Overexpression of the FERONIA receptor kinase MdMRLK2 enhances apple cold tolerance

Integrative analyses reveal Bna-miR397a-BnaLAC2 as a potential modulator of low-temperature adaptability in Brassica napus L

Brassica napus L. (B. napus) is a major edible oil crop grown around the southern part of China, which often faces cold stress, posing potential damage to vegetative tissues. To sustain growth and reproduction, a detailed understanding of fundamental regulatory processes in B. napus against long-term low temperature (LT) stress is necessary for breeders to adjust the level of LT adaption in a given region and is therefore of great economic importance. Till now, studies on microRNAs (miRNAs) in coping with LT adaption in B. napus are limited. Here, we performed an in-depth analysis on two B. napus varieties with distinct adaptability to LT stress. Through integration of RNA sequencing (RNA-seq) and small RNA-sequencing (sRNA-seq), we identified 106 modules comprising differentially expressed miRNAs and corresponding potential targets based on strong negative correlations between their dynamic expression patterns. Specifically, we demonstrated that Bna-miR397a post-transcriptionally regulates a LACCASE (LAC) gene, BnaLAC2, to enhance the adaption to LT stresses in B. napus by reducing the total lignin remodelling and ROS homeostasis. In addition, the miR397-LAC2 module was also proved to improve freezing tolerance of Arabidopsis, indicating a conserved role of miR397-LAC2 in Cruciferae plants. Overall, this work provides the first description of a miRNA-mediated-module signature for LT adaption and highlights the prominent role of laccase in future breeding programme of LT tolerant B. napus.

Jack of all trades: crosstalk between FERONIA signaling and hormone pathways

The receptor kinase FERONIA (FER) is a multifaceted regulator of plant growth, development, reproduction, and stress responses. FER is functionally connected to many plant hormones in diverse biological processes. This review summarizes the current understanding of the interplay between FER and phytohormones, with a focus on abscisic acid, ethylene, jasmonic acid, auxin, and brassinosteroid. The mutual regulation between FER and plant hormones happens at multiple levels including ligands, receptors, and downstream signaling components. Plant hormones can regulate the expression of genes encoding FER and its ligands RAPID ALKALINIZATION FACTORs (RALFs) as well as the abundance and kinase activity of FER proteins. On the other hand, FER can regulate hormone biosynthesis, transport, perception, and downstream signaling components such as transcription factors. Evidence of the crosstalk between FER and phytohormones is also emerging in crop species. Despite the rapid progress made in this field, more mechanistic studies are still needed to gain a comprehensive understanding of the FER-phytohormone crosstalk. Future research prospects and potential approaches are also discussed in this review.

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.

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.

VvbHLH036, a basic helix-loop-helix transcription factor regulates the cold tolerance of grapevine

Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix-loop-helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively. Transcriptome analysis of VvbHLH036-overexpressed roots identified threonine synthase (VvThrC1) as a potential downstream target of VvbHLH036. We confirmed that VvbHLH036 could bind the VvThrC1 promoter and activate its expression. Both the transcripts of VvThrC1 and the content of threonine were significantly induced in the leaves and roots of grapevine under cold treatment compared to controls. Conversely, these dynamics were significantly suppressed in the roots of CRISPR/Cas9-induced KO of VvbHLH036. These observations support the regulation of threonine accumulation by VvbHLH036 through VvThrC1 during cold stress in grapevine. Furthermore, overexpression and CRISPR/Cas9-mediated KO of VvThrC1 also confirmed its role in regulating threonine content and cold tolerance in transgenic roots at low temperature. Exogenous threonine treatment increased cold tolerance and reduced the accumulation of superoxide anions and hydrogen peroxide in grapevine leaves. Together, these findings point to the pivotal role of VvbHLH036 and VvThrC1 in the cold stress response in grapes by regulating threonine biosynthesis.

