Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis

CRISPR/Cas9 opens new horizon of crop improvement under stress condition

Plants are exposed to a myriad of stresses, stemming from abiotic and biotic sources, significantly threatening agricultural productivity. The low crop yield, coupled with the global burden of population has resulted in the scarcity of quality food, exacerbating socio-economic issues like poverty, hunger, and malnutrition. Conventional breeding methods for the generation of stress-tolerant plants are time-consuming, limit genetic diversity, and are not sustainable for the consistent production of high-yielding crops. In recent years, the use of high-throughput, genome editing (GE) technique has revolutionized the crop-improvement paradigm, ushering greater prospects for agricultural progress. Among these tools, the Clustered regularly interspaced short palindromic repeat (CRISPR), and its associated nuclease protein Cas9, have appeared as a ground-breaking technology, allowing precise knockout (KO), upregulation, and downregulation of target gene expression. Apart from its high efficacy and speed, this programmable nuclease offers exceptional specificity with minimal off-target effects. Here in, we aim to review the latest findings on the application of the CRISPR/Cas9 genome editing tool for generating resilience in plants against environmental stresses.

MYB Transcription Factor CDC5 Activates CBF3 Expression to Positively Regulates Freezing Tolerance via Cooperating With ICE1 and Histone Modification in Arabidopsis

The freezing temperature greatly limits the growth, development and productivity of plants. The C-repeat/DRE binding factor (CBF) plays a major role in cold acclimation, enabling plants to increase their freezing tolerance. Notably, the INDUCER OF CBF EXPRESSION1 (ICE1) protein has garnered attention for its pivotal role in bolstering plants' resilience against freezing through transcriptional upregulation of DREB1A/CBF3. However, the research on the interaction between ICE1 and other transcription factors and its function in regulating cold stress tolerance is largely inadequate. In this study, we found that a R2R3 MYB transcription factor CDC5 interacts with ICE1 and regulates the expression of CBF3 by recruiting RNA polymerase II, overexpression of ICE1 can complements the freezing deficient phenotype of cdc5 mutant. CDC5 increases the expression of CBF3 in response to freezing. Furthermore, CDC5 influences the expression of CBF3 by altering the chromatin status through H3K4me3 and H3K27me3 modifications. Our work identified a novel component that regulates CBF3 transcription in both ICE1-dependent and ICE1-independent manner, improving the understanding of the freezing signal transduction in plants.

Genome-wide analysis of the AP2/ERF gene family in Pennisetum glaucum and the negative role of PgRAV_01 in drought tolerance

APETALA2/ethylene-responsive (AP2/ERF) plays crucial roles in resisting diverse stresses and in regulating plant growth and development. However, little is known regarding the structure and function of the AP2/ERF genes in pearl millet (Pennisetum glaucum). The AP2/ERF gene family may be involved in the development and maintenance of P. glaucum resilience to abiotic stresses, central to its role as a vital forage and cereal crop. In this study, PgAP2/ERF family members were identified and comprehensive bioinformatics analyses were performed, including determination of phylogenetic relationships, gene structures, conserved motifs, chromosomal localization, gene duplication, expression pattern, protein interaction network, and functional characterization of PgRAV_01 (Related to ABI3/VP1). In total, 78 PgAP2/ERF members were identified in the P. glaucum genome and classified into five subfamilies: AP2, ERF, DREB, RAV, and soloist. Members within the same clade of the PgAP2/ERF family showed similar gene structures and motif compositions. Six duplication events were identified in the PgAP2/ERF family; calculation of Ka/Ks values showed that purification selection dominated the evolution of PgAP2/ERFs. Subsequently, a potential interaction network of PgAP2/ERFs was generated to predict the interaction relationships. Additionally, abiotic stress expression analysis showed that most PgAP2/ERFs were induced in response to drought and heat stresses. Furthermore, overexpression of PgRAV_01 negatively regulated drought tolerance in Nicotiana benthamiana by reducing its antioxidant capacity and osmotic adjustment. Taken together, these results provide valuable insights into the characteristics and functions of PgAP2/ERF genes, with implications for abiotic stress tolerance, and will ultimately contribute to the genetic improvement of cereal crop breeding.

Transcriptome analysis and genome-wide identification of the dehydration-responsive element binding gene family in jackfruit under cold stress

BACKGROUND

Jackfruit (Artocarpus heterophyllus Lam.) is the world's largest and heaviest fruit and adapts to hot, humid tropical climates. Low-temperature injury in winter is a primary abiotic stress, which affects jackfruit growth and development. Therefore, breeding cold-resistant varieties and identifying the vital genes in the process of cold resistance are essential. The dehydration-responsive element binding (DREB) gene family is among the subfamily of the APETALA2/ethylene response factor transcription factor family and is significant in plant abiotic stress responses.

METHODS

In this study, a comparative analysis of the cold resistance property of 'GuangXi' ('GX') and 'Thailand' ('THA') jackfruit strains with different cold resistance characteristics was performed through chlorophyll fluorescence and transcriptome sequencing.

RESULTS

We found that differentially expressed genes (DEGs) are significantly enriched in the metabolic processes. Here, 93 DREB genes were identified in the jackfruit genome, and phylogenetic analysis was used to classify them into seven groups. Gene structure, conserved motifs, chromosomal location, and homologous relationships were used to analyze the structural characteristics of the DREB family. Transcriptomics indicated that most of the AhDREB genes exhibited down-regulated expression in 'THA.' The DEGs AhDREB12, AhDREB21, AhDREB29, and AhDREB34 were selected for quantitative real-time PCR, and the results showed that these genes also had down-regulated expression in 'THA.'

CONCLUSIONS

The above results suggest the significance of the DREB family in improving the cold resistance property of 'GX.'

Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress

BACKGROUND

Phytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family.

RESULTS

In this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses.

