Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis

Genome-wide identification, expression analysis, and stress response analysis of the RdbZIP gene family in Rhododendron delavayi

BACKGROUND

Basic leucine zipper (bZIP) gene family members represent one of the most diverse and largest groups of transcription factors in eukaryotes. Research has demonstrated that bZIP transcription factors play crucial roles not only in plant growth and development but also in response to various abiotic stresses. However, studies focusing on bZIP factors in Rhododendron delavayi (RdbZIPs) remain limited.

RESULT

In this study, a total of 59 RdbZIPs were identified using bioinformatics approaches, and these could be classified into 13 subfamilies based on the genomic data of R. delavayi. Members of the same RdbZIP subfamily exhibited similar gene structures and conserved motifs, and were unevenly distributed across the 13 chromosomes of R. delavayi. Collinearity analysis revealed a total of 20 duplication events, comprising 3 pairs of tandem duplications and 17 pairs of segmental duplications. Additionally, cis-acting element analysis indicated that RdbZIP family members may be involved in various biological processes, including transcription, development, hormone regulation, and responses to biotic and abiotic stresses. Transcriptomic analysis revealed that RdbZIP family genes were highly expressed in reproductive tissues. RT-qPCR expression analysis revealed that many selected RdbZIP genes were significantly upregulated under high salinity and drought conditions, suggesting their potential involvement in stress-responsive regulatory networks.

CONCLUSION

This study provides the first comprehensive characterization of the bZIP transcription factor family in Rhododendron delavayi, laying a foundational framework for functional studies of individual RdbZIP genes. The results highlight the pivotal role of RdbZIP genes in abiotic stress tolerance, which is crucial for understanding the adaptive mechanisms of R. delavayi. Future research should focus on the functional validation of key RdbZIP genes and elucidation of their regulatory pathways, which may contribute to the genetic improvement of Rhododendron species under adverse environmental conditions.

CLINICAL TRIAL

Not applicable.

Genome-Wide identification and expression analysis of CsABF/AREB gene family in cucumber (Cucumis sativus L.) and in response to phytohormonal and abiotic stresses

Abscisic acid (ABA)-responsive element binding factors (ABF)/ABA-responsive element binding proteins (AREB)/ABA insensitive protein 5 (ABI5) all belong to the basic leucine zipper (bZIP) transcription factor A subfamily. The bZIP transcription factor family contains 13 subfamilies, namely groups A, B, C, D, E, F, G, H, I, J, K, M and S, and the ABF/AREB/ABI5 gene belongs to A subfamily of the bZIP transcription factor. However, genomic analysis of CsABF/AREB in cucumber (Cucumis sativus L.) has not been systematically studied. In this study, we analyzed the characterization of CsABF/AREB family members and their response to phytohormonal and abiotic stresses. The results showed that a total of 8 genes family members were identified in cucumber. Structural domain analysis showed that the proteins of these family members are highly similar, and all of them belong to the bZIP structural domain. qRT-PCR analysis showed that CsABF/AREB members are expressed in root, stem, and leaf, with the highest expression in root, followed by stem and leaf. In addition, all 8 CsABF/AREB genes respond to ABA and methyl jasmonate (Me-JA). Among them, CsABF7 has the highest expression under both ABA and Me-JA treatments. Drought and salt stress significantly induce CsABF1, CsABF2, CsABF7, and CsABF8 expression. Drought and NaC1 stresses significantly induce the expression of CsABF1, CsABF2, CsABF7, and CsABF8. This study provides a basis for a further understanding of the role of CsABF/AREB homologous genes in response to abiotic stress and lays the foundation for further research on the function of CsABF/AREB.

AREB/ABF/ABI5 transcription factors in plant defense: regulatory cascades and functional diversity

Basic leucine zipper transcription factors (TFs), also known as ABRE-BINDING PROTEINs/ABRE BINDING FACTORs (AREBs/ABFs), and ABA INSENSITIVE 5 (ABI5), show a great potential for the regulation of gene expressions in different crops under unfavorable conditions. These factors are involved in phytohormone signaling pathways, developmental metabolism, and growth regulation under environmental stresses. ABI5 functions alongside ABREs to regulate gene expression, with their promoter regions composed of the receptors PYR/PYL/RCAR, kinases (sucrose non-fermenting-1-related protein kinase 2) and phosphatases (PROTEIN PHOSPHATASE 2 C). These TFs participate in signaling pathways that regulate key genes and control numerous morphological, physiological, biochemical, and molecular processes under stressful environments. In this review, we studied ABFs/AREBs/ABI5s TFs, the phytohormone signaling pathways and their crosstalk, which play critical roles in regulating responses to abiotic stresses. The key TFs discussed in this work regulate various metabolic pathways and are promising candidates for the development of stress-resilient crops via CRISPR/CRISPR-associated protein technology to address threats to food security and sustainability in agriculture.

Plant Signaling Hormones and Transcription Factors: Key Regulators of Plant Responses to Growth, Development, and Stress

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change.

