Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis

Endophytic fungus Stagonosporopsis ajaci NEAU-BLH1 from Adonis amurensis enhances seed germination under low-temperature stress and increases grain yield in direct-seeded rice

Rice direct-seeding technology is regarded as a promising alternative to traditional transplanting due to its labor- and water-saving benefits. However, poor seedling emergence and growth under low-temperature stress remain major obstacles to its widespread adoption in Heilongjiang Province, China. Here, we isolated an endophytic fungus Stagonosporopsis ajaci NEAU-BLH1 from the cold-resistant plant Adonis amurensis, which effectively enhanced rice seed germination and seedling growth under low-temperature stress. Two years of pot and field experiments demonstrated that soaking rice seeds in a spore suspension of NEAU-BLH1 significantly increased tillering, resulting in a 16.0-47.8 % improvement in yield for direct-seeded rice. Mechanistic investigations revealed that NEAU-BLH1 treatment elevated gibberellin levels and reduced abscisic acid, accelerating starch hydrolysis into soluble sugars, thus improving germination under low temperature. Comprehensive physiological, transcriptomic, and metabolomic analyses indicated that NEAU-BLH1 enhances seedling growth by boosting respiratory metabolism, mitigating oxidative damage, and modulating hormone pathways. These findings indicate that seed-soaking with NEAU-BLH1 has good potential to enhance seed germination under low-temperature stress and increases grain yield in direct-seeded rice.

Role of jasmonates in plant response to temperature stress

The ambient temperature exerts a significant influence on the growth and development of plants, which are sessile organisms. Exposure to extreme temperatures, both low and high, has a detrimental impact on plant growth and development, crop yields, and even geographical distribution. Jasmonates constitute a class of lipid hormones that regulate plant tolerance to biotic and abiotic stresses. Recent studies have revealed that jasmonate biosynthesis and signaling pathways are integral to plant responses to both high and low temperatures. Exogenous application of jasmonate improves cold and heat tolerance in plants and reduces cold injury in fruits and vegetables during cold storage. Jasmonate interacts with low and high temperature key response factors and engages in crosstalk with primary and secondary metabolic pathways, including hormones, under conditions of temperature stress. This review presents a comprehensive summary of the jasmonate synthesis and signal transduction pathway, as well as an overview of the functions and mechanisms of jasmonate in response to temperature stress.

ICE1 (Inducer of CBF Expression 1) Is Essential for the Jasmonate-Regulated Development of Stamen in Arabidopsis thaliana

Floral organ development, pollen germination and pollen tube growth are crucial for plant sexual reproduction. Phytohormones maintain these processes by regulating the expression and activity of various transcription factors. ICE1, a MYC-like bHLH transcription factor, has been revealed to be involved in cold acclimatisation of Arabidopsis. This study shows that ICE1 regulates multiple aspects of sexual reproduction, including stamen development, pollen development and germination. Loss-of-function mutants of ICE1 exhibit floral organs with shorter filaments, defective anther dehiscence and lower pollen viability compared to the wild type. These abnormalities result in disrupted fertilisation, leading to short siliques, a high rate of seed abortion, and dark, shriveled mature seeds. JAZ proteins (JAZ1 and JAZ9) interact with ICE1, inhibiting its transcriptional activity on jasmonic acid (JA)-responsive genes, including MYB21, MYB24 and MYB108. This study highlights the essential role of ICE1 as a signalling agent in the JA-regulated maintenance of sexual reproduction in Arabidopsis thaliana.

ScDREBA5 Enhances Cold Tolerance by Regulating Photosynthetic and Antioxidant Genes in the Desert Moss Syntrichia caninervis

Extreme cold events, becoming more frequent, affect plant growth and development. Much is known about C-repeat binding transcription factor (CBF)-dependent cold-signaling pathways in plants. However, the CBF-independent regulatory pathway in angiosperms is unclear, and the cold-signaling pathways in non-angiosperms lacking CBFs, such as the extremely cold-tolerant desert moss Syntrichia caninervis, are largely unknown. In this study, we determined that fully hydrated S. caninervis without cold acclimation could tolerate a low-temperature of -16°C. Transcriptome analysis of S. caninervis under 4°C and -4°C treatments revealed that sugar and energy metabolism, lipid metabolism and antioxidant activity were altered in response to cold stress, and surprisingly, most photosynthesis-related genes were upregulated under cold treatment. Transcription factors analysis revealed that A-5 DREB genes, which share a common origin with CBFs, are the hubs in the freezing-stress response of S. caninervis, in which ScDREBA5 was upregulated ~1000-fold. Overexpressing ScDREBA5 significantly enhanced freezing tolerance in both S. caninervis and Physcomitrium patens by upregulating genes involved in photosynthetic and antioxidant pathways. This is the first study to uncover the mechanism regulating the cold-stress response in S. caninervis. Our findings increase our understanding of different cold-stress response strategies in non-angiosperms and provide valuable genetic resources for breeding cold-tolerant crops.

Divergent MYB paralogs determine spatial distribution of linalool mediated by JA and DNA demethylation participating in aroma formation and cold tolerance of tea plants

Linalool not only is one of characteristic flavour volatiles of tea, contributing to floral aroma, but also a kind of defensive compounds, playing essential roles in resistance against biotic/abiotic stresses. Although the linalool synthases have been identified, much is unknown about the regulation mechanism in tea plants. We identified two pairs of MYB paralogs as linalool biosynthesis activators, in which one pair (CsMYB148/CsMYB193) specifically expressed in flowers, and another (CsMYB68/CsMYB147) highly expressed in flowers, leaves, fruits and roots. These activators interacted with CsMYC2 to form MYC2-MYB complexes to regulate linalool synthase. While Jasmonate ZIM-domain (JAZ) proteins served as the linalool biosynthesis repressors by interfering MYC2-MYB complex. Further, we found that the transcripts of CsMYB68/CsMYB147 were significantly upregulated by jasmonic acid (JA) to improve linalool products during tea processing and that linalool pathway may as one of the downstream pathways of JA signalling and DNA methylation processes to participate in cold resistance. Under cold stress, JA signalling was activated to elevate the abundance of MYC-MYB complexes; meanwhile, DNA demethylation was also activated, leading to declining methylation levels and increasing transcripts of CsMYB68/CsMYB147. Our study provides a new insight into synergistically improving tea quality and tea plant resistance.

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.

Integrated transcriptomics and metabolomics analyses reveal jasmonic acid metabolic pathways for improving the chilling tolerance in cotton seedlings

Cotton (Gossypium spp.) originated in tropical and subtropical regions, spreading to higher latitudes through domestication while retaining thermophilic characteristics. Xinjiang, a major cotton-producing area in China, frequently experiences 'late spring cold snaps' due to its location, causing chilling injury during critical sowing periods. Current research on cotton chilling stress primarily focuses on physiological studies such as evaluations of chilling stress and biochemical indices but lacks systematic investigation into the difference among varieties. Phenotypic screening across seed germination, cotyledon, and seedling stages identified upland cotton (Gossypium hirsutum) cultivar, Junmian1 exhibits superior cold tolerance relative to the sensitive genotype C1470. Under chilling stress, Junmian1 protects chloroplasts and other cellular structures in its first true leaf to survive the chilling stress. Weighted gene co-expression network analysis (WGCNA) analysis pinpointed Module Brown as a chilling-tolerance responsive hub, with subsequent validation via virus-induced gene silencing (VIGS) confirming the regulatory roles of GhRBL (Ribulose-bisphosphate carboxylase), GhGI (GIGANTEA), and lncRNA MSTR.1631 in cold tolerance. Additionally, integrated metabolomic and transcriptomic analyses demonstrated that jasmonic acid plays a crucial role in enhancing cotton's chilling tolerance at seedling stage. The primary difference in chilling tolerance between Junmian1 and C1470 is attributed to the signaling efficiency of the jasmonic acid synthesis and metabolism pathways. These findings establish JA metabolic engineering as a viable approach for enhancing cold resilience in early-stage cotton seedlings.

