS5 in regulating plant cold adaptation. In summary, this study not only revealed the direct effect of exogenous galactinol on the low-temperature protection of apple saplings for the first time, but also explored a new mechanism of raffinose family oligosaccharides anabolism in plant low-temperature adaptation through overexpression of MdGolS5. These results provide a theoretical basis for the genetic improvement of apple cold resistance.

Multiple roles of NAC transcription factors in plant development and stress responses

NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are a family of plant-specific TFs that play crucial roles in various aspects of plant development and stress responses. Here, we provide an in-depth review of the structural characteristics, regulatory mechanisms, and functional roles of NACs in different plant species. One of the key features of NACs is their ability to regulate gene expression through a variety of mechanisms, including binding to DNA sequences in the promoter regions of target genes, interacting with other TFs, and modulating chromatin structure. We discuss these mechanisms in detail, providing insights into the complex regulatory networks that govern the activity of NACs. We explore the diverse functions of these TFs in plant growth and development processes, including embryogenesis, seed development, root and shoot development, floral development and fruit ripening, secondary cell wall formation, and senescence. We also discuss the diverse regulatory roles of NACs in response to various stresses, including drought, flooding, heat, cold, salinity, nutrient deficit, and diseases. Lastly, we emphasize the crosstalk role of NACs between developmental processes and stress responses. This integrated perspective highlights how NACs orchestrate plant growth and resilience. Overall, this review provides a comprehensive overview of the pivotal roles of NACs in plant development and stress responses, emphasizing their potential for engineering stress-resistant crops and enhancing agricultural productivity.

24-Epibrassinolide treatment alleviates frost damage of apple flower via regulating proline, ROS, and energy metabolism

Frost damage to apple flowers significantly affects both the quality and yield of apples, potentially leading to substantial economic losses. This study investigates the application of the environmentally friendly plant hormone 24-epibrassinolide (EBR) on apple flowers to assess its effects under frost stress conditions. The findings indicate that exogenous EBR treatment maintained favorable flower morphology, mitigated pistil browning, and reduced ion leakage. Furthermore, EBR enhanced the ICE-CBF-COR signaling pathway and increased proline accumulation by modulating gene expression and enzyme activity involved in proline metabolism, promoting osmotic adjustment ability of cells. Furthermore, EBR treatment retarded the increase of H2O2, O2·-, and malonaldehyde (MDA), and increased the enzymatic activity and gene expression of antioxidant enzymes such as superoxide dismutase (SOD), Catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD), thereby augmenting the antioxidant capacity of tissues. Additionally, the study found that exogenous EBR reduced AMP content, promoted ATP content and energy charge level, improved succinic dehydrogenase (SDH), cytochrome oxidase (CCO), H+-ATPase, Ca2+-ATPase enzyme activity, and enhanced the energy supply of the cells. Consequently, we hypothesized that EBR treatment could enhance the frost resistance in apple flowers by synergistically ameliorating cold signaling, osmotic adjustment, antioxidant capacity, and energy status.

GHCYP706A7 governs anthocyanin biosynthesis to mitigate ROS under alkali stress in cotton

KEY MESSAGE

Flavonoid 3'-hydroxylase synthesis gene-GHCYP706A7, enhanced cotton resistance to alkali stress by scavenging ROS to regulate anthocyanin synthesis. Anthocyanins are a class of flavonoids that play a significant role in mediating plant responses to adverse environmental conditions. Flavonoid 3'-hydroxylase (F3'H), a member of the cytochrome P-450 (CYP) family, is a pivotal enzyme involved in the biosynthesis of anthocyanins. The present study identified 398 CYPs in the Gossypium hirsutum genome, of which GHCYP706A7 was responsible for F3'H synthesis and its ability to respond to alkaline stress. GHCYP706A7 suppression through virus-induced gene silencing (VIGS) diminished tolerance to alkali stress in cotton, evidenced by significantly reduced anthocyanin synthesis, markedly decreased antioxidant capacity, notable increases in reactive oxygen species, severe cellular damage, and observably decreased stomatal opening. The cumulative effects of these physiological disruptions ultimately manifest in cotton wilting and fresh weight decline. These findings lay a foundation for further investigations into the role of CYPs in regulating anthocyanin synthesis and responding to alkali stress.

Genome-Wide Identification and Expression Divergence of CBF Family in Actinidia arguta and Functional Analysis of AaCBF4 Under Cold Stress