Genome-wide identification and analysis of autophagy-related (ATG) genes in Lycium ruthenicum Murray reveals their crucial roles in salt stress tolerance

Autophagy is a highly conserved intracellular degradation system that is crucial for nutrient recycling, thus regulating plant growth and development as well as in response to various stresses. Halophytic plant Lycium ruthenicum Murray (L. ruthenicum) is considered as a potential model plant for studying the physiological mechanisms of salt stress tolerance in plants. Although the genome sequence of L. ruthenicum is available, the characteristics and functions of the salt stress-related genes remain largely unknown. In the present study, a total of 36 AuTophaGy-related (ATG) genes were identified in L. ruthenicum and detailed characteristics of them were given. Quantitative real-time polymerase chain reaction analysis revealed that the expression of 25 LrATGs was significantly upregulated after salt stress treatments. Furthermore, the autophagic marker line pSuper:GFP-LrATG8g was generated and used to demonstrate the salt stress-induced autophagy, as revealed by measuring autophagic flux and observing autophagosome formation. The pSuper:LrATG5-GFP overexpression (OE) lines were also generated and further phenotypic analysis showed that OE-LrATG8g and OE-LrATG5 plants exhibited better salt tolerance than that of WT plants. To the best of our knowledge, this study firstly reports a detailed overview of LrATGs-mediated autophagy in L. ruthenicum response to salt stress. These findings contribute to a global understanding of the characteristics of ATG genes in L. ruthenicum and lay a foundation for future functional study.

Role of pepper bZIP transcription factor CaADBZ1 in abscisic acid signalling and drought stress response

In plants, basic-region/leucine-zipper (bZIP) transcription factors are key regulators of stress responses mediated by various phytohormone signalling pathways. However, the roles of bZIP transcription factors in pepper, particularly those associated with ABA signalling and drought stress, remain poorly understood. In this study, we isolated the CaADBZ1 (Capsicum annuum ABA and Dehydration-Induced bZIP transcription factor 1) gene, a member of the group A family, and analysed its functions in response to dehydration stress and ABA signalling. The expression of CaADBZ1 was specifically induced by dehydration and exogenous ABA treatment, not salinity and osmotic stress. CaADBZ1 was found to have transactivation activity in yeast cells, which was dependent on the N-terminal of CaADBZ1 (amino acids 1-112), harbouring a highly conserved C1 domain. Notably, a dual-luciferase reporter assay revealed that CaADBZ1 modulated the expression of CaOSR1, a dehydration stress-responsive gene in pepper plants. Functional studies in both pepper and Arabidopsis plants revealed that the modulation of CaADBZ1 expression level affected dehydration stress resistance in pepper and Arabidopsis plants. CaADBZ1-silenced pepper Arabidopsis plants showed dehydration stress-sensitive phenotypes characterized by higher transpiration rates and reduced expression of dehydration-responsive genes compared to control plants. Conversely, overexpression of the CaADBZ1 gene in Arabidopsis plants enhanced dehydration stress resistance. Moreover, CaADBZ1-overexpressing Arabidopsis transgenic plants showed increased ABA sensitivity during the seedling stage. Collectively, our findings suggest that CaADBZ1 plays a crucial role in enhancing dehydration stress tolerance in plants by positively regulating ABA sensitivity and dehydration-responsive gene expression.

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

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

The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume

Bud dormancy is a vital physiological process in woody perennials, facilitating their adaptation to seasonal environmental changes. Satisfying genotype-specific chilling requirements (CR) and heat requirements (HR) through exposure to specific chilling and warm temperatures is essential for dormancy release and the subsequent resumption of growth. The genetic mechanisms regulating bud dormancy traits in Prunus mume remain unclear. In this study, we first assembled the genome of 'Nanko', the leading P. mume cultivar in Japan, in a haplotype-resolved manner. Using an F1 segregating population from a cross between 'Nanko' (high-chill) and 'SC' (low-chill), a cultivar adapted to subtropical conditions, we identified quantitative trait loci (QTLs) for vegetative bud dormancy traits on chromosome 4 (LG4 QTLs) in the 'Nanko' genome and for CR and HR on chromosome 7 (LG7 QTL) in the 'SC' genome. A notable 5.6 Mb chromosome inversion was overlapped with LG4 QTL interval in one of the 'Nanko' haplotypes. We also identified candidate genes based on haplotyping, differential expression between the parents or the presence of trait-correlated variants in coding regions. Notably, genes such as PmuMAIN, PmuNAC2, PmuDOG1, PmuSUI1, PmuATG8CL, PmubZIP44, and PmuSAUR50 were identified. This study provides valuable insights into the genetic regulation of vegetative bud dormancy in Prunus species.

Transcriptional regulation and functional validation analysis of the McbZIP1 in Mentha canadensis L

Monoterpenoids are the main components of Mentha canadensis essential oil. Monoterpene biosynthetic pathways have been explored, but the regulatory mechanisms remain unclarified. We identified an abscisic acid (ABA)-inducible A-type basic leucine zipper (bZIP) transcription factor McbZIP1 that was localized in the nucleus and positively regulates monoterpene synthesis. McbZIP1 was expressed in most M. canadensis tissues and was induced under ABA, mannitol, and NaCl treatments. McbZIP1 had transcriptional activity in yeast and the N terminus (amino acids 75-117) was sufficient for transactivation. Yeast one-hybrid and Dual-Luciferase assays showed that McbZIP1 binds to ABA-responsive elements in the promoter region of limonene synthase gene. Yeast two-hybrid and biomolecular fluorescence complementation assays revealed that McbZIP1 interacts with McSnRK2.4. Overexpression of McbZIP1 in peppermint resulted in dramatically up-regulated monoterpene biosynthesis gene levels and increased menthol contents. The results support a transcriptional regulation mechanism in which McbZIP1 serves as a positive regulator of menthol biogenesis. These findings contribute to the molecular mechanism of monoterpenoid biogenesis, which may have uses in genetic engineering and menthol production.

Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (OsPR1)

Pathogenesis-related (PR) proteins, found in plants, play a crucial role in responding to both biotic and abiotic stresses and are categorized into 17 distinct families based on their properties and functions. We have conducted a phylogenetic analysis of OsPR1 genes (rice PR1 genes) in conjunction with 58 putative PR1 genes identified in Brachypodium distachyon, Hordeum vulgare, Brassica rapa, and Zea mays through BLASTP predictions. We extensively investigated the responses of the remaining 11 rice PR1 genes, using OsPR1a as a reference, under various stress conditions, including phytohormone treatments (salicylic acid and brassinosteroid [BR]), wounding, and heat stress (HS). In rice, of the 32 predicted OsPR1 genes, 12 have been well-characterized for their roles in disease resistance, while the functions of the remaining genes have not been studied extensively. In our study, we selected an additional 11 OsPR1 genes for further analysis and constructed a phylogenetic tree based on the presence of a 10-amino-acid-long conserved motif within these proteins. The phylogenetic analysis revealed that both OsPR1a from earlier studies and OsPR1-74 from our current study belong to the same clade. These genes consistently exhibit upregulation in response to diverse stress treatments such as biotic stress and abiotic stresses such as heat, drought, and salinity, indicating their potential roles in enhancing stress tolerance in rice. Significantly, this study delves into the previously unexplored role of OsPR1 genes in responding to Brassinosteroid (BR) and heat stress (HS) treatments, confirming their involvement in stress responses through qRT-PCR analysis. We found that seven genes were upregulated by EBR treatment. During heat stress (HS), six and seven genes were upregulated at 1hand 4h HS, respectively. The remaining genes OsPR1-22 and OsPR1-75 were upregulated at 1h but downregulated at 4h HS and under EBR treatment. In contrast, OsPR1-76 was upregulated at both 1h and 4h HS, but downregulated under EBR treatment. Promoters of PR1 genes in rice and other crops are rich in transcription factor binding sites (TFBSs) and feature a conserved Cysteine-rich secretory protein (SCP or CAP) motif. This study advances our understanding of PR1 gene regulation and its potential to enhance stress tolerance in rice.

Genome-wide analysis and expression profile of the bZIP gene family in Neopyropia yezoensis

The basic leucine zipper (bZIP) family consists of conserved transcription factors which are widely present in eukaryotes and play important regulatory roles in plant growth, development, and stress responses. Neopyropia yezoensis is a red marine macroalga of significant economic importance; however, their bZIP family members and functions have not been systematically identified and analyzed. In the present study, the bZIP gene family in Ny. yezoensis was characterized by investigating gene structures, conserved motifs, phylogenetic relationships, chromosomal localizations, gene duplication events, cis-regulatory elements, and expression profiles. Twenty-three Ny. yezoensis bZIP (NyybZIP) genes were identified and sorted into 13 out of 30 groups, which were classified based on the bZIPs of Ny. yezoensis and 15 other red algae species. Phylogenetic analysis revealed that bZIP genes may have a complex evolutionary pattern in red algae. Cross-species collinearity analysis indicated that the bZIP genes in Ny. yezoensis, Neoporphyra haitanensis, and Porphyra umbilicalis are highly evolutionarily conserved. In addition, we identified four main categories of cis-elements, including development-related, light-responsive, phytohormone-responsive and stress-responsive promoter sequences in NyybZIP genes. Finally, RNA sequencing data and quantitative real-time PCR (qRT-PCR) showed that NyybZIP genes exhibited different expression patterns depending on the life stage. NyybZIP genes were also found to be involved in the nitrogen stress response. We thought that bZIP genes may be involved in Ny. yezoensis growth and development, and play a significant role in nitrogen deficiency response. Taken together, our findings provide new insights into the roles of the bZIP gene family and provide a basis for additional research into its evolutionary history and biological functions.

bZIP Transcription Factor PavbZIP6 Regulates Anthocyanin Accumulation by Increasing Abscisic Acid in Sweet Cherry