Jasmonic Acid-Mediated Antioxidant Defense Confers Chilling Tolerance in Okra (Abelmoschus esculentus L.)

Chilling stress inhibits the growth of okra (Abelmoschus esculentus L.), reduces its overall agricultural yield, and deteriorates fruit quality. Therefore, it is crucial to elucidate the mechanism through which okra plants respond to chilling stress. This study investigates the molecular mechanisms of chilling tolerance by comparing the transcriptome and metabolome of chilling-tolerant (Ae182) and chilling-sensitive (Ae171) okra varieties. We found that Ae182 exhibits higher antioxidant enzyme activities, including SOD, POD, CAT, and APX, suggesting it mitigates oxidative stress more effectively than Ae171. Metabolomics analysis revealed that Ae182 produces higher levels of jasmonic acid (JA) and JA-isoleucine (JA-Ile) under chilling stress, potentially activating genes that alleviate oxidative damage. Additionally, integrated analyses identified key transcription factors, such as AP2, BHLH, and MYB, associated with JA and chilling stress. These findings provide candidate genes for further research on chilling resistance in okra.

The 14-3-3 gene AaGRF1 positively regulates cold tolerance in kiwifruit

Low temperatures severely threaten the growth and development of kiwifruit. Research has demonstrated that proteins belonging to the 14-3-3 family play a pivotal regulatory function in the ability of plants to resist stress. However, this specific roles of the genes in kiwifruit cold tolerance remain unclear. It had been identified that β-amylase gene, AaBAM3.1, exhibits a positive regulatory effect on kiwifruit's tolerance to low temperature. In our research, we obtained the Actinidia arguta 14-3-3 gene general regulatory factor 1 (AaGRF1) from yeast one-hybrid (Y1H) screening library of the AaBAM3.1 promoter; the expression level of AaGRF1 was enhanced by low-temperature stress. Subcellular localization, Y1H and dual-LUC assay indicated that the AaGRF1 protein resides within the nucleus and possesses the ability to interact with the AaBAM3.1 promoter. Moreover, we also studied the role of AaGRF1 gene in cold resistance of kiwifruit. When AaGRF1 was overexpressed in kiwifruit, the transgenic plants exhibited enhanced cold tolerance. The level of antioxidants and soluble sugars in these plants were elevated compared to wild-type (WT) lines. RNA-seq of the transgenic and WT lines revealed that AaGRF1 might interact with genes in the 'ascorbate-glutathione' and 'starch and sucrose' pathways, thereby enhancing the cold resistance of kiwifruit. In summary, we hypothesize that the 14-3-3 gene AaGRF1 may positively modulate the cold resistance in kiwifruit by accumulating more antioxidants and soluble sugars.

Phenotypic adaptation and genomic variation of Kandelia obovata associated with its northern introduction along southeastern coast of China

Introduction

Mangroves play a crucial role within coastal wetland ecosystems, with Kandelia obovata frequently utilized for introduction studies and cultivation research. Investigating the rapid adaptability of K. obovata across diverse environmental conditions offers valuable insights into how mangroves can effectively acclimate to global climate fluctuations.

Methods

In this study, following a common gardenexperiment, we investigated variations in morphological traits between twodistinct populations of K. obovata, Quanzhou (QZ) and Wenzhou (WZ),originating from the same introduction site Zhangzhou (ZZ). Then we performed the whole-genome resequencing on multiple populations along the southern coast of China to assess genetic divergence and diversity patterns in response to environmental factors.

Results

Our findings have uncovered divergent growth-defense trade-off mechanisms employed by these two populations when exposed to varying minimal temperatures in the coldest month within their respective habitats. Moreover, our observations have revealed discernible genetic divergence during the process of environmental acclimatization. Subsequent whole-genome re-sequencing have unveiled a significant decrease in genetic diversity within the northernmost population, suggesting that temperature plays a primary role in shaping genetic variability within the K. obovata species.

Discussion

These findings present new evidence for the rapid adaptation of K. obovata and contributes to our understanding of environmental adaptation characteristics during its introduction to northern regions, which holds significant implications for the conservation and sustainable development of mangroves.

Multi-omics reveal the molecular mechanisms of Sodium Nitrophenolate in enhancing cold tolerance through hormonal and antioxidant pathways in cucumber

Sodium nitrophenate (CSN) enhanced cold tolerance of cucumber. However, at the omics-level, the molecular mechanism of CSN to cold stress remains unclear. Here, we found that CSN was comparable to abscisic acid and much stronger than 2, 4-epibrassinolide (EBR) in enhancing cold tolerance. RNA-seq indicated that CSN regulated the brassinolides (BR) and cytokinin (CK) synthesis in the late stage of cold stress (LS-CS). CSN reduced the source of BR synthesis, accelerated the conversion of intermediate substances to BR and the deactivation of BR. While, CSN accelerated CK synthesis and CK deactivation by cytokinin dehydrogenase. Hormone content determination showed that CSN increased BR and decreased CK contents during most time-points of cold stress. Kinds of hormone signaling genes at LS-CS were activated by CSN, which may be due to changes in BR and CK contents. CSN also enhanced the expression of 90 % phenylalanine ammonia-lyase genes, participated in phenylpropanoid biosynthesis, at LS-CS. Genes of phenylpropanoid biosynthesis pathway and hormones signal were co-expression during cold stress. The metabolome also showed that CSN participated phenylpropanoid biosynthesis at LS-CS too. However, as for lipid metabolome, CSN up-regulated anthocyanin, flavones and flavonols metabolism at the early stage of cold stress. The autumn and winter field yield test showed that CSN increase cucumber yield by approximately 17.67 % and economic income by 207.67 dollars/667 m2. Collectedly, CSN may regulate lipid metabolism and hormone signaling mediated antioxidant pathways to enhance cold tolerance in the early and late stages of cold stress, respectively.

Transcriptome Analysis Reveals the Pivotal Genes and Regulation Pathways Under Cold Stress and Identifies SbERF027, an AP2/ERF Gene That Confers Cold Tolerance in Sorghum

Low temperature at the seedling stage adversely affects sorghum growth and development and limits its geographical distribution. APETALA2/Ethylene-Responsive transcription factors (AP2/ERFs), one of the largest transcription factor families in plants, play essential roles in growth, development, and responses to abiotic stresses. However, the roles of AP2/ERF genes in cold tolerance in sorghum and the mechanisms underlying their effects remain largely unknown. Here, transcriptome sequencing (RNA-seq) was performed on the leaves of sorghum seedlings before and after cold treatment. Several candidate genes for cold tolerance and regulation pathways involved in "photosynthesis" under cold stress were identified via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Additionally, the AP2/ERF family gene SbERF027, a novel regulator of cold tolerance, was functionally identified through a comprehensive analysis. The expression of SbERF027 was high in seedlings and panicles, and its expression was induced by low temperature; the cold-induced expression level of SbERF027 was markedly higher in cold-tolerant accession SZ7 than in cold-sensitive accession Z-5. SbERF027 was detected in the nucleus under both normal and cold stress conditions. In addition, the cold tolerance of SbERF027-overexpressing lines was higher than that of wild-type plants; while the cold tolerance of lines with SbERF027 silenced via virus-induced gene silencing (VIGS) was significantly lower than that of wild-type plants. Further research demonstrated that SNP-911 of the promoter was essential for enhancing cold tolerance by mediating SbERF027 expression. This study lays a theoretical foundation for dissecting the mechanism of cold tolerance in sorghum and has implications for the breeding and genetic improvement of cold-tolerant sorghum.