The C-repeat binding factors (CBFs) gene is essential for plants' cold response, which could not only be induced by the inducer of CBF expression (ICE) genes but also activated the expression of the cold-regulated (COR) gene, thereby participating in the ICE-CBF-COR cold response pathway. However, this gene family and its functions in Actinidia arguta remain unclear. In this study, whole-genome identification and functional analysis of CBF family members in A. arguta were performed. Eighteen CBF genes, which were located on four chromosomes and had five tandem repeats, were identified. The proteins encoded by the genes were predicted to be located in the nucleus and cytoplasm. The results of the promoter cis-acting element analysis revealed light response elements, low-temperature response elements, and hormone (methyl jasmonate, gibberellin, salicylic acid, etc.) response elements. We analyzed collinearity with other kiwifruit genomes, and, interestingly, the number of CBF family members differed across geographic locations of A. arguta. RT-qPCR revealed that the expression of the CBF gene family differed under low-temperature treatment; specifically, we observed differences in the expression of all the genes. Based on phylogenetic relationships and RT-qPCR analysis, the expression of AaCBF4.1 (AaCBF4) was found to be highly upregulated, and the function of this gene in cold resistance was further verified via overexpression in transgenic Arabidopsis. AaCBF4-overexpressing plants showed higher tolerance to cold stress, showing a higher germination rate, higher chlorophyll content and lower relative electrolyte leakage. In addition, compared with the wild-type Arabidopsis, the overexpressing plants exhibited significantly reduced oxidative damage due to the reduction in reactive oxygen species production under cold stress. Therefore, AaCBF4 plays an important role in improving the cold resistance of Actinidia arguta and can be further used to develop kiwifruit germplasm resources with strong cold resistance.

PiERF1 regulates cold tolerance in Plumbago indica L. through ethylene signalling

Ethylene is a signalling factor that plays a key role in the response of plants to abiotic stresses, such as cold stress. Recent studies have shown that the exogenous application of 1-aminocyclopropane-1-carboxylate (ACC), an ethylene promoter, affects plant cold tolerance. The cold-responsive specific gene DREB plays a crucial role in enhancing cold tolerance in plants by activating several cold-responsive (COR) genes. However, how the ethylene biosynthesis pathway regulates this gene in the cold response of thermophilic plants has yet to be fully elucidated. In this study, the thermophilic plant Plumbago indica L. was used as an example. Physiological experiments and transcriptomic analyses revealed that cold stress treatment induced the synthesis of endogenous ACC and regulated the ethylene signalling activator PiERF1, and cold signalling also activated PiDREB1A. Spray experiments also revealed that ACC-induced upregulation of the PiERF1 gene reduced the cold tolerance of P. indica and decreased the expression level of the PiDREB1A gene. These results indicate that ethylene signalling directly regulates the downstream gene PiERF1 and initiates the DREB‒COR cold-responsive signalling pathway to regulate cold tolerance, resulting in the negative regulation of cold tolerance in thermophilic plants.

Integrated Transcriptomic and Metabolomic Analysis Revealed Regulatory Mechanisms on Flavonoids Biosynthesis in the Skin of Passion Fruit (Passiflora spp.)

Passion fruit is one of the most famous fruit crops in tropical and subtropical regions due to its high edible, medicinal, and ornamental value. Flavonoids, a class of plant secondary metabolites, have important health-related roles. In this study, a total of 151 flavonoid metabolites were identified, of which 25 key metabolites may be the main contributors to the purple phenotype. Using RNA sequencing, 11,180 differentially expressed genes (DEGs) were identified. Among these, 48 flavonoid biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, DFR, ANS, and UFGT) and 123 transcription factors were identified. Furthermore, 12 distinct modules were identified through weighted gene coexpression network analysis, of which the brown module displays a robust positive correlation with numerous flavonoid metabolites. Overexpression of PeMYB114 significantly promoted flavonoids accumulation in tobacco leaves. Our study provided a key candidate gene for molecular breeding to improve color traits in passion fruit.

ERD14 regulation by the HY5- or HY5-MED2 module mediates the cold signal transduction of asparagus bean

Cold stress affects the growth, development, and yield of asparagus bean (Vigna unguiculata subsp. sesquipedalis). Mediator (MED) complex subunits regulate the cold tolerance of asparagus bean, but the underlying regulatory mechanisms remain unclear. Here, VunMED2 positively responds to cold stress of asparagus beans. Under cold acclimation and freezing treatment, the survival rate, ROS scavenging activity, and expression levels of VunMED2 were increased in VunMED2 transgenic plants. Natural variation in the promoter of VunMED2 in two different cold-tolerant asparagus beans was observed. Under cold stress, the expression of the GUS reporter gene was higher in cold-tolerant plants than in cold-sensitive plants, and the expression of the GUS reporter gene was tissue-specific. VunHY5 positively influenced the expression of VunMED2 by binding to the E-box motif, and the transcriptional activation of the promoter was stronger in the cold-tolerant variety than in cold-sensitive plants. VunHY5 overexpression improved plant freezing resistance by increasing the antioxidant capacity and expression of dehydrin genes. VunHY5 and VunMED2 play a synergistic role in binding to the G-box/ABRE motif and transcriptionally activating the expression of VunERD14. VunERD14 complemented the med2 mutant, which could positively respond to plant freezing resistance by reducing membrane lipid peroxidation and improving the antioxidant capacity. Therefore, the VunHY5-VunERD14 module and the VunHY5-VunMED2-VunERD14 positive cascade effect are involved in the cold signal transduction in asparagus bean. Our findings have implications for the breeding of asparagus bean varieties with improved cold tolerance.