CONCLUSION

This study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.

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.

An AP2/ERF transcription factor confers chilling tolerance in rice

Cold stress, a prominent adverse environmental factor, severely hinders rice growth and productivity. Unraveling the complex mechanisms governing chilling tolerance in rice is crucial for molecular breeding of cold-tolerant varieties. Here, we identify an APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor, OsERF52, as a positive modulator in response to low temperatures. OsERF52 directly regulates the expression of C-Repeat Binding Factor (CBF) genes in rice. In addition, Osmotic Stress/ABA-Activated Protein Kinase 9-mediated phosphorylation of OsERF52 at S261 enhances its stability and interaction with Ideal Plant Architecture 1 and OsbHLH002/OsICE1. This collaborative activation leads to the expression of OsCBFs, thereby initiating the chilling response in rice. Notably, plants with base-edited OsERF52S261D-3HA exhibit enhanced chilling resistance without yield penalty. Our findings unveil the mechanism orchestrated by a regulatory framework involving a protein kinase and transcription factors from diverse families, offering potential genetic resources for developing chilling-tolerant rice varieties.

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.

Exploring the puzzle of reactive oxygen species acting on root hair cells

Reactive oxygen species (ROS) are essential signaling molecules that enable cells to respond rapidly to a range of stimuli. The ability of plants to recognize various stressors, incorporate a variety of environmental inputs, and initiate stress-response networks depends on ROS. Plants develop resilience and defensive systems as a result of these processes. Root hairs are central components of root biology since they increase the surface area of the root, anchor it in the soil, increase its ability to absorb water and nutrients, and foster interactions between microorganisms. In this review, we specifically focused on root hair cells and we highlighted the identification of ROS receptors, important new regulatory hubs that connect ROS production, transport, and signaling in the context of two hormonal pathways (auxin and ethylene) and under low temperature environmental input related to nutrients. As ROS play a crucial role in regulating cell elongation rates, root hairs are rapidly gaining traction as a very valuable single plant cell model for investigating ROS homeostasis and signaling. These promising findings might soon facilitate the development of plants and roots that are more resilient to environmental stressors.

ICE1 interacts with IDD14 to transcriptionally activate QQS to increase pollen germination and viability

In flowering plants, sexual reproductive success depends on the production of viable pollen grains. However, the mechanisms by which QUA QUINE STARCH (QQS) regulates pollen development and how transcriptional activators facilitate the transcription of QQS in this process remain poorly understood. Here, we demonstrate that INDUCER OF CBF EXPRESSION 1 (ICE1), a basic helix-loop-helix (bHLH) transcription factor, acts as a key transcriptional activator and positively regulates QQS expression to increase pollen germination and viability in Arabidopsis thaliana by interacting with INDETERMINATE DOMAIN14 (IDD14). In our genetic and biochemical experiments, overexpression of ICE1 greatly promoted both the activation of QQS and high pollen viability mediated by QQS. IDD14 additively enhanced ICE1 function by promoting the binding of ICE1 to the QQS promoter. In addition, mutation of ICE1 significantly repressed QQS expression; the impaired function of QQS and the abnormal anther dehiscence jointly affected pollen development of the ice1-2 mutant. Our results also showed that the enhancement of pollen activity by ICE1 depends on QQS. Furthermore, QQS interacted with CUT1, the key enzyme for long-chain lipid biosynthesis. This interaction both promoted CUT1 activity and regulated pollen lipid metabolism, ultimately determining pollen hydration and fertility. Our results not only provide new insights into the key function of QQS in promoting pollen development by regulating pollen lipid metabolism, but also elucidate the mechanism that facilitates the transcription of QQS in this vital developmental process.

SlNAC3 suppresses cold tolerance in tomatoes by enhancing ethylene biosynthesis

Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.

EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors

Reconstructing functional gene regulatory networks (GRNs) is a primary prerequisite for understanding pathogenic mechanisms and curing diseases in animals, and it also provides an important foundation for cultivating vegetable and fruit varieties that are resistant to diseases and corrosion in plants. Many computational methods have been developed to infer GRNs, but most of the regulatory relationships between genes obtained by these methods are biased. Eliminating indirect effects in GRNs remains a significant challenge for researchers. In this work, we propose a novel approach for inferring functional GRNs, named EIEPCF (eliminating indirect effects produced by confounding factors), which eliminates indirect effects caused by confounding factors. This method eliminates the influence of confounding factors on regulatory factors and target genes by measuring the similarity between their residuals. The validation results of the EIEPCF method on simulation studies, the gold-standard networks provided by the DREAM3 Challenge and the real gene networks of Escherichia coli demonstrate that it achieves significantly higher accuracy compared to other popular computational methods for inferring GRNs. As a case study, we utilized the EIEPCF method to reconstruct the cold-resistant specific GRN from gene expression data of cold-resistant in Arabidopsis thaliana. The source code and data are available at https://github.com/zhanglab-wbgcas/EIEPCF.

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

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

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

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

A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold

Rice is susceptible to chilling stress. Identifying chilling tolerance genes and their mechanisms are key to improve rice performance. Here, we performed a genome-wide association study to identify regulatory genes for chilling tolerance in rice. One major gene for chilling tolerance variation in Indica rice was identified as a casein kinase gene OsCTK1. Its function and natural variation are investigated at the physiological and molecular level by its mutants and transgenic plants. Potential substrates of OsCTK1 were identified by phosphoproteomic analysis, protein-protein interaction assay, in vitro kinase assay, and mutant characterization. OsCTK1 positively regulates rice chilling tolerance. Three of its putative substrates, acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, and dual-specific mitogen-activated protein kinase phosphatase OsMKP1, are each involved in chilling tolerance. In addition, a natural OsCTK1 chilling-tolerant (CT) variant exhibited a higher kinase activity and conferred greater chilling tolerance compared with a chilling-sensitive (CS) variant. The CT variant is more prevalent in CT accessions and is distributed more frequently in higher latitude compared with the CS variant. This study thus enables a better understanding of chilling tolerance mechanisms and provides gene variants for genetic improvement of chilling tolerance in rice.