Basic leucine zipper (bZIP) transcription factors (TFs) play a crucial role in anthocyanin accumulation in plants. In addition to bZIP TFs, abscisic acid (ABA) increases anthocyanin biosynthesis. Therefore, this study aimed to investigate whether bZIP TFs are involved in ABA-induced anthocyanin accumulation in sweet cherry and elucidate the underlying molecular mechanisms. Specifically, the BLAST method was used to identify bZIP genes in sweet cherry. Additionally, we examined the expression of ABA- and anthocyanin-related genes in sweet cherry following the overexpression or knockdown of a bZIP candidate gene. In total, we identified 54 bZIP-encoding genes in the sweet cherry genome. Basic leucine zipper 6 (bZIP6) showed significantly increased expression, along with increased anthocyanin accumulation in sweet cherry. Additionally, yeast one-hybrid and dual-luciferase assays indicated that PavbZIP6 enhanced the expression of anthocyanin biosynthetic genes (PavDFR, PavANS, and PavUFGT), thereby increasing anthocyanin accumulation. Moreover, PavbZIP6 interacted directly with the PavBBX6 promoter, thereby regulating PavNCED1 to promote abscisic acid (ABA) synthesis and enhance anthocyanin accumulation in sweet cherry fruit. Conclusively, this study reveals a novel mechanism by which PavbZIP6 mediates anthocyanin biosynthesis in response to ABA and contributes to our understanding of the mechanism of bZIP genes in the regulation of anthocyanin biosynthesis in sweet cherry.

RNA-Seq and WGCNA Analyses Reveal Key Regulatory Modules and Genes for Salt Tolerance in Cotton

The problem of soil salinization has seriously hindered agricultural development. Cotton is a pioneering salinity-tolerant crop, so harvesting its key salinity-tolerant genes is important for improving crop salt tolerance. In this study, we analyzed changes in the transcriptome expression profiles of the salt-tolerant cultivar Lu Mian 28 (LM) and the salt-sensitive cultivar Zhong Mian Suo 12 (ZMS) after applying salt stress, and we constructed weighted gene co-expression networks (WGCNA). The results indicated that photosynthesis, amino acid biosynthesis, membrane lipid remodeling, autophagy, and ROS scavenging are key pathways in the salt stress response. Plant-pathogen interactions, plant hormone signal transduction, the mitogen-activated protein kinase (MAPK) signaling pathway, and carotenoid biosynthesis are the regulatory networks associated with these metabolic pathways that confer cotton salt tolerance. The gene-weighted co-expression network was used to screen four modules closely related to traits, identifying 114 transcription factors, including WRKYs, ERFs, NACs, bHLHs, bZIPs, and MYBs, and 11 hub genes. This study provides a reference for acquiring salt-tolerant cotton and abundant genetic resources for molecular breeding.

Transcription factor MdbZIP44 targets the promoter of MdPPO2 to regulate browning in Malus domestica Borkh

Apple (Malus domestica Borkh.) is among the most widely planted and economically valuable horticultural crops globally. Over time, the apple fruit's cut surface undergoes browning, and the degree of browning varies among different apple varieties. Browning not only affects the appearance of fruits but also adversely affects their taste and flavor. In the present study, we observed browning in different apple varieties over time and analyzed the expression of genes in the polyphenol oxidase gene family. The results indicated a strong correlation between the browning degree of the fruit and the relative expression of the polyphenol oxidase gene MdPPO2. With the MdPPO2 promoter as bait, the basic leucine zipper (bZIP) transcription factor MdbZIP44 was identified using the yeast single-hybrid screening method. Further investigation revealed that the overexpression of MdbZIP44 in 'Orin' callus could enhance the expression of MdPPO2 and promote browning of the callus. However, knocking out MdbZIP44 resulted in a callus with no apparent browning phenotype. In addition, our results confirmed the interaction between MdbZIP44 and MdbZIP11. In conclusion, the results indicated that MdbZIP44 can induce apple fruit browning by activating the MdPPO2 promoter. The results provide a theoretical basis for further clarifying the browning mechanism of apple fruit.

A soybean bZIP transcription factor is involved in submergence resistance

Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.

Regulatory Dynamics of Plant Hormones and Transcription Factors under Salt Stress

The negative impacts of soil salinization on ion homeostasis provide a significant global barrier to agricultural production and development. Plant physiology and biochemistry are severely affected by primary and secondary NaCl stress impacts, which damage cellular integrity, impair water uptake, and trigger physiological drought. Determining how transcriptional factors (TFs) and hormone networks are regulated in plants in response to salt stress is necessary for developing crops that tolerate salt. This study investigates the complex mechanisms of several significant TF families that influence plant responses to salt stress, involving AP2/ERF, bZIP, NAC, MYB, and WRKY. It demonstrates how these transcription factors (TFs) help plants respond to the detrimental effects of salinity by modulating gene expression through mechanisms including hormone signaling, osmotic stress pathway activation, and ion homeostasis. Additionally, it explores the hormonal imbalances triggered by salt stress, which entail complex interactions among phytohormones like jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) within the hormonal regulatory networks. This review highlights the regulatory role of key transcription factors in salt-stress response, and their interaction with plant hormones is crucial for developing genome-edited crops that can enhance agricultural sustainability and address global food security challenges.

QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis

The utilization of saline land is a global challenge, and cultivating salt-tolerant soybean varieties is beneficial for improving the efficiency of saline land utilization. Exploring the genetic basis of salt-tolerant soybean varieties and developing salt-tolerant molecular markers can effectively promote the process of soybean salt-tolerant breeding. In the study, the membership function method was used to evaluate seven traits related to salt tolerance and comprehensive salt tolerance at the soybean seedling stage; genome-wide association analysis (GWAS) was performed in a natural population containing 200 soybean materials; and linkage analysis was performed in 112 recombinant inbred lines (RIL) population to detect quantitative trait loci (QTLs) of salt tolerance. In the GWAS, 147 SNPs were mapped, explaining 5.28-17.16% of phenotypic variation. In the linkage analysis, 10 QTLs were identified, which could explain 6.9-16.16% of phenotypic variation. And it was found that there were two co-located regions between the natural population and the RIL population, containing seven candidate genes of salt tolerance in soybean. In addition, one colocalization interval was found to contain qZJS-15-1, rs47665107, and rs4793412, all of which could explain more than 10% of phenotypic variation rates, making it suitable for molecular marker development. The physical positions of rs47665107 and rs47934112 were included in qZJS-15-1. Therefore, a KASP marker was designed and developed using Chr. 15:47907445, which was closely linked to the qZJS-15-1. This marker could accurately and clearly cluster the materials of salt-tolerant genotypes in the heterozygous population tested. The QTLs and KASP markers found in the study provide a theoretical and technical basis for accelerating the salt-tolerant breeding of soybean.

Genome-wide identification, characterization and expression analysis of the bZIP transcription factors in garlic (Allium sativum L.)

Introduction

The bZIP genes (bZIPs) are essential in numerous biological processes, including development and stress responses. Despite extensive research on bZIPs in many plants, a comprehensive genome-wide analysis of bZIPs in garlic has yet to be undertaken.

Methods

In this study, we identified and classified 64 AsbZIP genes (AsbZIPs) into 10 subfamilies. A systematic analysis of the evolutionary characteristics of these AsbZIPs, including chromosome location, gene structure, conserved motifs, and gene duplication, was conducted. Furthermore, we also examined the nucleotide diversity, cis-acting elements, and expression profiles of AsbZIPs in various tissues and under different abiotic stresses and hormone treatments.

Results and Discussion

Our findings revealed that gene replication plays a crucial role in the expansion of AsbZIPs, with a minor genetic bottleneck observed during domestication. Moreover, the identification of cis-acting elements suggested potential associations of AsbZIPs with garlic development, hormone, and stress responses. Several AsbZIPs exhibited tissue-preferential and stress/hormone-responsive expression patterns. Additionally, Asa7G01972 and Asa7G01379 were notably differentially expressed under various stresses and hormone treatments. Subsequent yeast two-hybridization and yeast induction experiments validated their interactions with Asa1G01577, a homologue of ABI5, reinforcing their importance in hormone and abiotic stress responses. This study unveiled the characteristics of the AsbZIP superfamily and lays a solid foundation for further functional analysis of AsbZIP in garlic.

bZIP Transcription Factors: Structure, Modification, Abiotic Stress Responses and Application in Plant Improvement

Plant growth, yield, and distribution are significantly impacted by abiotic stresses, affecting global ecosystems and forestry practices. However, plants have evolved complex adaptation mechanisms governed by numerous genes and transcription factors (TFs) to manage these stresses. Among these, bZIP (basic leucine zipper) is a crucial regulator orchestrating morphological adaptations. This review aims to elucidate the multifaceted roles of bZIP TFs in plant species. We discuss the morphological changes induced by stress stimuli and the pivotal functions of bZIP TFs in mediating these responses. While several publications have explored the mechanisms of bZIP TFs in response to abiotic stresses, this review delves into the intricate regulatory networks, summarizing alternative splicing and post-translational modifications, signaling networks interacting with bZIP TFs, and genetic engineering of bZIP TFs. By synthesizing current research, this review provides an updated discussion on bZIP interactions with other proteins to regulate stresses such as cold, heat, drought, and salt. Additionally, it offers avenues for future research and applications of bZIP TFs to improve abiotic stress resilience in plants through genetic engineering.

Genome-Wide Identification of the Alfin-like Gene Family in Cotton (Gossypium hirsutum) and the GhAL19 Gene Negatively Regulated Drought and Salt Tolerance

Alfin-like (AL) is a small plant-specific gene family characterized by a PHD-finger-like structural domain at the C-terminus and a DUF3594 structural domain at the N-terminus, and these genes play prominent roles in plant development and abiotic stress response. In this study, we conducted genome-wide identification and analyzed the AL protein family in Gossypium hirsutum cv. NDM8 to assess their response to various abiotic stresses for the first time. A total of 26 AL genes were identified in NDM8 and classified into four groups based on a phylogenetic tree. Moreover, cis-acting element analysis revealed that multiple phytohormone response and abiotic stress response elements were highly prevalent in AL gene promoters. Further, we discovered that the GhAL19 gene could negatively regulate drought and salt stresses via physiological and biochemical changes, gene expression, and the VIGS assay. The study found there was a significant increase in POD and SOD activity, as well as a significant change in MDA in VIGS-NaCl and VIGS-PEG plants. Transcriptome analysis demonstrated that the expression levels of the ABA biosynthesis gene (GhNCED1), signaling genes (GhABI1, GhABI2, and GhABI5), responsive genes (GhCOR47, GhRD22, and GhERFs), and the stress-related marker gene GhLEA14 were regulated in VIGS lines under drought and NaCl treatment. In summary, GhAL19 as an AL TF may negatively regulate tolerance to drought and salt by regulating the antioxidant capacity and ABA-mediated pathway.