WD40 protein OsTTG1 promotes anthocyanin accumulation and CBF transcription factor-dependent pathways for rice cold tolerance

Temperature is a critical abiotic factor affecting rice (Oryza sativa L.) yields, and cold stress at the seedling stage can inhibit plant growth or even be fatal. Antioxidants such as anthocyanins accumulate in a variety of plants during cold stress, but the underlying mechanisms are not well understood. Here, we report that rice TRANSPARENT TESTA GLABRA 1 (OsTTG1), a major regulator of anthocyanin biosynthesis in rice, responds to short- and long-term cold stress at both the transcriptional and protein levels. Metabolomic and transcriptomic data indicate that OsTTG1 activates the expression of anthocyanidin synthase (OsANS) genes under cold stress. Our data also suggest that OsTTG1 forms a MYB-bHLH-WD (MBW) complex with Basic helix-loop-helix 148 (OsbHLH148) and Myb-related S3 (OsMYBS3), and this complex activates the expression of Dehydration-responsive element-binding protein 1 (OsDREB1) and OsANS genes. Together, our findings reveal the mechanisms by which OsTTG1 coordinates both anthocyanin biosynthesis and the expression of cold-responsive genes in colored rice, providing genetic resources for future cold resistance breeding in rice.

TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato

The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE 1) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.

Understanding cold stress response mechanisms in plants: an overview

Low-temperature stress significantly impacts plant growth, development, yield, and geographical distribution. However, during the long-term process of evolution, plants have evolved complicated mechanisms to resist low-temperature stress. The cold tolerance trait is regulated by multiple pathways, such as the Ca2+ signaling cascade, mitogen-activated protein kinase (MAPK) cascade, inducer of CBF expression 1 (ICE1)-C-repeat binding factor (CBF)-cold-reulated gene (COR) transcriptional cascade, reactive oxygen species (ROS) homeostasis regulation, and plant hormone signaling. However, the specific responses of these pathways to cold stress and their interactions are not fully understood. This review summarizes the response mechanisms of plants to cold stress from four aspects, including cold signal perception and transduction, ICE1-CBF-COR transcription cascade regulation, ROS homeostasis regulation and plant hormone signal regulation. It also elucidates the mechanism of cold stress perception and Ca2+ signal transduction in plants, and proposes the important roles of transcription factors (TFs), post-translational modifications (PTMs), light signals, circadian clock factors, and interaction proteins in the ICE1-CBF-COR transcription cascade. Additionally, we analyze the importance of ROS homeostasis and plant hormone signaling pathways in plant cold stress response, and explore the cross interconnections among the ICE1-CBF-COR cascade, ROS homeostasis, and plant hormone signaling. This comprehensive review enhances our understanding of the mechanism of plant cold tolerance and provides a molecular basis for genetic strategies to improve plant cold tolerance.

ATBS1-INTERACTING FACTOR 2 Positively Regulates Freezing Tolerance via INDUCER OF CBF EXPRESSION 1/C-REPEAT BINDING FACTOR-Induced Cold Acclimation Pathway

The INDUCER OF CBF EXPRESSION 1/C-REPEAT BINDING FACTOR (ICE1/CBF) pathway plays a crucial role in plant responses to cold stress, impacting growth and development. Here, we demonstrated that ATBS1-INTERACTING FACTOR 2 (AIF2), a non-DNA-binding basic helix-loop-helix transcription factor, positively regulates freezing tolerance through the ICE1/CBF-induced cold tolerance pathway in Arabidopsis. Cold stress transcriptionally upregulated AIF2 expression and induced AIF2 phosphorylation, thereby stabilizing the AIF2 protein during early stages of cold acclimation. The AIF2 loss-of-function mutant, aif2-1, exhibited heightened sensitivity to freezing before and after cold acclimation. In contrast, ectopic expression of AIF2, but not the C-terminal-deleted AIF2 variant, restored freezing tolerance. AIF2 enhanced ICE1 stability during cold acclimation and promoted the transcriptional expression of CBFs and downstream cold-responsive genes, ultimately enhancing plant tolerance to freezing stress. MITOGEN-ACTIVATED PROTEIN KINASES 3 and 6 (MPK3/6), known negative regulators of freezing tolerance, interacted with and phosphorylated AIF2, subjecting it to protein degradation. Furthermore, transient co-expression of MPK3/6 with AIF2 and ICE1 downregulated AIF2/ICE1-induced transactivation of CBF2 expression. AIF2 interacted preferentially with BRASSINOSTEROID-INSENSITIVE 2 (BIN2) and MPK3/6 during the early and later stages of cold acclimation, respectively, thereby differentially regulating AIF2 activity in a cold acclimation time-dependent manner. Moreover, AIF2 acted additively in a gain-of-function mutant of BRASSINAZOLE-RESISTANT 1 (BZR1; bzr1-1D) and a triple knockout mutant of BIN2 and its homologs (bin2bil1bil2) to induce CBFs-mediated freezing tolerance. This suggests that cold-induced AIF2 coordinates freezing tolerance along with BZR1 and BIN2, key positive and negative components, respectively, of brassinosteroid signaling pathways.