The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress

Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding

KEY MESSAGE

Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally. While ideally grown in 13-21 °C, its cultivation extends into winter in milder climates. However, occasional freezing temperatures can significantly reduce yields. Therefore, the development of freezing-tolerant lettuce varieties has become a long-term goal of lettuce breeding programs. Despite its significance, our understanding of freezing tolerance in lettuce remains limited. Plants have evolved a coping mechanism against freezing, known as cold acclimation, whereby they can increase freezing tolerance when pre-exposed to low nonfreezing temperatures. The CBF pathway is well-known for its central role in cold acclimation. Previously, we identified 14 CBF genes in lettuce and discovered that one of them, LsCBF7, had a loss-of-function mutation. In this study, we uncovered that accessions from colder regions carried the wild-type allele of LsCBF7 and this allele likely contributed to increased freezing tolerance, with 14% of the lettuce population carrying this allele. Interestingly, in wild lettuce (L. serriola) that is considered a progenitor of cultivated lettuce, this wild-type allele was much more common, with a frequency of 90%. This finding suggests that this wild-type allele may have undergone negative selection during the domestication or breeding of lettuce. Our data strongly indicate that this allele could be linked to early bolting, an undesirable trait in lettuce, which may have driven the negative selection. While this wild-type allele shows promise for improving freezing tolerance in lettuce, it is crucial to decouple it from the early bolting trait to fully harness its potential in lettuce breeding.

Functional Divergence in Orthologous Transcription Factors: Insights from AtCBF2/3/1 and OsDREB1C

Despite traditional beliefs of orthologous genes maintaining similar functions across species, growing evidence points to their potential for functional divergence. C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are critical in cold acclimation, with their overexpression enhancing stress tolerance but often constraining plant growth. In contrast, a recent study unveiled a distinctive role of rice OsDREB1C in elevating nitrogen use efficiency (NUE), photosynthesis, and grain yield, implying functional divergence within the CBF/DREB1 orthologs across species. Here, we delve into divergent molecular mechanisms of OsDREB1C and AtCBF2/3/1 by exploring their evolutionary trajectories across rice and Arabidopsis genomes, regulatomes, and transcriptomes. Evolutionary scrutiny shows discrete clades for OsDREB1C and AtCBF2/3/1, with the Poaceae-specific DREB1C clade mediated by a transposon event. Genome-wide binding profiles highlight OsDREB1C's preference for GCCGAC compared to AtCBF2/3/1's preference for A/GCCGAC, a distinction determined by R12 in the OsDREB1C AP2/ERF domain. Cross-species multiomic analyses reveal shared gene orthogroups (OGs) and underscore numerous specific OGs uniquely bound and regulated by OsDREB1C, implicated in NUE, photosynthesis, and early flowering, or by AtCBF2/3/1, engaged in hormone and stress responses. This divergence arises from gene gains/losses (∼16.7% to 25.6%) and expression reprogramming (∼62.3% to 66.2%) of OsDREB1C- and AtCBF2/3/1-regulated OGs during the extensive evolution following the rice-Arabidopsis split. Our findings illustrate the regulatory evolution of OsDREB1C and AtCBF2/3/1 at a genomic scale, providing insights on the functional divergence of orthologous transcription factors following gene duplications across species.

Regulatory networks in plant responses to drought and cold stress

Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.

Genome-Wide Analysis Elucidates the Roles of GhTIR1/AFB Genes Reveals the Function of Gh_D08G0763 (GhTIR1) in Cold Stress in G. hirsutum

This study identified 13 GhTIR1/AFB members in G. hirsutum through bioinformatics methods and divided them into three subgroups by phylogenetic tree analysis. Motif and gene structure analysis showed that the genes in this family were highly conserved. Promoter cis-acting element analysis found that the promoters of GhTIR1/AFBs contained a large number of cis-acting elements in response to growth and development and abiotic stress. Further RT-qPCR results showed that GhTIR1/AFB genes responded to various abiotic stresses such as IAA, ABA, cold, and heat, and the expression levels of each gene changed obviously, especially Gh_D08G0763 (GhTIR1), which responded significantly to cold injury. Using VIGS (virus-induced gene silencing) technology to silence Gh_D08G0763 in the cold-tolerant cotton variety ZM36, it was found that the resistance of ZM36 to cold damage was significantly reduced. The physiological response mechanism of the Gh_D08G0763 in resisting cold damage was further analyzed through trypan blue staining of leaves and determination of enzyme activity levels. This study provided effective genetic resources for cotton cold-tolerance breeding.

Effect of Low Temperature on Content of Primary Metabolites in Two Wheat Genotypes Differing in Cold Tolerance

The study of cold-tolerance mechanisms of wheat as a leading cereal crop is very relevant to science. Primary metabolites play an important role in the formation of increased cold tolerance. The aim of this research is to define changes in the content of primary metabolites (soluble proteins and sugars), growth, and photosynthetic apparatus of freezing-tolerant and cold-sustainable wheat (Triticum aestivum L.) genotypes under optimal conditions and after prolonged (7 days) exposure to low temperature (4 °C). In order to gain a deeper comprehension of the mechanisms behind wheat genotypes' adaptation to cold, we determined the expression levels of photosynthetic genes (RbcS, RbcL) and genes encoding cold-regulated proteins (Wcor726, CBF14). The results indicated different cold-adaptation strategies of freezing-tolerant and cold-sustainable wheat genotypes, with soluble proteins and sugars playing a significant role in this process. In plants of freezing-tolerant genotypes, the strategy of adaptation to low temperature was aimed at increasing the content of soluble proteins and modification of carbohydrate metabolism. The accumulation of sugars was not observed in wheat of cold-sustainable genotypes during chilling, but a high content of soluble proteins was maintained both under optimal conditions and after cold exposure. The adaptation strategies of wheat genotypes differing in cold tolerance were related to the expression of photosynthetic genes and genes encoding cold-regulated proteins. The data improve our knowledge of physiological and biochemical mechanisms of wheat cold adaptation.