Functional Characterization of the Soybean Glycine max Actin Depolymerization Factor GmADF13 for Plant Resistance to Drought Stress

Abiotic stress significantly affects plant growth and has devastating effects on crop production. Drought stress is one of the main abiotic stressors. Actin is a major component of the cytoskeleton, and actin-depolymerizing factors (ADFs) are conserved actin-binding proteins in eukaryotes that play critical roles in plant responses to various stresses. In this study, we found that GmADF13, an ADF gene from the soybean Glycine max, showed drastic upregulation under drought stress. Subcellular localization experiments in tobacco epidermal cells and tobacco protoplasts showed that GmADF13 was localized in the nucleus and cytoplasm. We characterized its biological function in transgenic Arabidopsis and hairy root composite soybean plants. Arabidopsis plants transformed with GmADF13 displayed a more robust drought tolerance than wild-type plants, including having a higher seed germination rate, longer roots, and healthy leaves under drought conditions. Similarly, GmADF13-overexpressing (OE) soybean plants generated via the Agrobacterium rhizogenes-mediated transformation of the hairy roots showed an improved drought tolerance. Leaves from OE plants showed higher relative water, chlorophyll, and proline contents, had a higher antioxidant enzyme activity, and had decreased malondialdehyde, hydrogen peroxide, and superoxide anion levels compared to those of control plants. Furthermore, under drought stress, GmADF13 OE activated the transcription of several drought-stress-related genes, such as GmbZIP1, GmDREB1A, GmDREB2, GmWRKY13, and GmANK114. Thus, GmADF13 is a positive regulator of the drought stress response, and it may play an essential role in plant growth under drought stress conditions. These results provide new insights into the functional elucidation of soybean ADFs. They may be helpful for breeding new soybean cultivars with a strong drought tolerance and further understanding how ADFs help plants adapt to abiotic stress.

Systematic characterization of CsbZIP transcription factors in Camelina sativa and functional analysis of CsbZIP-A12 mediating regulation of unsaturated fatty acid-enriched oil biosynthesis

The basic leucine zipper (bZIP) transcription factors (TFs) function importantly in numerous life processes in plants. However, bZIP members and their biological roles remain unknown in Camelina sativa, a worldwide promising oil crop. Here, 220 CsbZIP proteins were identified in camelina and classified into thirteen groups. Two and 347 pairs of tandem and segmental duplication genes were detected to be underwent purification selection, with segmental duplication as the main driven-force of CsbZIP gene family expansion. Most CsbZIP genes displayed a tissue-specific expression pattern. Particularly, CsbZIP-A12 significantly positively correlated with many FA/oil biosynthesis-related genes, indicating CsbZIP-A12 may regulate lipid biosynthesis. Notably, yeast one-hybrid (Y1H), β-Glucuronidase (GUS), dual-luciferase (LUC) and EMSA assays evidenced that CsbZIP-A12 located in nucleus interacted with the promoters of CsSAD2-3 and CsFAD3-3 genes responsible for unsaturated fatty acid (UFA) synthesis, thus activating their transcriptions. Overexpression of CsbZIP-A12 led to an increase of total lipid by 3.275 % compared to the control, followed with oleic and α-linolenic acid levels enhanced by 3.4 % and 5.195 %, and up-regulated the expressions of CsSAD2-3, CsFAD3-3 and CsPDAT2-3 in camelina seeds. Furthermore, heterogeneous expression of CsbZIP-A12 significantly up-regulated the expressions of NtSAD2, NtFAD3 and NtPDAT genes in tobacco plants, thereby improving the levels of total lipids and UFAs in both leaves and seeds without negative effects on other agronomic traits. Together, our findings suggest that CsbZIP-A12 upregulates FA/oil biosynthesis by activating CsSAD2-3 and CsFAD3-3 as well as possible other related genes. These data lay a foundation for further functional analyses of CsbZIPs, providing new insights into the TF-based lipid metabolic engineering to increase vegetable oil yield and health-beneficial quality in oilseeds.

A novel PGPR strain, Streptomyces lasalocidi JCM 3373T, alleviates salt stress and shapes root architecture in soybean by secreting indole-3-carboxaldehyde

While soybean (Glycine max L.) provides the most important source of vegetable oil and protein, it is sensitive to salinity, which seriously endangers the yield and quality during soybean production. The application of Plant Growth-Promoting Rhizobacteria (PGPR) to improve salt tolerance for plant is currently gaining increasing attention. Streptomycetes are a major group of PGPR. However, to date, few streptomycetes has been successfully developed and applied to promote salt tolerance in soybean. Here, we discovered a novel PGPR strain, Streptomyces lasalocidi JCM 3373T, from 36 strains of streptomycetes via assays of their capacity to alleviate salt stress in soybean. Microscopic observation showed that S. lasalocidi JCM 3373T does not colonise soybean roots. Chemical analysis confirmed that S. lasalocidi JCM 3373T secretes indole-3-carboxaldehyde (ICA1d). Importantly, IAC1d inoculation alleviates salt stress in soybean and modulates its root architecture by regulating the expression of stress-responsive genes GmVSP, GmPHD2 and GmWRKY54 and root growth-related genes GmPIN1a, GmPIN2a, GmYUCCA5 and GmYUCCA6. Taken together, the novel PGPR strain, S. lasalocidi JCM 3373T, alleviates salt stress and improves root architecture in soybean by secreting ICA1d. Our findings provide novel clues for the development of new microbial inoculant and the improvement of crop productivity under salt stress.