Regulatory Mechanisms of Bud Dormancy: Environmental, Hormonal, and Genetic Perspectives

Dormancy is a vital adaptive strategy in temperate and boreal plants, particularly fruit trees, enabling them to withstand harsh winter conditions and ensure survival and synchronized growth resumption in spring. This review comprehensively examines dormancy, focusing on its physiological, environmental, and molecular mechanisms. Dormancy is characterized by two distinct phases: endodormancy, which is regulated by internal plant signals and requires cold temperatures for release, and ecodormancy, which is influenced by external environmental factors. These stages are intricately linked to seasonal temperature fluctuations and the plant's ability to synchronize growth cycles, ensuring survival through harsh winters and optimal growth in warmer seasons. The review delves into the role of chilling requirements, temperature thresholds, and hormonal regulation in the dormancy process, highlighting how these factors influence critical growth events such as budbreak, flowering, and fruiting. Plant hormones, including abscisic acid, gibberellins, and cytokinins, regulate dormancy by modulating gene expression and growth activity. Additionally, we explore the historical development of dormancy research, from early observations of chilling requirements to the formulation of the chilling hours model. Considering ongoing climate change, the review examines how rising winter temperatures may disrupt dormancy cycles, potentially affecting the timing of flowering, fruiting, and overall crop productivity. This shift necessitates new strategies for managing dormancy, particularly in regions experiencing inconsistent or insufficient chilling. The review concludes by discussing practical approaches to enhance dormancy release and mitigate the impact of environmental stress on deciduous fruit tree growth, offering insights into improving agricultural practices amidst a changing climate.

Nitrate attenuates abscisic acid signaling via NIN-LIKE PROTEIN8 in Arabidopsis seed germination

Abscisic acid (ABA) suppresses Arabidopsis (Arabidopsis thaliana) seed germination and post-germinative growth. Nitrate stimulates seed germination, but whether it directly regulates ABA signaling and the associated underlying molecular mechanisms remain unknown. Here, we showed that nitrate alleviates the repressive effects of ABA on seed germination independently of the nitric oxide (NO) pathway. Moreover, nitrate attenuates ABA signaling activated by ABSCISIC ACID INSENSITIVE3 (ABI3) and ABI5, two critical transcriptional regulators of the ABA pathway. Mechanistic analyses demonstrated that ABI3 and ABI5 physically interact with the nitrate signaling-related core transcription factor NIN-LIKE PROTEIN 8 (NLP8). After ABA treatment, NLP8 suppresses ABA responses during seed germination without affecting ABA content. Notably, nitrate represses ABA signaling mainly through NLP8. Genetic analyses showed that NLP8 acts upstream of ABI3 and ABI5. Specifically, NLP8 inhibits the transcriptional functions of ABI3 and ABI5, as well as their ABA-induced accumulation. Additionally, NLP8 overexpression largely suppresses the ABA hypersensitivity of mutant plants exhibiting impaired NO biosynthesis or signaling. Collectively, our study reveals that nitrate counteracts the inhibitory effects of ABA signaling on seed germination and provides mechanistic insights into the NLP8-ABI3/ABI5 interactions and their antagonistic relationships in ABA signaling.

Effects of cold and methyl jasmonate on the expression of miRNAs and target genes in response to vernalisation in two wheat cultivars (Triticum aestivum L.)

Wheat undergoes significant physiological changes during winter, driven by processes such as cold acclimation and vernalisation that are regulated by gene expression and phytohormones. We investigate the effects of methyl jasmonate (MeJA) and cold treatments on the expression of three specific miRNAs and the associated target genes in Baz spring wheat and Norstar winter wheat using qRT-PCR analysis. Our objective was to examine the impact of MeJA on vernalisation and cold adaptation in these genotypes. Results showed that MeJA had no significant impact on vernalisation and acclimation in Baz, while the compound decreased these traits in Norstar. Additionally, the expression of miRNAs in Norstar was significantly reduced after a 2-day cold treatment, particularly for miR156 and further reduced after 14days for miR172 and miR319 . In contrast, Baz showed varied gene expression responses, with an increase in miRNA levels after the 14-day cold treatment. MeJA combined with a 2-day cold treatment suppressed the expression of SPL , AP2 and MYB3 target genes, with the most pronounced suppression observed in SPL . However, AP2 was induced after 14-day cold treatment in both cultivars. The study highlighted an inverse relationship between miRNAs and target genes under vernalisation conditions, underscoring the complex regulatory interactions between genotype, miRNAs and the associated target genes. Therefore, these findings provide new insights into how MeJA and cold treatments modulate miRNA and gene expression, enhancing our understanding of wheat's adaptive response mechanisms.

Integrative Profiling of Phytohormones, Metabolomics, and Transcriptomics Reveals Key Regulators of Cold Tolerance in Cucumber Leaves

A low-temperature condition in a root zone is a major abiotic stress that threatens cucumber (Cucumis sativus L.) growth and development, yet the molecular mechanism by which the leaf reacts to root zone chilling stress remains largely unknown. In this study, we applied three temperature treatments, including room temperature (20°C-22°C), suboptimal temperature (13°C-15°C), and low temperature (8°C-10°C), to investigate how root zone chilling affects hormone dynamics, metabolomics, and transcriptomics in the leaves of the cucumber variety "Jinyou 35", the main cultivar in northwest and southwest China. Through integrative physiological and biochemical analysis, auxin emerges as the most significant accumulated hormone, accounting for 88% in room temperature-treated leaves (RL), 99% in suboptimal temperature-treated leaves (SL), and 94% in low-temperature-treated leaves (LL). Under chilling stress, flavanones were the most abundant metabolite in cucumber leaves, constituting over 50% of total metabolites, while phenolic acids showed a marked decrease. Several differentially expressed transcription factors (DETFs), such as LOB (CsaV3_3G020650), MYB (CsaV3_3G043510), and bHLH (CsaV3_2G005070 and CsaV3_4G029740), were upregulated in SL and LL, potentially enhancing cucumber's defense against chilling injury. Additionally, terminal flower formation was observed under suboptimal and low-temperature conditions, with CsFT expression in SL and LL lower than in RL, and a significant negative correlation observed between CsFT and CsNAC6. These findings deepen our understanding of cucumber's resilience mechanisms to root zone chilling stress, shedding light on its cold tolerance strategies.

The transcription factor WRKY41-FLAVONOID 3'-HYDROXYLASE module fine-tunes flavonoid metabolism and cold tolerance in potato

Cold stress adversely affects crop growth and productivity. Resolving the genetic basis of freezing tolerance is important for crop improvement. Wild potato (Solanum commersonii) exhibits excellent freezing tolerance. However, the genetic factors underlying its freezing tolerance remain poorly understood. Here, we identified flavonoid 3'-hydroxylase (F3'H), a key gene in the flavonoid biosynthesis pathway, as highly expressed in S. commersonii compared with cultivated potato (S. tuberosum L.). Loss of ScF3'H function impaired freezing tolerance in S. commersonii, while ScF3'H overexpression in cultivated potato enhanced its freezing tolerance. Metabolic analysis revealed that F3'H generates more downstream products by adding hydroxyl (-OH) groups to the flavonoid ring structures. These flavonoids enhance reactive oxygen species scavenging, thereby contributing to freezing tolerance. Furthermore, the W-box element in the F3'H promoter plays a critical role in cold responses. Cold-induced transcription factor ScWRKY41 directly binds to the ScF3'H promoter region and recruits histone acetyltransferase 1 (ScHAC1), which enhances histone acetylation at the F3'H locus and activates its transcription. Overall, we identified the cold-responsive WRKY41-F3'H module that enhances freezing tolerance by augmenting the antioxidant capacity of flavonoids. This study reveals a valuable natural gene module for breeding enhanced freezing tolerance in potato and other crops.

miR166e/ZmATHB14 module contributes to drought tolerance in maize root

MicroRNAs significantly influence abiotic stress responses. A species-conserved miRNA implicated in the response to abiotic stress is maize miR166. Therefore, it is unknown whether miR166e plays a role in maize roots' reaction to drought stress. According to this study, drought stress lowers the expression of the miR166e precursor. According to genetic data, miR166e knockdown (KO) improved drought tolerance, while miR166e overexpression decreased it. Additionally, 5'-RACE and double luciferase tests have identified ZmATHB14, an HD-Zip III transcription factor, as a target of miR166e. Under drought stress, KO-miR166e alters ZmATHB14 expression and exhibits the opposite properties of miR166e. ZmATHB14 positively regulates the tolerance to drought stress. Furthermore, ZmATHB14, linked to the GTAATGATTAC cis-element, can activate transcription within the nucleus. Under drought stress, miR166e and ZmATHB14 contribute to vascular development and control ROS homeostasis. We discovered through metabolic targeting tests (Liquid chromatography-mass spectrometry, HPLC-MS) that ZmATHB14 modifies signaling pathways and hormone levels. Our findings strongly imply that the miR166e-ZmATHB14 module regulates drought tolerance.