ERF54 regulates cold tolerance in Rosa multiflora through DREB/COR signalling pathways

Ethylene-responsive factors (ERFs) participate in a wide range of physiological and biological processes. However, many of the functions of ERFs in cold stress responses remain unclear. We, therefore, characterised the cold responses of RmERF54 in Rosa multiflora, a rose-related cold-tolerant species. Overexpression of RmERF54, which is a nuclear transcription factor, increases the cold resistance of transgenic tobacco and rose somatic embryos. In contrast, virus-induced gene silencing (VIGS) of RmERF54 increased cold susceptibility of R. multiflora. The overexpression of RmERF54 resulted in extensive transcriptional reprogramming of stress response and antioxidant enzyme systems. Of these, the levels of transcripts encoding the PODP7 peroxidase and the cold-related COR47 protein showed the largest increases in the somatic embryos with ectopic expression of RmERF54. RmERF54 binds to the promoters of the RmPODP7 and RmCOR47 genes and activates expression. RmERF54-overexpressing lines had higher antioxidant enzyme activities and considerably lower levels of reactive oxygen species. Opposite effects on these parameters were observed in the VIGS plants. RmERF54 was identified as a target of Dehydration-Responsive-Element-Binding factor (RmDREB1E). Taken together, provide new information concerning the molecular mechanisms by which RmERF54 regulates cold tolerance.

Allelic variation of PmCBF03 contributes to the altitude and temperature adaptability in Japanese apricot (Prunus mume Sieb. et Zucc.)

Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03A type in high-altitude areas and PmCBF03T type in low-altitude areas. PmCBF03A gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03A gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03A directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03A lines. While PmCBF03T gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.

The cold-responsive C-repeat binding factors in Betula platyphylla Suk. positively regulate cold tolerance

Cold stress is one of the most destructive abiotic stresses limiting plant growth and development. CBF (C-repeat binding factor) transcription factors and their roles in cold response have been identified in Arabidopsis as well as several other plant species. However, the biological functions and related molecular mechanisms of CBFs in birch (Betula platyphylla Suk.) remain undetermined. In this study, five cold-responsive BpCBF genes, BpCBF1, BpCBF2, BpCBF7, BpCBF10 and BpCBF12 were cloned. Via protoplast transformation, BpCBF7 was found to be localized in nucleus. The result of yeast one hybrid assay validated the binding of BpCBF7 to the CRT/DRE (C-repeat/dehydration responsive element) elements in the promoter of BpERF1.1 gene. By overexpressing and repressing BpCBFs in birch plants, it was proven that BpCBFs play positive roles in the cold tolerance. At the metabolic level, BpCBFs OE lines had lower ROS accumulation, as well as higher activities of antioxidant enzymes (SOD, POD and CAT) and higher accumulation of protective substances (soluble sugar, soluble protein and proline). Via yeast one hybrid and co-transformation of effector and reporter vectors assay, it was proven that BpCBF7 can regulate the expression of BpERF5 and BpZAT10 genes by directly binding to their promoters. An interacting protein of BpCBF7, BpWRKY17, was identified by yeast two hybrid library sequencing and the interaction was validated with in vivo methods. These results indicates that BpCBFs can increase the cold tolerance of birch plants, partly by gene regulation and protein interaction. This study provides a reference for the research on CBF transcription factors and genetic improvement of forest trees upon abiotic stresses.

Regulation of the trade-off between cold stress and growth by glutathione S-transferase phi class 10 (BcGSTF10) in non-heading Chinese cabbage

Cold stress is a serious threat to global crop production and food security, but plant cold resistance is accompanied by reductions in growth and yield. In this study, we determined that the novel gene BcGSTF10 in non-heading Chinese cabbage [NHCC; Brassica campestris (syn. Brassica rapa) ssp. chinensis] is implicated in resistance to cold stress. Biochemical and genetic analyses demonstrated that BcGSTF10 interacts with BcICE1 to induce C-REPEAT BINDING FACTOR (CBF) genes that enhance freezing tolerance in NHCC and in Arabidopsis. However, BcCBF2 represses BcGSTF10 and the latter promotes growth in NHCC and Arabidopsis. This dual function of BcGSTF10 indicates its pivotal role in balancing cold stress and growth, and this important understanding has the potential to inform the future development of strategies to breed crops that are both climate-resilient and high-yielding.

Structural changes in cell wall pectic polymers contribute to freezing tolerance induced by cold acclimation in plants

Subzero temperatures are often lethal to plants. Many temperate herbaceous plants have a cold acclimation mechanism that allows them to sense a drop in temperature and prepare for freezing stress through accumulation of soluble sugars and cryoprotective proteins. As ice formation primarily occurs in the apoplast (the cell wall space), cell wall functional properties are important for plant freezing tolerance. Although previous studies have shown that the amounts of constituent sugars of the cell wall, in particular those of pectic polysaccharides, are altered by cold acclimation, the significance of this change during cold acclimation has not been clarified. We found that β-1,4-galactan, which forms neutral side chains of the acidic pectic rhamnogalacturonan-I, accumulates in the cell walls of Arabidopsis and various freezing-tolerant vegetables during cold acclimation. The gals1 gals2 gals3 triple mutant, which has reduced β-1,4-galactan in the cell wall, exhibited impaired freezing tolerance compared with wild-type Arabidopsis during initial stages of cold acclimation. Expression of genes involved in the galactan biosynthesis pathway, such as galactan synthases and UDP-glucose 4-epimerases, was induced during cold acclimation in Arabidopsis, explaining the galactan accumulation. Cold acclimation resulted in a decrease in extensibility and an increase in rigidity of the cell wall in the wild type, whereas these changes were not observed in the gals1 gals2 gals3 triple mutant. These results indicate that the accumulation of pectic β-1,4-galactan contributes to acquired freezing tolerance by cold acclimation, likely via changes in cell wall mechanical properties.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Genome-wide identification of DREB1 transcription factors in perennial ryegrass and functional profiling of LpDREB1H2 in response to cold stress