Genome-Wide Characterization of IQD Family Proteins in Apple and Functional Analysis of the Microtubule-Regulating Abilities of MdIQD17 and MdIQD28 under Cold Stress

Microtubules undergo dynamic remodeling in response to diverse abiotic stress in plants. The plant-specific IQ67 DOMAIN (IQD) family proteins serve as microtubule-associated proteins, playing multifaceted roles in plant development and response to abiotic stress. However, the biological function of IQD genes in apple remains unclear. In this study, we conducted a comprehensive analysis of the Malus domestica genome, identifying 42 IQD genes distributed across 17 chromosomes and categorized them into four subgroups. Promoter analysis revealed the presence of stress-responsive elements. Subsequent expression analysis highlighted the significant upregulation of MdIQD17 and MdIQD28 in response to cold treatments, prompting their selection for further functional investigation. Subcellular localization studies confirmed the association of MdIQD17 and MdIQD28 with microtubules. Crucially, confocal microscopy and quantification revealed diminished microtubule depolymerization in cells transiently overexpressing MdIQD17 and MdIQD28 compared to wild-type cells during cold conditions. In conclusion, this study provides a comprehensive analysis of IQD genes in apple, elucidating their molecular mechanism in response to cold stress.

Transcriptome and metabolome atlas reveals contributions of sphingosine and chlorogenic acid to cold tolerance in Citrus

Citrus is one of the most important fruit crop genera in the world, but many Citrus species are vulnerable to cold stress. Ichang papeda (Citrus ichangensis), a cold-hardy citrus species, holds great potential for identifying valuable metabolites that are critical for cold tolerance in Citrus. However, the metabolic changes and underlying mechanisms that regulate Ichang papeda cold tolerance remain largely unknown. In this study, we compared the metabolomes and transcriptomes of Ichang papeda and HB pummelo (Citrus grandis "Hirado Buntan", a cold-sensitive species) to explore the critical metabolites and genes responsible for cold tolerance. Metabolomic analyses led to the identification of common and genotype-specific metabolites, consistent with transcriptomic alterations. Compared to HB pummelo under cold stress, Ichang papeda accumulated more sugars, flavonoids, and unsaturated fatty acids, which are well-characterized metabolites involved in stress responses. Interestingly, sphingosine and chlorogenic acid substantially accumulated only in Ichang papeda. Knockdown of CiSPT (C. ichangensis serine palmitoyltransferase) and CiHCT2 (C. ichangensis hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyltransferase2), two genes involved in sphingosine and chlorogenic acid biosynthesis, dramatically decreased endogenous sphingosine and chlorogenic acid levels, respectively. This reduction in sphingosine and chlorogenic acid notably compromised the cold tolerance of Ichang papeda, whereas exogenous application of these metabolites increased plant cold tolerance. Taken together, our findings indicate that greater accumulation of a spectrum of metabolites, particularly sphingosine and chlorogenic acid, promotes cold tolerance in cold-tolerant citrus species. These findings broaden our understanding of plant metabolic alterations in response to cold stress and provide valuable targets that can be manipulated to improve Citrus cold tolerance.

MdSINA2-MdNAC104 Module Regulates Apple Alkaline Resistance by Affecting γ-Aminobutyric Acid Synthesis and Transport

Soil alkalization is an adverse factor limiting plant growth and yield. As a signaling molecule and secondary metabolite, γ-aminobutyric acid (GABA) responds rapidly to alkaline stress and enhances the alkaline resistance of plants. However, the molecular mechanisms by which the GABA pathway adapts to alkaline stress remain unclear. In this study, a transcription factor, MdNAC104 is identified, from the transcriptome of the alkaline-stressed roots of apple, which effectively reduces GABA levels and negatively regulates alkaline resistance. Nevertheless, applying exogenous GABA compensates the negative regulatory mechanism of overexpressed MdNAC104 on alkaline resistance. Further research confirms that MdNAC104 repressed the GABA biosynthetic gene MdGAD1/3 and the GABA transporter gene MdALMT13 by binding to their promoters. Here, MdGAD1/3 actively regulates alkaline resistance by increasing GABA synthesis, while MdALMT13 promotes GABA accumulation and efflux in roots, resulting in an improved resistance to alkaline stress. This subsequent assays reveal that MdSINA2 interacts with MdNAC104 and positively regulates root GABA content and alkaline resistance by ubiquitinating and degrading MdNAC104 via the 26S proteasome pathway. Thus, the study reveals the regulation of alkaline resistance and GABA homeostasis via the MdSINA2-MdNAC104-MdGAD1/3/MdALMT13 module in apple. These findings provide novel insight into the molecular mechanisms of alkaline resistance in plants.