In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa.

RESULT

In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns.

CONCLUSIONS

Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.

Enhancing drought tolerance in chilli pepper through AdDjSKI-mediated modulation of ABA sensitivity, photosynthetic preservation, and ROS scavenging

Drought stress threatens the productivity of numerous crops, including chilli pepper (Capsicum annuum). DnaJ proteins are known to play a protective role against a wide range of abiotic stresses. This study investigates the regulatory mechanism of the chloroplast-targeted chaperone protein AdDjSKI, derived from wild peanut (Arachis diogoi), in enhancing drought tolerance in chilli peppers. Overexpressing AdDjSKI in chilli plants increased chlorophyll content, reflected in the maximal photochemical efficiency of photosystem II (PSII) (Fv/Fm) compared with untransformed control (UC) plants. This enhancement coincided with the upregulated expression of PSII-related genes. Our subsequent investigations revealed that transgenic chilli pepper plants expressing AdDjSKI showed reduced accumulation of superoxide and hydrogen peroxide and, consequently, lower malondialdehyde levels and decreased relative electrolyte leakage percentage compared with UC plants. The mitigation of ROS-mediated oxidative damage was facilitated by heightened activities of antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, and peroxidase, coinciding with the upregulation of the expression of associated antioxidant genes. Additionally, our observations revealed that the ectopic expression of the AdDjSKI protein in chilli pepper plants resulted in diminished ABA sensitivity, consequently promoting seed germination in comparison with UC plants under different concentrations of ABA. All of these collectively contributed to enhancing drought tolerance in transgenic chilli plants with improved root systems when compared with UC plants. Overall, our study highlights AdDjSKI as a promising biotechnological solution for enhancing drought tolerance in chilli peppers, addressing the growing global demand for this economically valuable crop.

Molecular mechanism of abscisic acid signaling response factor VcbZIP55 to promote anthocyanin biosynthesis in blueberry (Vaccinium corymbosum)

A high content of anthocyanin in blueberry (Vaccinium corymbosum) is an important indicator to evaluate fruit quality. Abscisic acid (ABA) can promote anthocyanin biosynthesis, but since the molecular mechanism is unclear, clarifying the mechanism will improve for blueberry breeding and cultivation regulation. VcbZIP55 regulating anthocyanin synthesis in blueberry were screened and mined using the published Isoform-sequencing, RNA-Seq and qRT-PCR at different fruit developmental stages. Blueberry genetic transformation and transgenic experiments confirmed that VcbZIP55 could promote anthocyanin biosynthesis in blueberry adventitious buds, tobacco leaves, blueberry leaves and blueberry fruit. VcbZIP55 responded to ABA signals and its expression was upregulated in blueberry fruit. In addition, using VcbZIP55 for Yeast one hybrid assay (Y1H) and transient expression in tobacco leaves demonstrated an interaction between VcbZIP55 and a G-Box motif on the VcMYB1 promoter to activate the expression of VcMYB1. This study will lay the theoretical foundation for the molecular mechanisms of phytohormone regulation responsible for anthocyanin synthesis and provide theoretical support for blueberry quality improvement.

Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus

Background

Platycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus.

Methods

P. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses.

Conclusions

Forty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus's ability to cope with environmental stresses during growth and development.

PfbZIP85 Transcription Factor Mediates ω-3 Fatty Acid-Enriched Oil Biosynthesis by Down-Regulating PfLPAT1B Gene Expression in Plant Tissues

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the biggest TF families identified so far in the plant kingdom, functioning in diverse biological processes including plant growth and development, signal transduction, and stress responses. For Perilla frutescens, a novel oilseed crop abundant in polyunsaturated fatty acids (PUFAs) (especially α-linolenic acid, ALA), the identification and biological functions of bZIP members remain limited. In this study, 101 PfbZIPs were identified in the perilla genome and classified into eleven distinct groups (Groups A, B, C, D, E, F, G, H, I, S, and UC) based on their phylogenetic relationships and gene structures. These PfbZIP genes were distributed unevenly across 18 chromosomes, with 83 pairs of them being segmental duplication genes. Moreover, 78 and 148 pairs of orthologous bZIP genes were detected between perilla and Arabidopsis or sesame, respectively. PfbZIP members belonging to the same subgroup exhibited highly conserved gene structures and functional domains, although significant differences were detected between groups. RNA-seq and RT-qPCR analysis revealed differential expressions of 101 PfbZIP genes during perilla seed development, with several PfbZIPs exhibiting significant correlations with the key oil-related genes. Y1H and GUS activity assays evidenced that PfbZIP85 downregulated the expression of the PfLPAT1B gene by physical interaction with the promoter. PfLPAT1B encodes a lysophosphatidate acyltransferase (LPAT), one of the key enzymes for triacylglycerol (TAG) assembly. Heterogeneous expression of PfbZIP85 significantly reduced the levels of TAG and UFAs (mainly C18:1 and C18:2) but enhanced C18:3 accumulation in both seeds and non-seed tissues in the transgenic tobacco lines. Furthermore, these transgenic tobacco plants showed no significantly adverse phenotype for other agronomic traits such as plant growth, thousand seed weight, and seed germination rate. Collectively, these findings offer valuable perspectives for understanding the functions of PfbZIPs in perilla, particularly in lipid metabolism, showing PfbZIP85 as a suitable target in plant genetic improvement for high-value vegetable oil production.