Metabolic profiling and gene expression analyses shed light on the cold adaptation mechanisms of Saposhnikovia divaricata (Turcz.) Schischk

The northeastern region of China experiences a distinctly cold climate influenced by the Siberian High during the winter months, thus resulting in severe cold weather conditions. Snow cover is prevalent and can persist for several months. This prolonged exposure to low temperatures necessitates specific adaptations in terms of agriculture and plant life, particularly for perennial herbs. Saposhnikovia divaricate (Turcz.) Schischk (SD) is a widely distributed perennial herb in the northeastern and northern provinces of China. However, there is limited documentation on the molecular mechanism through which this plant adapts to cold stress. Therefore, we elucidated the SD response to cold stress by transcriptome and metabolome analysis. Cold stress induced chlorosis and wilting in plants, thus leading to added function of antioxidant enzymes and higher levels of malondialdehyde, proline, soluble sugars. Notably, the differentially expressed genes (DEGs) were primarily related with sugar metabolism, ROS sweep, flavonoid and terpenoid biosynthesis, plant hormone signalling pathways, lipid metabolism, and transcription factors. Additionally, the differentially expressed metabolites (DEMs) mainly included lipids, flavonoids, terpenoid compounds, sugar-related metabolites, alkaloids and other metabolites. Furthermore, integrated analysis revealed coexpression patterns between carbohydrate metabolism-related genes and genes reference flavonoid and terpenoid biosynthesis, along with their corresponding metabolites. Finally, the qPCR results revealed notable over-expression levels of stress-related genes, including those participated in plant hormone signalling pathways (PP2C and AUX), flavonoid biosynthesis (CH3), antioxidant enzymes (AOX and CAT), and sugar-related metabolite metabolism (TPS, SPS, and SS). In conclusion, our findings suggest that cold stress strongly affects plant hormone signalling pathways, ROS scavenging mechanisms, unsaturated fatty acid synthesis and flavonoid and terpenoid biosynthesis in SD. These discoveries provide valuable insights into the impact of cold climates on herbaceous plants.

Squalene acts as a feedback signaling molecule in facilitating bidirectional communication between tea plants

Plants respond to environmental stimuli by releasing volatile organic compounds (VOCs), which play diverse roles in plant-to-plant interactions. Previous studies have primarily focused on how receiving plants respond. However, little is known about how these receivers communicate back to the emitter plants and their subsequent impacts. Our findings indicated increased plant tolerance when neighboring plants were present, suggesting bidirectional plant communication. Furthermore, we established a model to explore the role of signals from receiver plants, identifying squalene as a crucial feedback signal enhancing the cold tolerance in emitter plants by up-regulating CsCBF5 expression. Further analysis using yeast one-hybrid analysis coupled with inhibition of brassinosteroid pathways suggested that squalene-induced castasterone (CS) accumulation directly activated CsCBF5 expression modulated by CsBES1/BZR1. Overall, these results demonstrated the role of the squalene-CS-BES1/BZR1-CBF5 pathway in the bidirectional communication between plants, expanding our understanding of plant interactions.

Phosphorylation-dependent VaMYB4a regulates cold stress in grapevine by inhibiting VaPIF3 and activating VaCBF4

Cold stress severely impacts the quality and yield of grapevine (Vitis L.). In this study, we extend our previous work to elucidate the role and regulatory mechanisms of Vitis amurensis MYB transcription factor 4a (VaMYB4a) in grapevine's response to cold stress. Our results identified VaMYB4a as a key positive regulator of cold stress. We demonstrated that VaMYB4a undergoes phosphorylation by V. amurensis calcineurin B-like (CBL) proteins-interacting protein kinase 18 (VaCIPK18) under cold stress, a process that activates VaMYB4a transcriptional activity. Using chromatin immunoprecipitation sequencing (ChIP-seq). We performed a comprehensive genomic search to identify downstream components that interact with VaMYB4a, leading to the discovery of a basic helix-loop-helix transcription factor, V. amurensis phytochrome-interacting factor 3 (VaPIF3). VaMYB4a attenuated the transcriptional activity of VaPIF3 through a phosphorylation-dependent interaction under cold conditions. Furthermore, VaPIF3, which interacts with and inhibits V. amurensis C-repeat binding factor 4 (VaCBF4, a known positive regulator of cold stress), has its activity attenuated by VaMYB4a, which mediates the modulation of this pathway. Notably, VaMYB4a also interacted with and promoted the expression of VaCBF4 in a phosphorylation-dependent manner. Our study shows that VaMYB4a positively modulates cold tolerance in plants by simultaneously downregulating VaPIF3 and upregulating VaCBF4. These findings provide a nuanced understanding of the transcriptional response in grapevine under cold stress and contribute to the broader field of plant stress physiology.

The ubiquitin ligase VviPUB19 negatively regulates grape cold tolerance by affecting the stability of ICEs and CBFs

Cold stress seriously affects plant growth and development. The ubiquitination system plays an important role by degrading and modifying substrates at the protein level. In this study, the U-box type ubiquitin ligase VviPUB19 gene was induced by low temperature (4°C) in grapevine. In Arabidopsis thaliana, the pub19 mutant, a homologous mutation of VviPUB19, exhibited enhanced cold tolerance, and the resistance phenotype of the mutant could be attenuated by VviPUB19. VviPUB19-overexpressing grape lines exhibited lower cold tolerance. Furthermore, it was revealed that VviPUB19 interacted with the cold-related transcription factors VviICE1, 2, and 3 and VviCBF1 and 2, and was involved in the degradation of them. This is the first time that an E3 ligase (VviPUB19) that interacts with CBFs and affects its protein stability has been identified. It was also shown that VviICE1, 2, and 3 positively regulated VviPUB19 promoter activity. Therefore, our results suggest that VviPUB19 reduces grape cold tolerance via participating in the CBF-dependent pathway.

Ethylene negatively regulates cold tolerance through HbEIN3-HbICE2 regulatory module in Hevea brasiliensis

Cold stress can result in reduced growth rates, decreased latex production, and restricted areas for the Para rubber tree (Hevea brasiliensis). However, the molecular mechanisms governing the response of Hevea brasiliensis to cold stress remain elusive. Here, we found that ethylene plays a negative role in Hevea brasiliensis responses to cold stress. Treatment with the ethylene synthesis precursor 1-aminocyclopropane-1-carboxylic acid (ACC) decreased the cold tolerance of Hevea brasiliensis, while exogenous treatment with Ag+ (an ethylene signal inhibitor) had the opposite effect. Additionally, overexpressing HbEIN3 decreased cold stress tolerance in Arabidopsis and Taraxacum koksaghyz plants. Quantitative real-time PCR analysis indicated that HbEIN3-1 and HbEIN3-2 repress the expression of the cold-responsive genes HbCBF1-3 in Hevea brasiliensis. Moreover, HbEIN3-1 and HbEIN3-2 directly bind to the HbCBF1 promoter to suppress its transcription. Further investigation revealed that HbEIN3s interact with and dampen the transcriptional activity of HbICE2, a crucial transcription factor that positively regulates the cold signaling pathway, thereby attenuating the expression of HbICE2-targeted genes. Collectively, these findings indicate that HbEIN3s play a crucial role in ethylene-regulated cold tolerance through the repression of HbCBF1 expression and HbICE2 transcriptional activity.