Perennial ryegrass (Lolium perenne L.) is an outstanding turfgrass and forage cultivated in temperate regions worldwide. However, poor tolerance to extreme cold, heat, or drought limits wide extension and cultivation. DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR1s (DREB1s) play a vital role in enhancing plant tolerance to abiotic stress, specifically for low-temperature stress. In this study, a total of 24 LpDREB1 family members were identified from the released genome of perennial ryegrass. Phylogenetic analysis showed that the LpDREB1 genes are divided into 7 groups that have close relationships with rice homologues. Conserved motif analysis revealed that members within the same group have similar conserved motif compositions. All LpDREB1s lack introns, and the promoter sequences of LpDREB1 genes contain multiple cis-acting elements associated with stress response, phytohormone signal transduction and plant growth and development. The majority of LpDREB1 genes were upregulated by drought, submergence, heat and cold stress treatments, including LpDREB1H2. Further investigation showed that LpDREB1H2 is localized in the nucleus. Overexpression of LpDREB1H2 in Arabidopsis induced the expression of cold-responsive (COR) genes, increased the levels of osmotic adjusting substances, and enhanced antioxidant enzyme activities, thus improving the cold tolerance of Arabidopsis. This study lays a foundation for further understanding the function of LpDREB1 genes in perennial ryegrass and provides insights for plant stress tolerance breeding.

A comprehensive analysis of transcriptomic data for comparison of cold tolerance in two Brassica napus genotypes

Brassica napus is an important oil crop and cold stress severely limits its productivity. To date, several studies have reported the regulatory genes and pathways involved in cold-stress responses in B. napus. However, transcriptome-scale identification of the regulatory genes is still lacking. In this study, we performed comparative transcriptome analysis of cold-tolerant C18 (CT - C18) and cold-sensitive C6 (CS - C6) Brassica napus genotypes under cold stress for 7 days, with the primary purpose of identifying cold-responsive transcription in B. napus. A total of 6061 TFs belonging to 58 families were annotated in the B. napus genome, of which 3870 were expressed under cold stress in both genotypes. Among these, 451 TFs were differentially expressed (DE), with 21 TF genes expressed in both genotypes. Most TF members of the MYB (26), bHLH (23), and NAC (17) families were significantly expressed in the CT - C18 genotype compared with the CS - C6 B. napus genotype. GO classification showed a significant role in transcription regulation, DNA-binding transcription factor activity, response to chitin, and the ethylene-activated signaling pathway. KEGG pathway annotation revealed these TFs are involved in regulating more pathways, resulting in more tolerance. In conclusion, the results provide insights into the molecular regulation mechanisms of B. napus in response to freezing treatment, expanding our understanding of the complex molecular mechanisms in plants' response to freezing stress.

Cold acclimation alleviates photosynthetic inhibition and oxidative damage induced by cold stress in citrus seedlings

Cold stress seriously inhibits plant growth and development, geographical distribution, and yield stability of plants. Cold acclimation (CA) is an important strategy for modulating cold stress, but the mechanism by which CA induces plant resistance to cold stress is still not clear. The purpose of this study was to investigate the effect of CA treatment on the cold resistance of citrus seedlings under cold stress treatment, and to use seedlings without CA treatment as the control (NA). The results revealed that CA treatment increased the content of photosynthetic pigments under cold stress, whereas cold stress greatly reduced the value of gas exchange parameters. CA treatment also promoted the activity of Rubisco and FBPase, as well as led to an upregulation of the transcription levels of photosynthetic related genes (rbcL and rbcS)，compared to the NA group without cold stress. In addition, cold stress profoundly reduced photochemical chemistry of photosystem II (PSII), especially the maximum quantum efficiency (Fv/Fm) in PSII. Conversely, CA treatment improved the chlorophyll a fluorescence parameters, thereby improving electron transfer efficiency. Moreover, under cold stress, CA treatment alleviated oxidative stress damage to cell membranes by inhibiting the concentration of H2O2 and MDA, enhancing the activities of superoxide dismutase (SOD), catalase (CAT), ascorbic acid peroxidase (APX) and glutathione reductase (GR), accompanied by an increase in the expression level of antioxidant enzyme genes (CuZnSOD1, CAT1, APX and GR). Additionally, CA also increased the contents of abscisic acid (ABA) and salicylic acid (SA) in plants under cold stress. Overall, we concluded that CA treatment suppressed the negative effects of cold stress by enhancing photosynthetic performance, antioxidant enzymes functions and plant hormones contents.

Genome-wide identification and expression analysis of the CBF transcription factor family in Lolium perenne under abiotic stress

C-repeat binding factor (CBF) subfamily genes encoding transcriptional activators are members of the AP2/ERF superfamily. CBFs play important roles in plant tolerance to abiotic stress. In this study, we identified and analyzed the structure, phylogeny, conserved motifs, and expression profiles of 12 CBFs of the grass species Lolium perenne cultured under abiotic stress. The identified LpCBFs were grouped into three phylogenetic clades according to their protein structures and motif organizations. LpCBF expression was differentially induced by cold, heat, water deficit, salinity, and abscisic acid, among which cold treatment induced LpCBF gene expression significantly. Furthermore, association network analysis indicated that different proteins, including certain stress-related proteins, potentially interact with LpCBFs. Altogether, these findings will enhance our understanding of LpCBFs protein structure and function in the regulation of L. perenne stress responses. Our results will provide valuable information for further functional research of LpCBF proteins in L. perenne stress resistance.

