Overexpression of TaMYC2 confers freeze tolerance by ICE-CBF-COR module in Arabidopsis thaliana

The Role of MYC2 Transcription Factors in Plant Secondary Metabolism and Stress Response Mechanisms

Jasmonates (JAs) are essential signaling molecules that orchestrate plant responses to abiotic and biotic stresses and regulate growth and developmental processes. MYC2, a core transcription factor in JA signaling, plays a central role in mediating these processes through transcriptional regulation. However, the broader regulatory functions of MYC2, particularly in secondary metabolism and stress signaling pathways, are still not fully understood. This review broadens that perspective by detailing the signaling mechanisms and primary functions of MYC2 transcription factors. It specifically emphasizes their roles in regulating the biosynthesis of secondary metabolites such as alkaloids, terpenes, and flavonoids, and in modulating plant responses to environmental stresses. The review further explores how MYC2 interacts with other transcription factors and hormonal pathways to fine-tune defense mechanisms and secondary metabolite production. Finally, it discusses the potential of MYC2 transcription factors to enhance plant metabolic productivity in agriculture, considering both their applications and limitations in managing secondary metabolite synthesis.

The brassinosteroid-mediated Camellia sinensis synthase kinase1 and Camellia sinensis sumo conjugation enzyme1 module positively regulates the cold tolerance of tea plant

Plant glycogen synthase kinase 3 (GSK3) is involved in germinal development and stress response. In the present study, 15 GSK3 members were identified in tea plants and categorised into four subfamilies. During brassinosteroid (BR)-mediated cold stress, the expression levels of the Camellia sinensis synthase kinase1(CsSK1) gene was significantly down-regulated. This gene is highly homologous to the gene encoding BRASSINOSTEROID INSENSITIVE (BIN2) in Arabidopsis (Arabidopsis thaliana). These results suggest that CsSK1 is a candidate gene involved in BR-mediated cold stress in tea plants. Overexpression of the CsSK1 gene in A. thaliana reduced the survival rate of plants at low temperatures, thereby weakening cold tolerance. However, after silencing the CsSK1 in tea plants, cold tolerance was enhanced. In this study, we determined that the protein Camellia sinensis sumo conjugation enzyme1 (CsSCE1) interacts with CsSK1. Silencing of CsSCE1 weakened the cold tolerance of tea plants, indicating that CsSCE1 positively regulates plant cold resistance. Additionally, silencing of CsSCE1 enhanced the expression of CsSK1; similarly, the expression of CsSCE1 increased after CsSK1 was silenced. In summary, CsSK1 interacts with CsSCE1 and plays a negative regulatory role in cold tolerance in tea plants. This study provides new insights into the role of BRs in the regulation of cold tolerance in plants.

Mining genomic regions associated with stomatal traits and their candidate genes in bread wheat through genome-wide association study (GWAS)

KEY MESSAGE

112 candidate quantitative trait loci (QTLs) and 53 key candidate genes have been identified as associated with stomatal traits in wheat. These include bHLH, MADS-box transcription factors, and mitogen-activated protein kinases (MAPKs). Stomata is a common feature of the leaf surface of plants and serve as vital conduits for the exchange of gases (primarily CO₂ and water vapor) between plants and the external environment. In this study, a comprehensive genome analysis was conducted by integrating genome-wide association study (GWAS) and genome prediction to identify the genomic regions and candidate genes of stomatal traits associated with drought resistance and water-saving properties in a panel of 184 diverse bread wheat genotypes. There were significant variations on stomatal traits in the wheat panel across different environmental conditions. GWAS was conducted with the genotypic data from the wheat 660 K single-nucleotide polymorphism (SNP) chip, and the stomatal traits conducted across three environments during two growing seasons. The final GWAS identified 112 candidate QTLs that exhibited at least two significant marker-trait associations. Subsequent analysis identified 53 key candidate genes, including 13 bHLH transcription factor, 2 MADS-box transcription factors, and 4 mitogen-activated protein kinase genes, which may be strongly associated with stomatal traits. The application of Bayesian ridge regression for genomic prediction yielded an accuracy rate exceeding 60% for all four stomatal traits in both SNP matrices, with stomatal width achieving a rate in excess of 70%. Additionally, three Kompetitive allele-specific PCR markers were developed and validated, representing a significant advancement in marker-assisted prediction. Overall, these results will contribute to a more comprehensive understanding of wheat stomatal traits and provide a valuable reference for germplasm screening and innovation in wheat germplasm with novel stomatal traits.