Discovery of candidate genes involved in ethylene biosynthesis and signal transduction pathways related to peach bud cold resistance

Background: Low temperature pose significant challenges to peach cultivation, causing severe damage to peach buds and restricting production and distribution. Ethylene, an important phytohormone, plays a critical role in enhancing plant cold resistance. Structural genes and transcription factors involved in ethylene biosynthesis and signal transduction pathways are associated with cold resistance. However, no research has specifically addressed their roles in peach cold resistance. Methods: In this study, we aimed for cold-resistance gene discovery in cold-sensitive peach cultivar "21Shiji" (21SJ) and cold-resistance cultivar "Shijizhixing" (SJZX) using RNA-seq and gas chromatography. Results: The findings revealed that under cold stress conditions, ethylene biosynthesis in "SJZX" was significantly induced. Subsequently, a structural gene, PpACO1-1, involved in ethylene biosynthesis in peach buds was significantly upregulated and showed a higher correlation with ethylene release rate. To identify potential transcription factors associated with PpACO1-1 expression and ethylene signal transduction, weighted gene co-expression network analysis was conducted using RNA-seq data. Four transcription factors: PpERF2, PpNAC078, PpWRKY65 and PpbHLH112, were identified. Conclusion: These findings provide valuable theoretical insights for investigating the regulatory mechanisms of peach cold resistance and guiding breeding strategies.

Integrated Metabolomics and Transcriptomics Reveal the Key Role of Flavonoids in the Cold Tolerance of Chrysanthemum

Chrysanthemum (Chrysanthemum morifolium, ground-cover Chrysanthemums), one of the important garden flowers, has a high ornamental and economic value. However, its ornamental value is significantly diminished by the low temperature experienced in northeastern China. Here, metabolomics and transcriptomics were performed on three Chrysanthemum cultivars before and after a low temperature to investigate the dynamic metabolite changes and the molecular regulatory mechanisms. The results showed that 1324 annotated metabolites were detected, among which 327 were identified as flavonoids derived from Chrysanthemum. The accumulation of metabolites and gene expression related to the flavonoid biosynthesis pathway significantly increased in the three cultivars under the low temperature, indicating flavonoid metabolism actively participates in the Chrysanthemum cold response. Specifically, the content of cyanidin and pelargonidin derivatives and the expression of anthocyanin biosynthesis genes significantly increases in XHBF, providing a reasonable explanation for the change in petal color from white to purple under the low temperature. Six candidate UDP-glycosyltransferase genes involved in the glycosylation of flavonoids were identified through correlation networks and phylogenetic analysis. CmNAC1, CmbZIP3, and other transcription factors potentially regulating flavonoid metabolism and responding to low temperatures were discovered by correlation analysis and weighted gene co-expression network analysis (WGCNA). In conclusion, this study elucidated the specific response of flavonoids to low temperatures in Chrysanthemums, providing valuable insights and metabolic data for investigating cold tolerance.

The miR6445-NAC029 module regulates drought tolerance by regulating the expression of glutathione S-transferase U23 and reactive oxygen species scavenging in Populus

MicroRNAs are essential in plant development and stress resistance, but their specific roles in drought stress require further investigation. Here, we have uncovered that a Populus-specific microRNAs (miRNA), miR6445, targeting NAC (NAM, ATAF, and CUC) family genes, is involved in regulating drought tolerance of poplar. The expression level of miR6445 was significantly upregulated under drought stress; concomitantly, seven targeted NAC genes showed significant downregulation. Silencing the expression of miR6445 by short tandem target mimic technology significantly decreased the drought tolerance in poplar. Furthermore, 5' RACE experiments confirmed that miR6445 directly targeted NAC029. The overexpression lines of PtrNAC029 (OE-NAC029) showed increased sensitivity to drought compared with knockout lines (Crispr-NAC029), consistent with the drought-sensitive phenotype observed in miR6445-silenced strains. PtrNAC029 was further verified to directly bind to the promoters of glutathione S-transferase U23 (GSTU23) and inhibit its expression. Both Crispr-NAC029 and PtrGSTU23 overexpressing plants showed higher levels of PtrGSTU23 transcript and GST activity while accumulating less reactive oxygen species (ROS). Moreover, poplars overexpressing GSTU23 demonstrated enhanced drought tolerance. Taken together, our research reveals the crucial role of the miR6445-NAC029-GSTU23 module in enhancing poplar drought tolerance by regulating ROS homeostasis. This finding provides new molecular targets for improving the drought resistance of trees.