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

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

OsMAPK6 positively regulates rice cold tolerance at seedling stage via phosphorylating and stabilizing OsICE1 and OsIPA1

Rice is a chilling-sensitive plant, and extremely low temperatures seriously decrease rice production. Several genes involved in chilling stress have been reported in rice; however, the chilling signaling in rice remains largely unknown. Here, we investigated the chilling tolerance phenotype of overexpression of constitutive active OsMAPK6 (CAMAPK6-OE) and OsMAPK6 mutant dsg1, and demonstrated that OsMAPK6 positively regulated rice chilling tolerance. It was shown that, under cold stress, the survival rate of dsg1 was significantly lower than that of WT, whereas CAMAPK6-OE display higher survival rate than WT. Physiological assays indicate that ion leakage and dead cell in dsg1 was much more severe than those in WT and CAMAPK6-OE. Consistently, expression of chilling responsive genes in dsg1, including OsCBFs and OsTPP1, was significantly lower than that of in WT and CAMAPK6-OE. Biochemical analyses revealed that chilling stress promotes phosphorylation of OsMAPK6. Besides, we found that OsMAPK6 interacts with and phosphorylates two key regulators in rice cold signaling, OsIPA1 and OsICE1, and then enhance their protein stability. Overall, our results revealed a cold-induced OsMAPK6-OsICE1/OsIPA1 signaling cascade by which OsMAPK6 was involved in rice chilling tolerance, which provides novel insights to understand rice cold response at seedling stage.

Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.

Jasmonate: A Hormone of Primary Importance for Temperature Stress Response in Plants

Temperature is a critical environmental factor that plays a vital role in plant growth and development. Temperatures below or above the optimum ranges lead to cold or heat stress, respectively. Temperature stress retards plant growth and development, and it reduces crop yields. Jasmonates (JAs) are a class of oxylipin phytohormones that play various roles in growth, development, and stress response. In recent years, studies have demonstrated that cold and heat stress affect JA biosynthesis and signaling, and JA plays an important role in the response to temperature stress. Recent studies have provided a large body of information elucidating the mechanisms underlying JA-mediated temperature stress response. In the present review, we present recent advances in understanding the role of JA in the response to cold and heat stress, and how JA interacts with other phytohormones during this process.

Comprehensive genome-wide analysis of the DREB gene family in Moso bamboo (Phyllostachys edulis): evidence for the role of PeDREB28 in plant abiotic stress response

Dehydration response element binding (DREB) proteins are vital for plant abiotic stress responses, but the understanding of DREBs in bamboo, an important sustainable non-timber forest product, is limited. Here we conducted a comprehensive genome-wide analysis of the DREB gene family in Moso bamboo, representing the most important running bamboo species in Asia. In total, 44 PeDREBs were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress-related cis-regulatory elements (CREs) was provided. Based on the bioinformatical analysis, we further analyzed PeDREBs from the A5 group and found that four of five PeDREB transcripts were induced by salt, drought, and cold stresses, and their proteins could bind to stress-related CREs. Among these, PeDREB28 was selected as a promising candidate for further functional characterization. PeDREB28 is localized in nucleus, has transcriptional activation activity, and could bind to the DRE- and coupling element 1- (CE1) CREs. Overexpression of PeDREB28 in Arabidopsis and bamboo improved plant abiotic stress tolerance. Transcriptomic analysis showed that broad changes due to the overexpression of PeDREB28. Furthermore, 628 genes that may act as the direct PeDREB28 downstream genes were identified by combining DAP-seq and RNA-seq analysis. Moreover, we confirmed that PeDREB28 could bind to the promoter of pyrabactin-resistance-like gene (DlaPYL3), which is a homolog of abscisic acid receptor in Arabidopsis, and activates its expression. In summary, our study provides important insights into the DREB gene family in Moso bamboo, and contributes to their functional verification and genetic engineering applications in the future.

Auxin and abiotic stress responses

Plants are exposed to a variety of abiotic stresses; these stresses have profound effects on plant growth, survival, and productivity. Tolerance and adaptation to stress require sophisticated stress sensing, signaling, and various regulatory mechanisms. The plant hormone auxin is a key regulator of plant growth and development, playing pivotal roles in the integration of abiotic stress signals and control of downstream stress responses. In this review, we summarize and discuss recent advances in understanding the intersection of auxin and abiotic stress in plants, with a focus on temperature, salt, and drought stresses. We also explore the roles of auxin in stress tolerance and opportunities arising for agricultural applications.

Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus

MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.

CsBPC2 is essential for cucumber survival under cold stress

Cold stress affects the growth and development of cucumbers. Whether the BPC2 transcription factor participates in cold tolerance and its regulatory mechanism in plants have not been reported. Here, we used wild-type (WT) cucumber seedlings and two mutant Csbpc2 lines as materials. The underlying mechanisms were studied by determining the phenotype, physiological and biochemical indicators, and transcriptome after cold stress. The results showed that CsBPC2 knockout reduced cucumber cold tolerance by increasing the chilling injury index, relative electrical conductivity and malondialdehyde (MDA) content and decreasing antioxidant enzyme activity. We then conducted RNA sequencing (RNA-seq) to explore transcript-level changes in Csbpc2 mutants. A large number of differentially expressed genes (1032) were identified and found to be unique in Csbpc2 mutants. However, only 489 down-regulated genes related to the synthesis and transport of amino acids and vitamins were found to be enriched through GO analysis. Moreover, both RNA-seq and qPT-PCR techniques revealed that CsBPC2 knockout also decreased the expression of some key cold-responsive genes, such as CsICE1, CsCOR413IM2, CsBZR1 and CsBZR2. These results strongly suggested that CsBPC2 knockout not only affected cold function genes but also decreased the levels of some key metabolites under cold stress. In conclusion, this study reveals for the first time that CsBPC2 is essential for cold tolerance in cucumber and provides a reference for research on the biological function of BPC2 in other plants.