Genome-Wide Identification and Analysis of the MYC Gene Family in Cotton: Evolution and Expression Profiles During Normal Growth and Stress Response

BACKGROUND

The gene family of myelomatosis (MYC), serving as a transcription factor in the jasmonate (JA) signaling pathway, displays a significant level of conservation across diverse animal and plant species. Cotton is the most widely used plant for fiber production. Nevertheless, there is a paucity of literature reporting on the members of MYCs and how they respond to biotic stresses in cotton.

METHODS

Bioinformatics analysis was used to mine the MYC gene family in cotton based on InterPro, cottongen, etc. Results: The gene structure, conserved motifs, and upstream open reading frames of 32 GhMYCs in Gossypium hirsutum were identified. Moreover, it was anticipated that the GT1-motif is the most abundant in GhMYCs, indicating that the GT1-motif plays a significant role in light-responsive GhMYCs. The expression patterns of GhMYCs under biotic stresses including V. dahliae and Aphid gossypii were evaluated, suggesting that GhMYCs in class-1 and -3 GhMYCs, which function as negative regulators, are involved in resistance to verticillium wilt and aphids. The class-3 GhMYCs genes were found to be mostly expressed in female tissues. Interestingly, it was also determined that the homeologous expression bias within GhMYCs in cotton was uncovered, and results showed that the gene expression of class-1A and class-2 GhMYCs in the Dt sub-genome may have a direct impact on gene function.

CONCLUSIONS

This study provides a research direction for researchers and breeders to enhance cotton traits through manipulating individual or multiple homeologs, which laid a foundation for further study of the molecular characteristics and biological functions of GhMYC gene.

Physiological characteristics and transcriptomic analyses of alfalfa root crown in wintering

Background

Alfalfa, scientifically identified as Medicago sativa, is repeatedly referred to as the "king of forages". Because of its tight relationship to winter hardiness, the alfalfa's root crown plays a significant role as a storage organ over the winter. At present, it is still unknown what molecular process makes the alfalfa root crown resistant to cold. This study was aimed to study these knowledge gaps. Using RNA sequencing (RNA-Seq) technology, significant genes associated with cold hardiness were found.

Methods

According to the random block design, Longmu 806 alfalfa and Sardi alfalfa were planted in regional experiments. Under the condition of low-temperature treatment in winter, the differentially expressed genes (DEGs), winter survival rate (WSR), and physiological characteristics were, in turn, calculated by RNA-Seq, chemical analysis, and field investigation.

Results

The WSR of the Longmu 806 alfalfa was 3.68-fold greater than that of the Sardi alfalfa. The jasmonic acid (JA), soluble sugar (SS), proline (Pro), and glutathione (GSH) concentration in the roots of Longmu 806 alfalfa was more than the same amount in Sardi alfalfa in other words P is less than 0.05. An entire set of 878 DEGs related to winter hardiness was found by statistical analysis. Among them, 463 DEGs showed an increase in expression, whereas 415 DEGs showed a decrease in expression. The metabolic pathways' examination presented that the DEGs (MsERF1, MsCHIB, MsJAZ, MsAOC, MsGST, MsINV, MsTPS, and MsOAT) were linked to the pathways of "plant hormone signaling transduction", "Amino sugar and nucleotide sugar metabolism", and "glutathione metabolism". Furthermore, the physiological changes in JA, SS, Pro content, and GSH were influenced by the dynamic transcription profile of LT (low- temperature) resistance-related genes.