CRF12 specifically regulates the flowering time of Arabidopsis thaliana under non-inductive conditions

The flowering time of Arabidopsis thaliana, a model plant, is significantly accelerated when exposed to long-day (LD) conditions, as it is a typical LD plant. Consequently, the investigation of the flowering regulatory network in A. thaliana under LD conditions has garnered considerable attention in the study of flowering signals, resulting in a significant breakthrough. While many LD plants, including A. thaliana, exhibit delayed flowering under non-inductive short-day (SD) conditions, they are still capable of flowering. Nevertheless, research on the regulation of flowering induction in LD plants under non-inductive SD conditions has been limited. This study demonstrated the involvement of CYTOKININ RESPONSE FACTORS 12 (CRF12) in the regulation of flowering in A. thaliana under non-inductive conditions. Analysis of the expression patterns revealed that the activation of CRF12 expression and protein stability occurred exclusively in non-inductive environments. Molecular and genetic analyses revealed that under a non-inductive photoperiod of 12 h of light and 12 h of darkness, CRF12, CONSTANS (CO), and TARGET OF EAT 1/2 (TOE1/2) engage in competitive interactions to regulate flowering time, while in a SD photoperiod of 8 h of light and 16 h of darkness, CRF12 modulates flowering time by inhibiting the activity of TOE1/2.

Strigolactones positively regulate HY5-dependent autophagy and the degradation of ubiquitinated proteins in response to cold stress in tomato

Autophagy, involved in protein degradation and amino acid recycling, plays a key role in plant development and stress responses. However, the relationship between autophagy and phytohormones remains unclear. We used diverse methods, including CRISPR/Cas9, ultra-performance liquid chromatography coupled with tandem mass spectrometry, chromatin immunoprecipitation, electrophoretic mobility shift assays, and dual-luciferase assays to explore the molecular mechanism of strigolactones in regulating autophagy and the degradation of ubiquitinated proteins under cold stress in tomato (Solanum lycopersicum). We show that cold stress induced the accumulation of ubiquitinated proteins. Mutants deficient in strigolactone biosynthesis were more sensitive to cold stress with increased accumulation of ubiquitinated proteins. Conversely, treatment with the synthetic strigolactone analog GR245DS enhanced cold tolerance in tomato, with elevated levels of accumulation of autophagosomes and transcripts of autophagy-related genes (ATGs), and reduced accumulation of ubiquitinated proteins. Meanwhile, cold stress induced the accumulation of ELONGATED HYPOCOTYL 5 (HY5), which was triggered by strigolactones. HY5 further trans-activated ATG18a transcription, resulting in autophagy formation. Mutation of ATG18a compromised strigolactone-induced cold tolerance, leading to decreased formation of autophagosomes and increased accumulation of ubiquitinated proteins. These findings reveal that strigolactones positively regulate autophagy in an HY5-dependent manner and facilitate the degradation of ubiquitinated proteins under cold conditions in tomato.

Combined Bulked Segregant Analysis-Sequencing and Transcriptome Analysis to Identify Candidate Genes Associated with Cold Stress in Brassica napus L

Cold tolerance in rapeseed is closely related to its growth, yield, and geographical distribution. However, the mechanisms underlying cold resistance in rapeseed remain unclear. This study aimed to explore cold resistance genes and provide new insights into the molecular mechanisms of cold resistance in rapeseed. Rapeseed M98 (cold-sensitive line) and D1 (cold-tolerant line) were used as parental lines. In their F2 population, 30 seedlings with the lowest cold damage levels and 30 with the highest cold damage levels were selected to construct cold-tolerant and cold-sensitive pools, respectively. The two pools and parental lines were analyzed using bulk segregant sequencing (BSA-seq). The G'-value analysis indicated a single peak on Chromosome C09 as the candidate interval, which had a 2.59 Mb segment with 69 candidate genes. Combined time-course and weighted gene co-expression network analyses were performed at seven time points to reveal the genetic basis of the two-parent response to low temperatures. Twelve differentially expressed genes primarily involved in plant cold resistance were identified. Combined BSA-seq and transcriptome analysis revealed BnaC09G0354200ZS, BnaC09G0353200ZS, and BnaC09G0356600ZS as the candidate genes. Quantitative real-time PCR validation of the candidate genes was consistent with RNA-seq. This study facilitates the exploration of cold tolerance mechanisms in rapeseed.

Plant Coping with Cold Stress: Molecular and Physiological Adaptive Mechanisms with Future Perspectives

Cold stress strongly hinders plant growth and development. However, the molecular and physiological adaptive mechanisms of cold stress tolerance in plants are not well understood. Plants adopt several morpho-physiological changes to withstand cold stress. Plants have evolved various strategies to cope with cold stress. These strategies included changes in cellular membranes and chloroplast structure, regulating cold signals related to phytohormones and plant growth regulators (ABA, JA, GA, IAA, SA, BR, ET, CTK, and MET), reactive oxygen species (ROS), protein kinases, and inorganic ions. This review summarizes the mechanisms of how plants respond to cold stress, covering four main signal transduction pathways, including the abscisic acid (ABA) signal transduction pathway, Ca2+ signal transduction pathway, ROS signal transduction pathway, and mitogen-activated protein kinase (MAPK/MPK) cascade pathway. Some transcription factors, such as AP2/ERF, MYB, WRKY, NAC, and bZIP, not only act as calmodulin-binding proteins during cold perception but can also play important roles in the downstream chilling-signaling pathway. This review also highlights the analysis of those transcription factors such as bHLH, especially bHLH-type transcription factors ICE, and discusses their functions as phytohormone-responsive elements binding proteins in the promoter region under cold stress. In addition, a theoretical framework outlining plant responses to cold stress tolerance has been proposed. This theory aims to guide future research directions and inform agricultural production practices, ultimately enhancing crop resilience to cold stress.

Transcriptome sequencing reveals jasmonate playing a key role in ALA-induced osmotic stress tolerance in strawberry

BACKGROUND

Strawberry (Fragaria × annanasa Duch.) is an important economic fruit worldwide, whose growth and development are often hindered by water deficiency. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, has been suggested to mitigate the osmotic damages by promoting root water absorption, osmotic adjustment, photosynthetic capacity, and antioxidant improvement. However, the regulatory mechanism remains unclear.

RESULTS

In the current study, the underlying mechanism by determination of various physiological indices, as well as transcriptome sequencing and the weighted gene correlation network analysis (WGCNA) of 10 mg L- 1 ALA treated strawberry leaves and roots stressed by 20% polyethylene glycol 6000 (PEG) treatment. The findings indicated that ALA enhanced osmotic stress tolerance reflected by enhancing relative water content (RWC), root development, gas exchange parameters and antioxidant enzyme activities, and decreasing the leaf H2O2 and malondialdehyde (MDA) content. Transcriptome analysis showed that the differentially expressed genes (DEGs) stimulated by exogenous ALA were mostly associated with the secondary biosynthesis and hormones signaling pathways, especially jasmonates (JAs). The JA derivative (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile) was found to be elevated in the strawberry leaves and roots treated with ALA under PEG stress. Additionally, exogenous methyl jasmonate (MeJA) alleviated osmotic stress damages similarly to ALA, while its synthesis inhibitor diethyldithiocarbamate (DIECA) led to adverse effects on strawberries, which can be relieved by further additional application of ALA.

CONCLUSIONS

Theses findings suggest that JAs can act as the necessary signaling molecules involved in ALA-improved osmotic stress tolerance networks. This provides a new insight for further study on how ALA can help plants cope with water stress.

Transcriptomic and metabolomic analysis reveals the molecular mechanism of exogenous melatonin improves salt tolerance in eggplants

Introduction

Melatonin significantly enhances the tolerance of plants to biotic and abiotic stress, and plays an important role in plant resistance to salt stress. However, its role and molecular mechanisms in eggplant salt stress resistance have been rarely reported. In previous studies, we experimentally demonstrated that melatonin can enhance the salt stress resistance of eggplants.

Methods

In this study, we treated salt-stressed eggplant plants with melatonin and a control treatment with water, then conducted physiological and biochemical tests, transcriptomic and metabolomic sequencing, and RT-qPCR validation at different stages after treatment.