Transcriptomic Analysis Reveals the Flavonoid Biosynthesis Pathway Involved in Rhizome Development in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua (P. cyrtonema) rhizomes are rich in flavonoids and other secondary metabolites, exhibiting remarkable antioxidant, anti-tumor, and immunomodulatory effects. Polygonatum flavonoid-biosynthesis-related genes have been characterized already. However, a comprehensive overview of Polygonatum flavonoid biosynthesis pathways is still absent. To articulate the accumulation of the flavonoid biosynthesis pathways, we examined transcriptome changes using Illumina HiSeq from five different tissues and the RNA-seq of 15 samples had over 105 Gb of a clean base, generating a total of 277,955 unigenes. The cDNA libraries of the fruits (F), leaves (L), roots (R), stems (S), and rhizomes (T) of three-year-old P. cyrtonema plants generated 57,591, 53,578, 60,321, 51,530, and 54,935 unigenes. Comparative transcriptome analysis revealed that 379 differentially expressed genes (DEGs) were in the group of F _vs_ T, L _vs_ T, R _vs_ T, and S _vs_ T, and the transcripts of flavonoid-biosynthesis-related DEGs were principally enriched in rhizomes. In addition, combined with WGCNA and the FPKM of five tissues' transcription, nine differentially expressed transcription factor families (MYB, WRKY, AP2/ERF, etc.) were characterized in the red module, the red module positively correlated with rhizome flavonoid accumulation. Quantitative real-time PCR (qRT-PCR) further indicated that BZIP1, C3H31, ERF114, and DREB21 are differentially expressed in rhizomes, accompanied in rhizome development in P. cyrtonema. Therefore, this study provides a foundation for further research into uncovering the accumulation of flavonoid biosynthesis in the rhizomes of P. cyrtonema.

Physiological and transcriptomic analysis revealed that the accumulation of reactive oxygen species caused the low temperature sensitivity of Liriodendron × sinoamericanum

Liriodendron × sinoamericanum is widely cultivated in southern China as an excellent wood and garden ornamental trees. However, its intolerance to low temperature limits its application to high latitudes. Understanding the molecular mechanism of low temperature sensitivity of Liriodendron × sinoamericanum is very important for its further application. In this study, combined with physiological and transcriptomic analysis, it was revealed that low temperature stress can lead to water loss and decreased photosynthetic capacity of Liriodendron × sinoamericanum leaves. The accelerated accumulation of reactive oxygen species (ROS) caused by the imbalance of cell REDOX homeostasis is one of the important reasons for the low temperature sensitivity. Further analysis showed that several transcription factors could be involved in regulating the synthesis and degradation of ROS, among which LsNAC72 and LsNAC73a could regulate the accumulation of O2- and H2O2 in leaves by affecting the expression level of LsAPX, LsSOD, LsPAO, and LsPOD.

Soybean RVE8a confers salt and drought tolerance in Arabidopsis

Soybean is an economically important crop, which often suffers various abiotic stresses. REVEILLE (RVE) genes have been generally considered as circadian oscillators to mediate diverse developmental processes and plant response to environmental stresses. Addressing their roles is of significance for utilizing them to enhance agronomic traits in crops. However, our understanding of soybean RVEs is extremely limited. In the study, we investigated the expression patterns of soybean CCA1-like genes under salt stress using our RNA-Seq data. Subsequently, a salt stress-inducible gene, GmRVE8a, was chosen for further study. Phylogenetic analysis indicated that GmRVE8a is most closely related to Arabidopsis RVE4 and RVE8. Also, GmRVE8a showed circadian expression pattern with 24 h rhythmic period, suggesting that it might be a clock-regulated gene. Moreover, transgenic Arabidopsis lines over-expressing GmRVE8a were generated. It was observed that ectopic over-expression of GmRVE8a caused a significant delay in flowering. Further observation indicated that under salt and drought stress, transgenic seedlings were stronger than wild type. Consistently, three-week-old transgenic plants grew better than wild type under salt and drought conditions, and the MDA content in transgenic lines was significantly lower than wild type, suggesting that GmRVE8a might be a positive regulator in response to salt and drought stress. Intriguingly, Y2H assay indicated that GmRVE8a physically interacted with a drought-tolerant protein, GmNAC17. Overall, our findings provided preliminary information regarding the functional roles of GmRVE8a in response to salt and drought stress.

Overexpression of a Fragaria vesca NAM, ATAF, and CUC (NAC) Transcription Factor Gene (FvNAC29) Increases Salt and Cold Tolerance in Arabidopsis thaliana

The NAC (NAM, ATAF1/2, CUC2) family of transcription factors (TFs) is a vital transcription factor family of plants. It controls multiple parts of plant development, tissue formation, and abiotic stress response. We cloned the FvNAC29 gene from Fragaria vesca (a diploid strawberry) for this research. There is a conserved NAM structural domain in the FvNAC29 protein. The highest homology between FvNAC29 and PaNAC1 was found by phylogenetic tree analysis. Subcellular localization revealed that FvNAC29 is localized onto the nucleus. Compared to other tissues, the expression level of FvNAC29 was higher in young leaves and roots. In addition, Arabidopsis plants overexpressing FvNAC29 had higher cold and high-salinity tolerance than the wild type (WT) and unloaded line with empty vector (UL). The proline and chlorophyll contents of transgenic Arabidopsis plants, along with the activities of the antioxidant enzymes like catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) under 200 mM NaCl treatment or -8 °C treatment, were higher than those activities of the control. Meanwhile, malondialdehyde (MDA) and the reactive oxygen species (ROS) content were higher in the WT and UL lines. FvNAC29 improves transgenic plant resistance to cold and salt stress by regulating the expression levels of AtRD29a, AtCCA1, AtP5CS1, and AtSnRK2.4. It also improves the potential to tolerate cold stress by positively regulating the expression levels of AtCBF1, AtCBF4, AtCOR15a, and AtCOR47. These findings suggest that FvNAC29 may be related to the processes and the molecular mechanisms of F. vesca response to high-salinity stress and LT stress, providing a comprehensive understanding of the NAC TFs.