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

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

Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress

Salt stress is one of the primary environmental stresses limiting plant growth and production and adversely affecting the growth, development, yield, and fruit quality of Citrus sinensis. bHLH (basic helix-loop-helix) genes are involved in many bioregulatory processes in plants, including growth and development, phytohormone signaling, defense responses, and biosynthesis of specific metabolites. In this study, by bioinformatics methods, 120 CsbHLHgenes were identified, and phylogenetic analysis classified them into 18 subfamilies that were unevenly distributed on nine chromosomes. The cis-acting elements of the CsbHLH genes were mainly hormone-related cis-acting elements. Seventeen CsbHLH genes exhibited significant differences in expression under salt stress. Six CsbHLH genes with significant differences in expression were randomly selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The qRT-PCR results showed a strong correlation with the transcriptome data. Phytohormones such as jasmonic acid (JA) are essential for biotic and abiotic stress responses in plants, and CsbHLH55 and CsbHLH87 are considered candidate target genes for sweet orange MYC2 transcription factors involved in the JA signaling pathway. These genes are the main downstream effectors in the JA signaling pathway and can be activated to participate in the JA signaling pathway. Activation of the JA signaling pathway inhibits the production of reactive oxygen species and improves the salt tolerance of sweet orange plants. The CsbHLH55 and CsbHLH87 genes could be candidate genes for breeding new transgenic salt-resistant varieties of sweet orange.

Advances in functional studies of plant MYC transcription factors

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Crop-Specific Responses to Cold Stress and Priming: Insights from Chlorophyll Fluorescence and Spectral Reflectance Analysis in Maize and Soybean

This study aimed to investigate the impact of cold stress and priming on photosynthesis in the early development of maize and soybean, crops with diverse photosynthetic pathways. The main objectives were to determine the effect of cold stress on chlorophyll a fluorescence parameters and spectral reflectance indices, to determine the effect of cold stress priming and possible stress memory and to determine the relationship between different parameters used in determining the stress response. Fourteen maize inbred lines and twelve soybean cultivars were subjected to control, cold stress, and priming followed by cold stress in a walk-in growth chamber. Measurements were conducted using a portable fluorometer and a handheld reflectance instrument. Cold stress induced an overall downregulation of PSII-related specific energy fluxes and efficiencies, the inactivation of RCs resulting in higher energy dissipation, and electron transport chain impairment in both crops. Spectral reflectance indices suggested cold stress resulted in pigment differences between crops. The effect of priming was more pronounced in maize than in soybean with mostly a cumulatively negative effect. However, priming stabilized the electron trapping efficiency and upregulated the electron transfer system in maize, indicating an adaptive response. Overall, this comprehensive analysis provides insights into the complex physiological responses of maize and soybean to cold stress, emphasizing the need for further genotype-specific cold stress response and priming effect research.

Overexpression of TaMPK3 enhances freezing tolerance by increasing the expression of ICE-CBF-COR related genes in the Arabidopsis thaliana

Mitogen-activated protein kinases (MAPKs) play important roles in plant stress response. As a major member of the MAPK family, MPK3 has been reported to participate in the regulation of chilling stress. However, the regulatory function of wheat (Triticum aestivum ) mitogen-activated protein kinase TaMPK3 in freezing tolerance remains unknown. Dongnongdongmai No.1 (Dn1) is a winter wheat variety with strong freezing tolerance; therefore, it is important to explore the mechanisms underlying this tolerance. In this study, the expression of TaMPK3 in Dn1 was detected under low temperature and hormone treatment. Gene cloning, bioinformatics and subcellular localisation analyses of TaMPK3 in Dn1 were performed. Overexpressed TaMPK3 in Arabidopsis thaliana was obtained, and freezing tolerance phenotype observations, physiological indices and expression levels of ICE-C-repeat binding factor (CBF)-COR -related genes were determined. In addition, the interaction between TaMPK3 and TaICE41 proteins was detected. We found that TaMPK3 expression responds to low temperatures and hormones, and the TaMPK3 protein is localised in the cytoplasm and nucleus. Overexpression of TaMPK3 in Arabidopsis significantly improves freezing tolerance. TaMPK3 interacts with the TaICE41 protein. In conclusion, TaMPK3 is involved in regulating the ICE-CBF-COR cold resistance module through its interaction with TaICE41, thereby improving freezing tolerance in Dn1 wheat.

Genome-wide identification of the bHLH transcription factor family in Rosa persica and response to low-temperature stress

Background

Basic helix-loop-helix (bHLH) transcription factors are involved in plant growth and development, secondary metabolism, and abiotic stress responses have been studied in a variety of plants. Despite their importance in plant biology, the roles and expression patterns of bHLH family genes in Rosa persica have not been determined.