Results

The results showed that exogenous melatonin can alleviate the adverse effects of salt stress on plants by increasing the activity of antioxidant enzymes, reducing the content of reactive oxygen species in plants, and increasing the content of organic osmoprotectants. Transcriptomic and metabolomic data, as well as combined analysis, indicate that melatonin can activate the metabolic pathways of plant resistance to adverse stress. Compared to the control treatment with water, melatonin can activate the genes of the α-linolenic acid metabolism pathway and promote the accumulation of metabolites in this pathway, with significant effects observed 48 hours after treatment, and significantly activates the expression of genes such as SmePLA2, SmeLOXs and SmeOPR et al. and the accumulation of metabolites such as α-Linolenic acid, (9R,13R)-12-oxophytodienoic acid, 9(S)-HpOTrE and (+)-7-iso-Jasmonic acid. RT-qPCR validated the activating effect of melatonin on the candidate genes of the a-linolenic acid metabolism pathway.

Discussion

This study analyzed the molecular mechanism of melatonin in alleviating eggplant salt stress, providing a theoretical foundation for the application of melatonin in enhancing eggplant salt stress resistance in production.

Evolution and functional divergence of glycosyltransferase genes shaped the quality and cold tolerance of tea plants

Plant uridine diphosphate-dependent glycosyltransferases (UGTs) play a key role in plant growth and metabolism. Here, we examined the evolutionary landscape among UGTs in 28 fully sequenced species from early algae to angiosperms. Our findings revealed a distinctive expansion and contraction of UGTs in the G and H groups in tea (Camellia sinensis), respectively. Whole-genome duplication and tandem duplication events jointly drove the massive expansion of UGTs, and the interplay of natural and artificial selection has resulted in marked functional divergence within the G group of the sinensis-type tea population. In Cluster II of group G, differences in substrate selection (e.g. abscisic acid) of the enzymes encoded by UGT genes led to their functional diversification, and these genes influence tolerance to abiotic stresses such as low temperature and drought via different modes of positive and negative regulation, respectively. UGTs in Cluster III of the G group have diverse aroma substrate preferences, which contribute a diverse aroma spectrum of the sinensis-type tea population. All Cluster III genes respond to low-temperature stress, whereas UGTs within Cluster III-1, shaped by artificial selection, are unresponsive to drought. This suggests that artificial selection of tea plants focused on improving quality and cold tolerance as primary targets.

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.

Integrating physiological and transcriptomic analyses explored the regulatory mechanism of cold tolerance at seedling emergence stage in upland cotton (Gossypium hirsutum L.)

Cold stress is one of the major abiotic stressor that profoundly impacts plant growth. Cotton, a widely cultivated variety, is particularly susceptible to cold stress. Unraveling the responses to cold stress is critical for cotton demand. In this investigation, we conducted comparative physiological and transcriptomic analyses of the cold-tolerant variety XLZ16 and cold-sensitive variety XLZ84 at seedling emergence stage under cold stress. Following exposure to cold stress, XLZ16 exhibited a markedly higher growth phenotype and increased activity of antioxidant enzymes, while simultaneously showing reduced cellular oxidative damage and apoptosis. Furthermore, the levels of auxin (IAA), cytokinin (CTK), and salicylic acid (SA) significantly increased during cold stress, whereas the contents of catendorsterol (TY), brassinosterone (CS), and jasmonic acid (JA) significantly decreased. Integrated with stoichiometric analysis, these findings definitively demonstrated significant differences in antioxidant capacity and hormone content between the two varieties during their response to cold stress. A total of 6207 potential cold-responsive differentially expressed genes (DEGs) were identified through transcriptome sequencing analysis. Enrichment analyses of these DEGs revealed that pathways related to "hormones biosynthesis and signaling" as well as "circadian rhythm" were associated with cold response. Notably, the hub gene Gh_D12G2567 (GhJAZ3), encoding jasmonate ZIM-domain (JAZ) proteins, was found to influence the JA signal transduction pathway and regulate cotton growth under cold stress within the MEred module network. Furthermore, suppressing the expression level of GhJAZ3 by virus-induced gene silencing led to the reduction of cold resistance, implying GhJAZ3 as a positive regulator of cold tolerance. This study provides valuable insights into the response mechanisms of cotton under cold stress. It also serves as a reference and foundation for further enhancing cold tolerance of new cotton varieties.

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.

Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes

It is essential for the survival of grapevines in cool climate viticultural regions where vines properly acclimate in late fall and early winter and develop freezing tolerance. Climate change-associated abnormities in temperature during the dormant season, including oscillations between prolonged warmth in late fall and extreme cold in midwinter, impact cold acclimation and threaten the sustainability of the grape and wine industry. We conducted two experiments in controlled environment to investigate the impacts of different temperature regimes on cold acclimation ability in endodormant grapevine buds through a combination of freezing tolerance-based physiological and RNA-seq-based transcriptomic monitoring. Results show that exposure to a constant temperature, whether warm (22 and 11°C), moderate (7°C), or cool (4 and 2°C) was insufficient for triggering cold acclimation and increasing freezing tolerance in dormant buds. However, when the same buds were exposed to temperature cycling (7±5°C), acclimation occurred, and freezing tolerance was increased by 5°C. We characterized the transcriptomic response of endodormant buds to high and low temperatures and temperature cycling and identified new potential roles for the ethylene pathway, starch and sugar metabolism, phenylpropanoid regulation, and protein metabolism in the genetic control of endodormancy maintenance. Despite clear evidence of temperature-responsive transcription in endodormant buds, our current understanding of the genetic control of cold acclimation remains a challenge when generalizing across grapevine tissues and phenological stages.

Transcription factor ABF3 modulates salinity stress-enhanced jasmonate signaling in Arabidopsis

Salinity is a severe abiotic stress that affects plant growth and yield. Salinity stress activates jasmonate (JA) signaling in Arabidopsis thaliana, but the underlying molecular mechanism remains to be elucidated. In this study, we confirmed the activation of JA signaling under saline conditions and demonstrated the importance of the CORONATINE INSENSITIVE1 (COI1)-mediated JA signaling for this process. Phenotypic analyses reflected the negative regulation of JASMONATE ZIM-DOMAIN (JAZ) repressors during salinity stress-enhanced JA signaling. Mechanistic analyses revealed that JAZ proteins physically interact with ABSCISIC ACID-RESPONSIVE ELEMENT BINDING FACTOR1 (ABF1), AREB1/ABF2, ABF3, and AREB2/ABF4, which belong to the basic leucine zipper (bZIP) transcription factor family and respond to salinity stress. Analyses on the ABF3 overexpression plants and ABF mutants indicated the positive role of ABF3 in regulating JA signaling under saline condition. Furthermore, ABF3 overexpression partially recovered the JA-related phenotypes of JAZ1-Δ3A plants. Moreover, ABF3 was observed to indirectly activate ALLENE OXIDE SYNTHASE (AOS) transcription, but this activation was inhibited by JAZ1. In addition, ABF3 competitively bind to JAZ1, thereby decreasing the interaction between JAZ1 and MYC2, which is the master transcription factor controlling JA signaling. Collectively, our findings have clarified the regulatory effects of ABF3 on JA signaling and provide new insights into how JA signaling is enhanced following an exposure to salinity stress.

Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress

Cold is an important environmental factor limiting plant growth and development. Recent studies have revealed the complex regulatory networks associated with plant responses to cold and identified their interconnections with signaling pathways related to light, the circadian clock, plant hormones, and pathogen defense. In this article, we review recent advances in understanding the molecular basis of cold perception and signal transduction pathways. We also summarize recent developments in the study of cold-responsive growth and flowering. Finally, we propose future directions for the study of long-term cold sensing, RNA secondary structures in response to cold, and the development of cold-tolerant and high-yield crops.