The unequal functional redundancy of Arabidopsis INCURVATA11 and CUPULIFORMIS2 is not dependent on genetic background

The paralogous genes INCURVATA11 (ICU11) and CUPULIFORMIS2 (CP2) encode components of the epigenetic machinery in Arabidopsis and belong to the 2-oxoglutarate and Fe (II)-dependent dioxygenase superfamily. We previously inferred unequal functional redundancy between ICU11 and CP2 from a study of the synergistic phenotypes of the double mutant and sesquimutant combinations of icu11 and cp2 mutations, although they represented mixed genetic backgrounds. To avoid potential confounding effects arising from different genetic backgrounds, we generated the icu11-5 and icu11-6 mutants via CRISPR/Cas genome editing in the Col-0 background and crossed them to cp2 mutants in Col-0. The resulting mutants exhibited a postembryonic-lethal phenotype reminiscent of strong embryonic flower (emf) mutants. Double mutants involving icu11-5 and mutations affecting epigenetic machinery components displayed synergistic phenotypes, whereas cp2-3 did not besides icu11-5. Our results confirmed the unequal functional redundancy between ICU11 and CP2 and demonstrated that it is not allele or genetic background specific. An increase in sucrose content in the culture medium partially rescued the post-germinative lethality of icu11 cp2 double mutants and sesquimutants, facilitating the study of their morphological phenotypes throughout their life cycle, which include floral organ homeotic transformations. We thus established that the ICU11-CP2 module is required for proper flower organ identity.

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

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

The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold

Plant growth and development involve the specification and regeneration of stem cell niches (SCNs). Although plants are exposed to disparate environmental conditions, how environmental cues affect developmental programs and stem cells is not well understood. Root stem cells are accommodated in meristems in SCNs around the quiescent center (QC), which maintains their activity. Using a combination of genetics and confocal microscopy to trace morphological defects and correlate them with changes in gene expression and protein levels, we show that the cold-induced transcription factor (TF) C-REPEAT BINDING FACTOR 3 (CBF3), which has previously been associated with cold acclimation, regulates root development, stem cell activity, and regeneration. CBF3 is integrated into the SHORT-ROOT (SHR) regulatory network, forming a feedback loop that maintains SHR expression. CBF3 is primarily expressed in the root endodermis, whereas the CBF3 protein is localized to other meristematic tissues, including root SCNs. Complementation of cbf3-1 using a wild-type CBF3 gene and a CBF3 fusion with reduced mobility show that CBF3 movement capacity is required for SCN patterning and regulates root growth. Notably, cold induces CBF3, affecting QC activity. Furthermore, exposure to moderate cold around 10°C-12°C promotes root regeneration and QC respecification in a CBF3-dependent manner during the recuperation period. By contrast, CBF3 does not appear to regulate stem cell survival, which has been associated with recuperation from more acute cold (∼4°C). We propose a role for CBF3 in mediating the molecular interrelationships among the cold response, stem cell activity, and development.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.

Histone deacetylase MdHDA6 is an antagonist in regulation of transcription factor MdTCP15 to promote cold tolerance in apple

Understanding the molecular regulation of plant cold response is the basis for cold resistance germplasm improvement. Here, we revealed that the apple histone deacetylase MdHDA6 can perform histone deacetylation on cold-negative regulator genes and repress their expression, leading to the positive regulation of cold tolerance in apples. Moreover, MdHDA6 directly interacts with the transcription factor MdTCP15. Phenotypic analysis of MdTCP15 transgenic apple lines and wild types reveals that MdTCP15 negatively regulates cold tolerance in apples. Furthermore, we found that MdHDA6 can facilitate histone deacetylation of MdTCP15 and repress the expression of MdTCP15, which positively contributes to cold tolerance in apples. Additionally, the transcription factor MdTCP15 can directly bind to the promoter of the cold-negative regulator gene MdABI1 and activate its expression, and it can also directly bind to the promoter of the cold-positive regulator gene MdCOR47 and repress its expression. However, the co-expression of MdHDA6 and MdTCP15 can inhibit MdTCP15-induced activation of MdABI1 and repression of MdCOR47, suggesting that MdHDA6 suppresses the transcriptional regulation of MdTCP15 on its downstream genes. Our results demonstrate that histone deacetylase MdHDA6 plays an antagonistic role in the regulation of MdTCP15-induced transcriptional activation or repression to positively regulate cold tolerance in apples, revealing a new regulatory mechanism of plant cold response.

Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice

Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.

Plant breeding for harmony between sustainable agriculture, the environment, and global food security: an era of genomics-assisted breeding

MAIN CONCLUSION

Genomics-assisted breeding represents a crucial frontier in enhancing the balance between sustainable agriculture, environmental preservation, and global food security. Its precision and efficiency hold the promise of developing resilient crops, reducing resource utilization, and safeguarding biodiversity, ultimately fostering a more sustainable and secure food production system. Agriculture has been seriously threatened over the last 40 years by climate changes that menace global nutrition and food security. Changes in environmental factors like drought, salt concentration, heavy rainfalls, and extremely low or high temperatures can have a detrimental effects on plant development, growth, and yield. Extreme poverty and increasing food demand necessitate the need to break the existing production barriers in several crops. The first decade of twenty-first century marks the rapid development in the discovery of new plant breeding technologies. In contrast, in the second decade, the focus turned to extracting information from massive genomic frameworks, speculating gene-to-phenotype associations, and producing resilient crops. In this review, we will encompass the causes, effects of abiotic stresses and how they can be addressed using plant breeding technologies. Both conventional and modern breeding technologies will be highlighted. Moreover, the challenges like the commercialization of biotechnological products faced by proponents and developers will also be accentuated. The crux of this review is to mention the available breeding technologies that can deliver crops with high nutrition and climate resilience for sustainable agriculture.