Methods

In this study, the RbebHLH family genes were systematically analyzed using bioinformatics methods, and their expression patterns under low-temperature stress were analyzed by transcriptome and related physiological index measurements.

Results

In total, 142 RbebHLHs were identified in the genome of R. persica, distributed on seven chromosomes. Phylogenetic analysis including orthologous genes in Arabidopsis divided RbebHLHs into 21 subfamilies, with similar structures and motifs within a subfamily. A collinearity analysis revealed seven tandem duplications and 118 segmental duplications in R. persica and 127, 150, 151, 172, and 164 segmental duplications between R. persica and Arabidopsis thaliana, Prunus mume, Fragaria vesca, Rosa chinensis, and Prunus persica, respectively. A number of cis-regulatory elements associated with abiotic stress response and hormone response were identified in RbebHLHs, and 21 RbebHLHs have potential interactions with the CBF family. In addition, the expression results showed that part of bHLH may regulate the tolerance of R. persica to low-temperature stress through the jasmonic acid and pathway. Transcriptomic data showed that the expression levels of different RbebHLHs varied during overwintering, and the expression of some RbebHLHs was significantly correlated with relative conductivity and MDA content, implying that RbebHLHs play important regulatory roles in R. persica response to low-temperature stress. Overall, this study provides valuable insights into the study of RbebHLHs associated with low-temperature stress.

The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change

BACKGROUND

Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to species geographic range shifts, population declines, and even extinctions. The rare and endangered species, being critical components of regional biodiversity, hold the key to understanding local adaptation and evolutionary processes shaping species distributions. Therefore, assessing the evolutionary mechanisms of local adaptation and population vulnerability under climate change is crucial for developing conservation strategies of endangered species.

RESULTS

In this study, we assembled a high-quality, chromosome-level genome of the rare and endangered herb Bergenia scopulosa in the Qinling Mountains in East Asia and resequenced 37 individual genomes spanning its entire geographic distributional ranges. By integrating population genetics, landscape genomics, and climate datasets, a substantial number of adaptive single-nucleotide polymorphism loci associated with climate variables were identified. The genotype-environment association analysis showed that some cold-tolerant genes have played pivotal roles in cold environmental adaptation of B. scopulosa. These findings are further corroborated through evolutionary analysis of gene family and quantitative PCR validation. Population genomic analysis revealed 2 distinct genetic lineages in B. scopulosa. The western lineage showed higher genomic vulnerability and more rare cold-tolerance alleles, suggesting its heightened sensitivity to impending climate shifts, and should be given priority conservation in the management practices.

CONCLUSIONS

These findings provide novel insights into local adaptation and genomic vulnerability of B. scopulosa under climate change in the Qinling Mountains in East Asia. Additionally, the study also offers valuable guidance for formulating conservation strategies for the rare and endangered plants.

Overexpression of TaMYB4 Confers Freezing Tolerance in Arabidopsis thaliana

Freezing stress is one of the main factors limiting the growth and yield of wheat. In this study, we found that TaMYB4 expression was significantly upregulated in the tillering nodes of the strong cold-resistant winter wheat variety Dongnongdongmai1 (Dn1) under freezing stress. Weighted gene co-expression network analysis, qRT-PCR and protein-DNA interaction experiments demonstrated that monodehydroascorbate reductase (TaMDHAR) is a direct target of TaMYB4. The results showed that overexpression of TaMYB4 enhanced the freezing tolerance of transgenic Arabidopsis. In TaMYB4 overexpression lines (OE-TaMYB4), AtMDHAR2 expression was upregulated and ascorbate-glutathione (AsA-GSH) cycle operation was enhanced. In addition, the expression of cold stress marker genes such as AtCBF1, AtCBF2, AtCBF3, AtCOR15A, AtCOR47, AtKIN1 and AtRD29A in OE-TaMYB4 lines was significantly upregulated. Therefore, TaMYB4 may increase freezing tolerance as a transcription factor (TF) in Arabidopsis through the AsA-GSH cycle and DREB/CBF signaling pathway. This study provides a potential gene for molecular breeding against freezing stress.

Responses of sorghum to cold stress: A review focused on molecular breeding

Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.