Current status for utilization of cold resistance genes and strategies in wheat breeding program

Low temperature chilling is one of the major abiotic stresses affecting growth and yield of Triticum aestivum L. With global climate change, the risk of cold damage in wheat production has increased. In recent years, with the extensive research on wheat chilling resistance, especially the development of genetic engineering technology, the research on wheat chilling resistance has made great progress. This paper describes the mechanism of wheat cold damage, including cell membrane injury, cytoplasmic concentration increased as well as the imbalance of the ROS system. Mechanisms of cold resistance in wheat are summarised, including hormone signalling, transcription factor regulation, and the role of protective enzymes of the ROS system in cold resistanc. Functions of cloned wheat cold resistance genes are summarised, which will provide a reference for researchers to further understand and make use of cold resistance related genes in wheat. The current cold resistant breeding of wheat relies on the agronomic traits and observable indicators, molecular methods are lacked. A strategy for wheat cold-resistant breeding based on QTLs and gene technologies is proposed, with a view to breeding more cold-resistant varieties of wheat with the deepening of the research.

A systematic regulatory network related to bulbil formation in Lilium lancifolium based on metabolome and transcriptome analyses

BACKGROUND

Lilium lancifolium is a special wild triploid species native to China and can produce abundant bulbils on its stem under natural conditions, which is very valuable to study bulbil organogenesis in plants. Although similar to the lateral and tillering principles, the molecular mechanism underlying bulbil formation has remained incompletely understood.

RESULTS

The metabolome and transcriptome of L. lancifolium bulbils across four development stages were analyzed. The pairwise comparison of metabolomes across the four stages identified 17 differential hormones, predominantly auxin (IAA), cytokinin (CK), and jasmonic acid (JA). Short Time-series Expression Miner (STEM) trend analysis of differential genes revealed four significant trends across these stages. The KEGG enrichment analysis of the four clusters highlighted pathways, such as plant hormone signal transduction, which were speculated to play a crucial role in development stages. these pathways were speculated to play a crucial role in development stages. To explore the key differential expressed genes and transcription factors associated with bulbil occurrence, two periods were focused on: Ll_UN and Ll_DN, which represented the stages with and without bulbils, respectively. Through correlation analysis and qRT-PCR analysis, 11 candidate differentially expressed genes and 27 candidate transcription factors were selected. By spraying exogenous hormones to validate these candidates, LlbHLH128, LlTIFY10A, LlbHLH93, and LlMYB108, were identified as the key genes for L. lancifolium bulbils.

CONCLUSION

A regulatory network of L. lancifolium bulbil development was predicted. LlTIFY10A and LlbHLH93 might be involved in the JA and auxin signal transduction pathways, which jointly formed a regulatory network to affect the occurrence of L. lancifolium bulbil. This study not only provided more information about the differentially expressed genes and metabolites through transcriptome and metabolomics analyses, but also provided a clearer understanding of the effect of hormones on bulbil formation in lily.

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.

Salicylic acid improves chilling tolerance via CsNPR1-CsICE1 interaction in grafted cucumbers

Salicylic acid (SA) plays a role in the regulation of grafting-induced cold tolerance. However, the molecular mechanism behind it is still unknown. Here, we established that the phenylalanine ammonia-lyase (PAL) pathway-dependent elevate in SA content in grafted cucumber leaves was not only synthesized in the leaves but also transported from the roots under chilling stress. RNAi-CsPAL with low SA content as rootstock reduced SA accumulation in grafted seedling leaves while decreasing rootstock-induced cold tolerance, as evidenced by higher electrolyte leakage (EL), hydrogen peroxide (H2O2), and superoxide anion (O2 ·-) contents and lower expression of cold-responsive genes (CsICE1, CsDREB1A, CsDREB1B, and CsCOR47), whereas OE-CsPAL with high SA content as rootstock improved the cold tolerance of grafted plants in comparison with the wild type (WT). In addition, CsNPR1 was significantly upregulated in grafted cucumber under chilling stress, with exogenous and endogenous overexpressed SA inducing its transcriptional expression and protein stability, which exhibited higher expression in grafted plants than in self-root plants. While CsNPR1-overexpression (OE-CsNPR1) seedlings as scions were more tolerant to chilling stress than WT seedlings, CsNPR1-suppression (Anti-CsNPR1) seedlings as scions were more vulnerable to chilling stress. Notably, CsNPR1-CsICE1 interactions alleviated ROS accumulation and activated the expression of CsDREB1A, CsDREB1B, CsCOR47, CsCOR15, CsCOR413, and CsKIN1 to enhance SA-mediated chilling tolerance in grafted cucumber. Overall, our findings reveal that SA enhances chilling tolerance in grafted cucumbers via the model of the CsNPR1-CsICE1 transcriptional regulatory cascade.

LUX ARRHYTHMO links CBF pathway and jasmonic acid metabolism to regulate cold tolerance of tea plants

Cold stress declines the quality and yield of tea, yet the molecular basis underlying cold tolerance of tea plants (Camellia sinensis) remains largely unknown. Here, we identified a circadian rhythm component LUX ARRHYTHMO (LUX) that potentially regulates cold tolerance of tea plants through a genome-wide association study and transcriptomic analysis. The expression of CsLUX phased with sunrise and sunset and was strongly induced by cold stress. Genetic assays indicated that CsLUX is a positive regulator of freezing tolerance in tea plants. CsLUX was directly activated by CsCBF1 and repressed the expression level of CsLOX2, which regulates the cold tolerance of tea plants through dynamically modulating jasmonic acid content. Furthermore, we showed that the CsLUX-CsJAZ1 complex attenuated the physical interaction of CsJAZ1 with CsICE1, liberating CsICE1 with transcriptional activities to withstand cold stress. Notably, a single-nucleotide variation of C-to-A in the coding region of CsLUX was functionally validated as the potential elite haplotype for cold response, which provided valuable molecular markers for future cold resistance breeding in tea plants.

KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes

Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.

Comparison of transcriptome and metabolome analysis revealed cold-resistant metabolic pathways in cucumber roots under low-temperature stress in root zone

Introduction

Low ground temperature is a major factor limiting overwintering in cucumber cultivation facilities in northern alpine regions. Lower temperatures in the root zone directly affect the physiological function of the root system, which in turn affects the normal physiological activity of plants. However, the importance of the ground temperature in facilities has not attracted sufficient attention.

Methods

Therefore, this study tested the cucumber variety Jinyou 35 under three root zone temperatures (room temperature, 20-22°C; suboptimal temperature, 13- 15°C; and low temperature, 8-10°C) to investigated possible cold resistance mechanisms in the root of cucumber seedlings through hormone, metabolomics, and transcriptomics analyses.

Results and discussion

The results showed that cucumber roots were subjected to chilling stress at different temperatures. Hormone analysis indicated that auxin content was highest in the roots. Jasmonic acid and strigolactone participated in the low-temperature stress response. Auxin and jasmonate are key hormones that regulate the response of cucumber roots to low temperatures. Phenolic acid was the most abundant metabolite in cucumber roots under chilling stress. Additionally, triterpenes may play an important role in chilling resistance. Differentially expressed genes and metabolites were significantly enriched in benzoxazinoid biosynthesis in the room temperature vs. suboptimal temperature groups and the room temperature vs. low temperature groups. Most differentially expressed transcription factor genes in AP2/ERF were strongly induced in cucumber roots by both suboptimal and low-temperature stress conditions. These results provide guidance for the cultivation of cucumber in facilities.

CaAOS as a hub gene based on physiological and transcriptomic analyses of cold-resistant and cold-sensitive pepper cultivars

The yield and quality of pepper are considerably influenced by the cold conditions. Herein, we performed morphological, physiological and transcriptomic analyses by using two pepper seedlings, '2379' (cold-resistant) and '2380' (cold-sensitive). Briefly, 60 samples from each cultivar were analyzed at four distinct time points (0, 6, 24 and 48 h) at 5 °C in darkness. The physiological indices and activities of enzymes exhibited marked differences between the two cultivars. Transcriptomic analysis indicated that, compared to the control group, 11,415 DEGs were identified in '2379' and '2380' at 24 h. In the early stage, the number of DEGs in '2379' was 5.68 times higher than that in '2380', potentially explaining the observed differences in tolerance to colds. Processes such as protein targeting to membranes, jasmonic acid (JA)-mediated signalling, cold response and abscisic acid-activated signalling were involved. Subsequently, we identified a hub gene, CaAOS, that is involved in JA biosynthesis, positively influences cold tolerance and is a target of CaMYC2. Variations in the GC-motif of the CaAOS's promoter may influence the expression levels of CaAOS under cold treatment. The result of this study may lead to the development of more effective strategies for enhancing cold tolerance, potentially benefitting pepper breeding in cold regions.