CsWAK12, a novel cell wall-associated receptor kinase gene from Camellia sinensis, promotes growth but reduces cold tolerance in Arabidopsis

Cold significantly impacts the growth and development of tea plants, thereby affecting their economic value. Receptor-like kinases (RLKs) are thought to play a pivotal role in signaling the plant's response to cold and regulating cold tolerance. Among the RLK subfamilies, wall-associated receptor-like kinases (WAKs) have been investigated across various plant species and have been shown to regulate cell growth and stress responses. However, the function of WAK genes in response to cold stress in tea has yet to be studied. In a previous investigation, we identified the WAK gene family from Camellia sinensis and isolated a specific WAK gene, CsWAK12, which is induced by abiotic stresses. Here, we demonstrate that CsWAK12 is involved in the regulation of cold tolerance in tea plants. CsWAK12 was rapidly induced by cold, peaking at 3 hours after treatment at 4°C (10-fold increase). Heterologous overexpression of CsWAK12 (35S:CsWAK12) in Arabidopsis promoted plant growth by enhancing root length and seed size under normal conditions, although it reduced cold resistance compared to the wild type. Under cold stress, the transgenic plants exhibited a lower survival rate and significantly altered levels of superoxide dismutase (SOD) activity and malondialdehyde (MDA) content compared to the wild type (WT). Furthermore, the expression of C-repeat/dehydration-responsive element binding factor (CBF) genes was diminished in CsWAK12-overexpressing transgenic Arabidopsis plants following cold treatment. Transcriptome analysis revealed that genes associated with the CBF pathway, such as transcription factor genes (ERF53, ERF54, and DREB2A) were markedly reduced in the overexpression line. These data suggest that CsWAK12 acts as a negative regulator, reducing the cold tolerance of transgenic Arabidopsis by mediating the CBF pathway. Therefore, CsWAK12 may serve as a candidate gene for the molecular breeding of cold resistance in tea plants.

γ-Aminobutyric acid mediated by MdCBF3- MdGAD1 mitigates low temperature damage in apple

Low temperatures can seriously affect apple yield and can also cause chilling injury to apple fruit. γ-aminobutyric acid (GABA) plays an important role in improving plant stress resistance. Some studies have reported that GABA can improve cold resistance in plants, only through exogenous treatment; however, the molecular mechanism of its resistance to low temperature is still unknown. This result suggested that exogenous GABA treatment of both apple seedlings and fruit could improve the resistance of apple to low temperatures. MdGAD1, a key gene involved in GABA synthesis, was overexpressed in tomato plants and apple callus to improve their cold tolerance. Both yeast one-hybrid and luciferase assay showed that MdCBF3 could bind to the MdGAD1 promoter to activate its expression and promote GABA synthesis. These results revealed a molecular mechanism utilizing the MdCBF3-MdGAD1 regulatory module that can enhance cold resistance by increasing endogenous GABA synthesis in apple.

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.

Transcription factor DcbZIPs regulate secondary metabolism in Dendrobium catenatum during cold stress

Cold stress seriously affects plant development and secondary metabolism. The basic region/leucine zipper (bZIP) is one of the largest transcription factor (TFs) family and widely involved in plant cold stress response. However, the function of bZIP in Dendrobium catenatum has not been well-documented. Cold inhibited the growth of D. catenatum and increased total polysaccharide and alkaloid contents in stems. Here, 62 DcbZIP genes were identified in D. catenatum, which were divided into 13 subfamilies. Among them, 58 DcbZIPs responded to cold stress, which were selected based on the transcriptome database produced from cold-treated D. catenatum seedlings. Specifically, the expression of DcbZIP3/6/28 was highly induced by cold treatment in leaves or stems. Gene sequence analysis indicated that DcbZIP3/6/28 contains the bZIP conserved domain and is localized to the cell nucleus. Co-expression networks showed that DcbZIP6 was significantly negatively correlated with PAL2 (palmitoyl-CoA), which is involved in flavonoid metabolism. Moreover, DcbZIP28 has significant negative correlations with various metabolism-related genes in the polysaccharide metabolic pathway, including PFKA1 (6-phosphofructokinase), ALDO2 (aldose-6-phosphate reductase) and SCRK5 (fructokinase). These results implied that DcbZIP6 or DcbZIP28 are mainly involved in flavonoid or polysaccharide metabolism. Overall, these findings provide new insights into the roles of the DcbZIP gene family in secondary metabolism in D. catenatum under cold stress.