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Plants possess the remarkable ability to sense detrimental environmental stimuli and launch sophisticated signal cascades that culminate in tailored responses to facilitate their survival, and transcription factors (TFs) are closely involved in these processes. Phytochrome interacting factors (PIFs) are among these TFs and belong to the basic helix-loop-helix family. PIFs are initially identified and have now been well established as core regulators of phytochrome-associated pathways in response to the light signal in plants. However, a growing body of evidence has unraveled that PIFs also play a crucial role in adapting plants to various biological and environmental pressures. In this review, we summarize and highlight that PIFs function as a signal hub that integrates multiple environmental cues, including abiotic (i.e., drought, temperature, and salinity) and biotic stresses to optimize plant growth and development. PIFs not only function as transcription factors to reprogram the expression of related genes, but also interact with various factors to adapt plants to harsh environments. This review will contribute to understanding the multifaceted functions of PIFs in response to different stress conditions, which will shed light on efforts to further dissect the novel functions of PIFs, especially in adaption to detrimental environments for a better survival of plants.

IbMYC2 Contributes to Salt and Drought Stress Tolerance via Modulating Anthocyanin Accumulation and ROS-Scavenging System in Sweet Potato

Basic helix-loop-helix (bHLH) transcription factors extensively affect various physiological processes in plant metabolism, growth, and abiotic stress. However, the regulation mechanism of bHLH transcription factors in balancing anthocyanin biosynthesis and abiotic stress in sweet potato (Ipomoea batata (L.) Lam.) remains unclear. Previously, transcriptome analysis revealed the genes that were differentially expressed among the purple-fleshed sweet potato cultivar 'Jingshu 6' and its anthocyanin-rich mutant 'JS6-5'. Here, we selected one of these potential genes, IbMYC2, which belongs to the bHLH transcription factor family, for subsequent analyses. The expression of IbMYC2 in the JS6-5 storage roots is almost four-fold higher than Jingshu 6 and significantly induced by hydrogen peroxide (H2O2), methyl jasmonate (MeJA), NaCl, and polyethylene glycol (PEG)6000. Overexpression of IbMYC2 significantly enhances anthocyanin production and exhibits a certain antioxidant capacity, thereby improving salt and drought tolerance. In contrast, reducing IbMYC2 expression increases its susceptibility. Our data showed that IbMYC2 could elevate the expression of anthocyanin synthesis pathway genes by binding to IbCHI and IbDFR promoters. Additionally, overexpressing IbMYC2 activates genes encoding reactive oxygen species (ROS)-scavenging and proline synthesis enzymes under salt and drought conditions. Taken together, these results demonstrate that the IbMYC2 gene exercises a significant impact on crop quality and stress resistance.

MdbHLH160 is stabilized via reduced MdBT2-mediated degradation to promote MdSOD1 and MdDREB2A-like expression for apple drought tolerance

Drought stress is a key environmental factor limiting the productivity, quality, and geographic distribution of crops worldwide. Abscisic acid (ABA) plays an important role in plant drought stress responses, but the molecular mechanisms remain unclear. Here, we report an ABA-responsive bHLH transcription factor, MdbHLH160, which promotes drought tolerance in Arabidopsis (Arabidopsis thaliana) and apple (Malus domestica). Under drought conditions, MdbHLH160 is directly bound to the MdSOD1 (superoxide dismutase 1) promoter and activated its transcription, thereby triggering reactive oxygen species (ROS) scavenging and enhancing apple drought tolerance. MdbHLH160 also promoted MdSOD1 enzyme activity and accumulation in the nucleus through direct protein interactions, thus inhibiting excessive nuclear ROS levels. Moreover, MdbHLH160 directly upregulated the expression of MdDREB2A-like, a DREB (dehydration-responsive element binding factor) family gene that promotes apple drought tolerance. Protein degradation and ubiquitination assays showed that drought and ABA treatment stabilized MdbHLH160. The BTB protein MdBT2 was identified as an MdbHLH160-interacting protein that promoted MdbHLH160 ubiquitination and degradation, and ABA treatment substantially inhibited this process. Overall, our findings provide insights into the molecular mechanisms of ABA-modulated drought tolerance at both the transcriptional and post-translational levels via the ABA-MdBT2-MdbHLH160-MdSOD1/MdDREB2A-like cascade.