Azospirillum brasilense improves rice growth under salt stress by regulating the expression of key genes involved in salt stress response, abscisic acid signaling, and nutrient transport, among others

Major food crops, such as rice and maize, display severe yield losses (30-50%) under salt stress. Furthermore, problems associated with soil salinity are anticipated to worsen due to climate change. Therefore, it is necessary to implement sustainable agricultural strategies, such as exploiting beneficial plant-microbe associations, for increased crop yields. Plants can develop associations with beneficial microbes, including arbuscular mycorrhiza and plant growth-promoting bacteria (PGPB). PGPB improve plant growth via multiple mechanisms, including protection against biotic and abiotic stresses. Azospirillum brasilense, one of the most studied PGPB, can mitigate salt stress in different crops. However, little is known about the molecular mechanisms by which A. brasilense mitigates salt stress. This study shows that total and root plant mass is improved in A. brasilense-inoculated rice plants compared to the uninoculated plants grown under high salt concentrations (100 mM and 200 mM NaCl). We observed this growth improvement at seven- and fourteen days post-treatment (dpt). Next, we used transcriptomic approaches and identified differentially expressed genes (DEGs) in rice roots when exposed to three treatments: 1) A. brasilense, 2) salt (200 mM NaCl), and 3) A. brasilense and salt (200 mM NaCl), at seven dpt. We identified 786 DEGs in the A. brasilense-treated plants, 4061 DEGs in the salt-stressed plants, and 1387 DEGs in the salt-stressed A. brasilense-treated plants. In the A. brasilense-treated plants, we identified DEGs involved in defense, hormone, and nutrient transport, among others. In the salt-stressed plants, we identified DEGs involved in abscisic acid and jasmonic acid signaling, antioxidant enzymes, sodium and potassium transport, and calcium signaling, among others. In the salt-stressed A. brasilense-treated plants, we identified some genes involved in salt stress response and tolerance (e.g., abscisic acid and jasmonic acid signaling, antioxidant enzymes, calcium signaling), and sodium and potassium transport differentially expressed, among others. We also identified some A. brasilense-specific plant DEGs, such as nitrate transporters and defense genes. Furthermore, our results suggest genes involved in auxin and ethylene signaling are likely to play an important role during these interactions. Overall, our transcriptomic data indicate that A. brasilense improves rice growth under salt stress by regulating the expression of key genes involved in defense and stress response, abscisic acid and jasmonic acid signaling, and ion and nutrient transport, among others. Our findings will provide essential insights into salt stress mitigation in rice by A. brasilense.

Jasmonate biosynthesis enzyme allene oxide cyclase 2 mediates cold tolerance and pathogen resistance

Allene oxide cyclase (AOC) is a key enzyme in the biosynthesis of jasmonic acid (JA), which is involved in plant growth and development as well as adaptation to environmental stresses. We identified the cold- and pathogen-responsive AOC2 gene from Medicago sativa subsp. falcata (MfAOC2) and its homolog MtAOC2 from Medicago truncatula. Heterologous expression of MfAOC2 in M. truncatula enhanced cold tolerance and resistance to the fungal pathogen Rhizoctonia solani, with greater accumulation of JA and higher transcript levels of JA downstream genes than in wild-type plants. In contrast, mutation of MtAOC2 reduced cold tolerance and pathogen resistance, with less accumulation of JA and lower transcript levels of JA downstream genes in the aoc2 mutant than in wild-type plants. The aoc2 phenotype and low levels of cold-responsive C-repeat-binding factor (CBF) transcripts could be rescued by expressing MfAOC2 in aoc2 plants or exogenous application of methyl jasmonate. Compared with wild-type plants, higher levels of CBF transcripts were observed in lines expressing MfAOC2 but lower levels of CBF transcripts were observed in the aoc2 mutant under cold conditions; superoxide dismutase, catalase, and ascorbate-peroxidase activities as well as proline concentrations were higher in MfAOC2-expressing lines but lower in the aoc2 mutant. These results suggest that expression of MfAOC2 or MtAOC2 promotes biosynthesis of JA, which positively regulates expression of CBF genes and antioxidant defense under cold conditions and expression of JA downstream genes after pathogen infection, leading to greater cold tolerance and pathogen resistance.

Oligogalactolipid production during cold challenge is conserved in early diverging lineages

Severe cold, defined as a damaging cold beyond acclimation temperatures, has unique responses, but the signaling and evolution of these responses are not well understood. Production of oligogalactolipids, which is triggered by cytosolic acidification in Arabidopsis (Arabidopsis thaliana), contributes to survival in severe cold. Here, we investigated oligogalactolipid production in species from bryophytes to angiosperms. Production of oligogalactolipids differed within each clade, suggesting multiple evolutionary origins of severe cold tolerance. We also observed greater oligogalactolipid production in control samples than in temperature-challenged samples of some species. Further examination of representative species revealed a tight association between temperature, damage, and oligogalactolipid production that scaled with the cold tolerance of each species. Based on oligogalactolipid production and transcript changes, multiple angiosperm species share a signal of oligogalactolipid production initially described in Arabidopsis, namely cytosolic acidification. Together, these data suggest that oligogalactolipid production is a severe cold response that originated from an ancestral damage response that remains in many land plant lineages and that cytosolic acidification may be a common signaling mechanism for its activation.