Global insights into intermediate metabolites: Signaling, metabolic divergence and stress response modulation in plants

Climate change-induced environmental stresses pose significant challenges to plant survival and agricultural productivity. In response, many plants undergo genetic reprogramming, resulting in profound alterations in metabolic pathways and the production of diverse secondary metabolites. As a critical molecular junction, intermediate metabolites by targeted intensification or suppression of subpathways channel cell resources into a multifaceted array of functions such as cell signals, photosynthesis, energy metabolism, ROS homeostasis, producing defensive and protective molecules, epigenetic regulation and stress memory, phytohormones biosynthesis and cell wall architecture under stress conditions. Unlike the well-established functions of end products, intermediate metabolites are context-dependent and produce enigmatic alternatives during stress. As key components of signal transduction pathways, intermediate metabolites with relay and integration of stress signals ensure responses to stress combinations. Investigating efficient metabolic network pathways and their role in regulating unpredictable paths from upstream to downstream levels can unlock their full potential to shape the future of agriculture and ensure global food security. Here, we summarized the activity of some intermediate metabolites, from the perception step to tolerance responses to stress factors.

FERONIA homologs in stress responses of horticultural plants: current knowledge and missing links

Owing to its versatile roles in almost all aspects of plants, FERONIA (FER), a receptor-like kinase of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) subfamily, has received extensive research interests during the past decades. Accumulating evidence has been emerged that FER homologs in horticultural crops also play crucial roles in reproductive biology and responses to environmental stimuli (abiotic and biotic stress factors). Here, we provide a review for the latest advances in the studies on FER homologs in modulating stress responses in horticultural crops, and further analyze the underlying mechanisms maintained by FER. Moreover, we also envisage the missing links in current work and provide a perspective for future studies on this star protein.

Effects of chronic cold stress on tissue structure, antioxidant response, and key gene expression in the warm-water bivalve Chlamys nobilis

As ectothermic invertebrates, mollusks are regarded as good environmental indicator species for determining the adverse effects of climate change on marine organisms. In the present study, the effects of cold stress on the tissue structure, antioxidant activity, and expression levels of genes were evaluated in the warm-water noble scallop Chlamys nobilis by simulating natural seawater cooled down during winter from 17 °C to 14 °C, 12 °C, 10 °C, and 9 °C. Firstly, the gill was severely damaged at 10 °C and 9 °C, indicating that it could be used as a visually indicative organ for monitoring cold stress. The methylenedioxyamphetamine (MDA) content significantly increased with the temperatures decreasing, meanwhile, the antioxidant enzyme activities superoxide dismutase (SOD) and catalase (CAT) showed a similar pattern, suggesting that the scallop made a positive response. More importantly, 6179 genes related to low temperatures were constructed in a module-gene clustering heat map including 10 modules. Furthermore, three gene modules about membrane lipid metabolism, amino acid metabolism, and molecular defense were identified. Finally, six key genes were verified, and HEATR1, HSP70B2, PI3K, and ATP6V1B were significantly upregulated, while WNT6 and SHMT were significantly downregulated under cold stress. This study provides a dynamic demonstration of the major gene pathways' response to various low-temperature stresses from a transcriptomic perspective. The findings shed light on how warm-water bivalves can tolerate cold stress and can help in breeding new strains of aquatic organisms with low-temperature resistance.

Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses

Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.

VvWRKY5 positively regulates wounding-induced anthocyanin accumulation in grape by interplaying with VvMYBA1 and promoting jasmonic acid biosynthesis

Wounding stress induces the biosynthesis of various secondary metabolites in plants, including anthocyanin. However, the underlying molecular mechanism remains elusive. Here, we reported that a transcription factor, VvWRKY5, promotes wounding-induced anthocyanin accumulation in grape (Vitis vinifera). Biochemical and molecular analyses demonstrated that wounding stress significantly increased anthocyanin content, and VvMYBA1 plays an essential role in this process. VvWRKY5 could interact with VvMYBA1 and amplify the activation effect of VvMYBA1 on its target gene VvUFGT. The transcript level of VvWRKY5 was notably induced by wounding treatment. Moreover, our data demonstrated that VvWRKY5 could promote the synthesis of jasmonic acid (JA), a phytohormone that acts as a positive modulator in anthocyanin accumulation, by directly binding to the W-box element in the promoter of the JA biosynthesis-related gene VvLOX and enhancing its activities, and this activation was greatly enhanced by the VvWRKY5-VvMYBA1 protein complex. Collectively, our findings show that VvWRKY5 plays crucial roles in wounding-induced anthocyanin synthesis in grape and elucidates the transcriptional regulatory mechanism of wounding-induced anthocyanin accumulation.

Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances

Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.

Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses

Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.