Research progress on the physiological response and molecular mechanism of cold response in plants

Low temperature is a critical environmental stress factor that restricts crop growth and geographical distribution, significantly impacting crop quality and yield. When plants are exposed to low temperatures, a series of changes occur in their external morphology and internal physiological and biochemical metabolism. This article comprehensively reviews the alterations and regulatory mechanisms of physiological and biochemical indices, such as membrane system stability, redox system, fatty acid content, photosynthesis, and osmoregulatory substances, in response to low-temperature stress in plants. Furthermore, we summarize recent research on signal transduction and regulatory pathways, phytohormones, epigenetic modifications, and other molecular mechanisms mediating the response to low temperatures in higher plants. In addition, we outline cultivation practices to improve plant cold resistance and highlight the cold-related genes used in molecular breeding. Last, we discuss future research directions, potential application prospects of plant cold resistance breeding, and recent significant breakthroughs in the research and application of cold resistance mechanisms.

A novel R2R3-MYB transcription factor PbMYB1L of Pyrus bretschneideri regulates cold tolerance and anthocyanin accumulation

KEY MESSAGE

PbMYB1L enhances the cold tolerance and anthocyanin accumulation of transgenic Arabidopsis by regulating the expression of genes related to the cold-responsive genes pathway and anthocyanin synthesis pathway. MYB transcription factors (TFs) have been demonstrated to play diverse roles in plant growth and development. In the present study, we identified a novel R2R3-MYB transcription factor, PbMYB1L, from the peel of 'Red Zaosu' pear (Pyrus bretschneideri), which was induced by cold stress and acted as a positive regulator in anthocyanin biosynthesis. Notably, the transgenic Arabidopsis lines exhibited enhanced tolerance to cold stress. Compared to the Arabidopsis wild-type plants, the transgenic lines displayed longer primary roots and reduced reactive oxygen species (ROS) levels including O2-, hydrogen peroxide (H2O2), and malondialdehyde (MDA). Furthermore, significant upregulation of key cold-responsive genes AtCBF1, AtCBF2, AtCBF3, AtCBF4, and AtKIN1 was observed in the transgenic plants under cold stress conditions compared to wild type. Arabidopsis plants overexpressing PbMYB1L had significant anthocyanin accumulation in leaves after cold treatment with quantitative results indicating higher expression of anthocyanin structural genes compared to wild type. These findings suggest that PbMYB1L not only plays a vital role in conferring cold tolerance but also acts as a crucial regulator of anthocyanin biosynthesis.

The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants

Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.

RsCDF3, a member of Cycling Dof Factors, positively regulates cold tolerance via auto-regulation and repressing two RsRbohs transcription in radish (Raphanus sativus L.)

Radish is one of the most economical root vegetable crops worldwide. Cold stress dramatically impedes radish taproot formation and development as well as reduces its yield and quality. Although the Cycling Dof Factors (CDFs) play crucial roles in plant growth, development and abiotic stress responses, how CDF TFs mediate the regulatory network of cold stress response remains largely unexplored in radish. Herein, a total of nine RsCDF genes were identified from the radish genome. Among them, the RsCDF3 exhibited obviously up-regulated expression under cold stress, especially at 12 h and 24 h. RsCDF3 was localized to the nucleus and displayed dramatic cold-induced promoter activity in tobacco leaves. Moreover, overexpression of RsCDF3 significantly enhanced cold tolerance of radish plants, whereas its knock-down plants exhibited the opposite phenotype. Interestingly, both in vitro and in vivo assays indicated that the RsCDF3 repressed the transcription of RsRbohA and RsRbohC via directly binding to their promoters, which contributed to maintaining the cellular homeostasis of reactive oxygen species (ROS) production and scavenging in radish. In addition, the RsCDF3 bound to its own promoter to mediate its transcription, thereby forming an autoregulatory feedback loop to cooperatively trigger RsRbohs-dependent cold tolerance. Together, we revealed a novel RsCDF3-RsRbohs module to promote the cold tolerance in radish plants. These findings would facilitate unveiling the molecular mechanism governing RsCDF3-mediated cold stress response in radish.

Genome-Wide Identification of Catalase Gene Family and the Function of SmCAT4 in Eggplant Response to Salt Stress

Salinity is an important abiotic stress, damaging plant tissues by causing a burst of reactive oxygen species (ROS). Catalase (CAT) enzyme coded by Catalase (CAT) genes are potent in reducing harmful ROS and hydrogen peroxide (H2O2) produced. Herein, we performed bioinformatics and functional characterization of four SmCAT genes, retrieved from the eggplant genome database. Evolutionary analysis CAT genes revealed that they are divided into subgroups I and II. The RT-qPCR analysis of SmCAT displayed a differential expression pattern in response to abiotic stresses. All the CAT proteins of eggplant were localized in the peroxisome, except for SmCAT4, which localized in the cytomembrane and nucleus. Silencing of SmCAT4 compromised the tolerance of eggplant to salt stress. Suppressed expression levels of salt stress defense related genes SmTAS14 and SmDHN1, as well as increase of H2O2 content and decrease of CAT enzyme activity was observed in the SmCAT4 silenced eggplants. Our data provided insightful knowledge of CAT gene family in eggplant. Positive regulation of eggplant response to salinity by SmCAT4 provides resource for future breeding programs.