Transcriptomic and Physiological Studies Unveil that Brassinolide Maintains the Balance of Maize's Multiple Metabolisms under Low-Temperature Stress

Low-temperature (LT) is one of the major abiotic stresses that restrict the growth and development of maize seedlings. Brassinolides (BRs) have been shown to enhance LT tolerance in several plant species; the physiological and molecular mechanisms by which BRs enhance maize tolerance are still unclear. Here, we characterized changes in the physiology and transcriptome of N192 and Ji853 seedlings at the three-leaf stage with or without 2 μM 2,4-epibrassinolide (EBR) application at 25 and 15 °C environments via high-performance liquid chromatography and RNA-Sequencing. Physiological analyses revealed that EBR increased the antioxidant enzyme activities, enhanced the cell membrane stability, decreased the malondialdehyde formation, and inhibited the reactive oxygen species (ROS) accumulation in maize seedlings under 15 °C stress; meanwhile, EBR also maintained hormone balance by increasing indole-3-acetic acid and gibberellin 3 contents and decreasing the abscisic acid level under stress. Transcriptome analysis revealed 332 differentially expressed genes (DEGs) enriched in ROS homeostasis, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) cascade. These DEGs exhibited synergistic and antagonistic interactions, forming a complex LT tolerance network in maize. Additionally, weighted gene co-expression network analysis (WGCNA) revealed that 109 hub genes involved in LT stress regulation pathways were discovered from the four modules with the highest correlation with target traits. In conclusion, our findings provide new insights into the molecular mechanisms of exogenous BRs in enhancing LT tolerance of maize at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to LT stress.

Transcriptome dynamics in Artemisia annua provides new insights into cold adaptation and de-adaptation

Plants adapt to cold stress through a tightly regulated process involving metabolic reprogramming and tissue remodeling to enhance tolerance within a short timeframe. However, the precise differences and interconnections among various organs during cold adaptation remain poorly understood. This study employed dynamic transcriptomic and metabolite quantitative analyses to investigate cold adaptation and subsequent de-adaptation in Artemisia annua, a species known for its robust resistance to abiotic stress. Our findings revealed distinct expression patterns in most differentially expressed genes (DEGs) encoding transcription factors and components of the calcium signal transduction pathway within the two organs under cold stress. Notably, the long-distance transport of carbon sources from source organs (leaves) to sink organs (roots) experienced disruption followed by resumption, while nitrogen transport from roots to leaves, primarily in the form of amino acids, exhibited acceleration. These contrasting transport patterns likely contribute to the observed differences in cold response between the two organs. The transcriptomic analysis further indicated that leaves exhibited increased respiration, accumulated anti-stress compounds, and initiated the ICE-CBF-COR signaling pathway earlier than roots. Differential expression of genes associated with cell wall biosynthesis suggests that leaves may undergo cell wall thickening while roots may experience thinning. Moreover, a marked difference was observed in phenylalanine metabolism between the two organs, with leaves favoring lignin production and roots favoring flavonoid synthesis. Additionally, our findings suggest that the circadian rhythm is crucial in integrating temperature fluctuations with the plant's internal rhythms during cold stress and subsequent recovery. Collectively, these results shed light on the coordinated response of different plant organs during cold adaptation, highlighting the importance of inter-organ communication for successful stress tolerance.

Improved pokeweed genome assembly and early gene expression changes in response to jasmonic acid

BACKGROUND

Jasmonic acid (JA) is a phytohormone involved in regulating responses to biotic and abiotic stress. Although the JA pathway is well characterized in model plants such as Arabidopsis thaliana, less is known about many non-model plants. Phytolacca americana (pokeweed) is native to eastern North Americana and is resilient to environmental stress. The goal of this study was to produce a publicly available pokeweed genome assembly and annotations and use this resource to determine how early response to JA changes gene expression, with particular focus on genes involved in defense.

RESULTS

We assembled the pokeweed genome de novo from approximately 30 Gb of PacBio Hifi long reads and achieved an NG50 of ~ 13.2 Mb and a minimum 93.9% complete BUSCO score for gene annotations. With this reference, we investigated the early changes in pokeweed gene expression following JA treatment. Approximately 5,100 genes were differentially expressed during the 0-6 h time course with almost equal number of genes with increased and decreased transcript levels. Cluster and gene ontology analyses indicated the downregulation of genes associated with photosynthesis and upregulation of genes involved in hormone signaling and defense. We identified orthologues of key transcription factors and constructed the first JA gene response network integrated with our transcriptomic data from orthologues of Arabidopsis genes. We discovered that pokeweed did not use leaf senescence as a means of reallocating resources during stress; rather, most secondary metabolite synthesis genes were constitutively expressed, suggesting that pokeweed directs its resources for survival over the long term. In addition, pokeweed synthesizes several RNA N-glycosylases hypothesized to function in defense, each with unique expression profiles in response to JA.

CONCLUSIONS

Our investigation of the early response of pokeweed to JA illustrates patterns of gene expression involved in defence and stress tolerance. Pokeweed provides insight into the defense mechanisms of plants beyond those observed in research models and crops, and further study may yield novel approaches to improving the resilience of plants to environmental changes. Our assembled pokeweed genome is the first within the taxonomic family Phytolaccaceae to be publicly available for continued research.

The Role of Brassinosteroids in Plant Cold Stress Response

Temperature affects plant growth and geographical distribution. Cold stress occurs when temperatures fall below the physiologically optimal range for plants, causing permanent and irreversible damage to plant growth, development, and production. Brassinosteroids (BRs) are steroid hormones that play an important role in plant growth and various stress responses. Recent studies have shown that low temperatures affect BR biosynthesis in many plant species and that BR signaling is involved in the regulation of plant tolerance to low temperatures, both in the CBF-dependent and CBF-independent pathways. These two regulatory pathways correspond to transient and acclimation responses of low temperature, respectively. The crosstalk between BRs and other hormones is a significant factor in low-temperature tolerance. We provide an overview of recent developments in our knowledge of BRs' function in plant responses to cold stress and how they interact with other plant hormones in this review.

UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development

Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.

Crosstalk between Ethylene, Jasmonate and ABA in Response to Salt Stress during Germination and Early Plant Growth in Cucurbita pepo

The crosstalk of phytohormones in the regulation of growth and development and the response of plants to environmental stresses is a cutting-edge research topic, especially in crop species. In this paper, we study the role and crosstalk between abscisic acid (ABA), ethylene (ET), and jasmonate (JA) in the control of germination and seedling growth in water or in standard nutrient solution and under salt stress (supplemented with 100-200 mM NaCl). The roles of ET and JA were studied using squash ET- and JA-deficient mutants aco1a and lox3a, respectively, while the crosstalk between ET, JA, and ABA was determined by comparing the expression of the key ABA, JA, and ET genes in wild-type (WT) and mutant genotypes under standard conditions and salt stress. Data showed that ET and JA are positive regulators of squash germination, a function that was found to be mediated by downregulating the ABA biosynthesis and signaling pathways. Under salt stress, aco1a germinated earlier than WT, while lox3a showed the same germination rate as WT, indicating that ET, but not JA, restricts squash germination under unfavorable salinity conditions, a function that was also mediated by upregulation of ABA. ET and JA were found to be negative regulators of plant growth during seedling establishment, although ET inhibits both the aerial part and the root, while JA inhibits only the root. Both aco1a and lox3a mutant roots showed increased tolerance to salt stress, a phenotype that was found to be mainly mediated by JA, although we cannot exclude that it is also mediated by ABA.