A novel maize F-bZIP member, ZmbZIP76, functions as a positive regulator in ABA-mediated abiotic stress tolerance by binding to ACGT-containing elements

The group F-bZIP transcription factors (TFs) in Arabidopsis are involved in nutrient deficiency or salt stress responses. Nevertheless, our learning about the functions of group F-bZIP genes in maize remains limited. Here, we cloned a new F-bZIP gene (ZmbZIP76) from maize inbred line He344. The expression of ZmbZIP76 in maize was dramatically induced by high salt, osmotic stress and abscisic acid. Accordingly, overexpression of ZmbZIP76 increased tolerance of transgenic plants to salt and osmotic stress. In addition, ZmbZIP76 functions as a nuclear transcription factor and upregulates the expression of a range of abiotic stress-responsive genes by binding to the ACGT-containing elements, leading to enhanced reactive oxygen species (ROS) scavenging capability, increased abscisic acid level, proline content, and ratio of K+/Na+, reduced water loss rate, and membrane damage. These physiological changes caused by ZmbZIP76 ultimately enhanced tolerance of transgenic plants to salt and osmotic stress.

"Genome-wide identification of bZIP gene family in Pearl millet and transcriptional profiling under abiotic stress, phytohormonal treatments; and functional characterization of PgbZIP9"

Abiotic stresses are major constraints in crop production, and are accountable for more than half of the total crop loss. Plants overcome these environmental stresses using coordinated activities of transcription factors and phytohormones. Pearl millet an important C4 cereal plant having high nutritional value and climate resilient features is grown in marginal lands of Africa and South-East Asia including India. Among several transcription factors, the basic leucine zipper (bZIP) is an important TF family associated with diverse biological functions in plants. In this study, we have identified 98 bZIP family members (PgbZIP) in pearl millet. Phylogenetic analysis divided these PgbZIP genes into twelve groups (A-I, S, U and X). Motif analysis has shown that all the PgbZIP proteins possess conserved bZIP domains and the exon-intron organization revealed conserved structural features among the identified genes. Cis-element analysis, RNA-seq data analysis, and real-time expression analysis of PgbZIP genes suggested the potential role of selected PgbZIP genes in growth/development and abiotic stress responses in pearl millet. Expression profiling of selected PgbZIPs under various phytohormones (ABA, SA and MeJA) treatment showed differential expression patterns of PgbZIP genes. Further, PgbZIP9, a homolog of AtABI5 was found to localize in the nucleus and modulate gene expression in pearl millet under stresses. Our present findings provide a better understanding of bZIP genes in pearl millet and lay a good foundation for the further functional characterization of multi-stress tolerant PgbZIP genes, which could become efficient tools for crop improvement.

Functional Analysis of PbbZIP11 Transcription Factor in Response to Cold Stress in Arabidopsis and Pear

Cold stress is a prominent abiotic factor that adversely affects the growth and yield of pears, consequently restricting the cultivation range and resulting in substantial economic losses for the pear industry. Basic region-leucine zipper (bZIP) transcription factors are widely involved in multiple physiological and biochemical activities of plants, particularly in response to cold stress. In this study, the responsiveness of PbbZIP11 in pear to cold stress was investigated, and its role was explored by using pear callus and Arabidopsis thaliana. The findings revealed that overexpression of PbbZIP11 enhanced the tolerance of pear callus and Arabidopsis thaliana to cold stress. The antioxidant enzyme activities of transgenic plants were enhanced and the expression of C-repeat binding transcription factor (CBF) genes was increased as compared to wild-type plants. To better understand the biological function of PbbZIP11, mRNAs were isolated from overexpressed and wild-type Arabidopsis thaliana after cold stress for whole-genome sequencing. The results showed that the expression of some CBF downstream target genes changed after exposure to cold stress. The results suggested that the PbbZIP11 gene could participate in cold-stress signaling through the CBF-dependent pathway, which provides a theoretical basis for the PbbZIP11-mediated response to cold stress and for the genetic breeding of pear varieties with low-temperature tolerance.

Involvement of Dynamic Adjustment of ABA, Proline and Sugar Levels in Rhizomes in Effective Acclimation of Solidago gigantea to Contrasting Weather and Soil Conditions in the Country of Invasion

Giant goldenrod (Solidago gigantea Aiton) is one of the most invasive plant species occurring in Europe. Since little is known about the molecular mechanisms contributing to its invasiveness, we examined the natural dynamics of the content of rhizome compounds, which can be crucial for plant resistance and adaptation to environmental stress. We focused on rhizomes because they are the main vector of giant goldenrod dispersion in invaded lands. Water-soluble sugars, proline, and abscisic acid (ABA) were quantified in rhizomes, as well as ABA in the rhizosphere from three different but geographically close natural locations in Poland (50°04'11.3″ N, 19°50'40.2″ E) under extreme light, thermal, and soil conditions, in early spring, late summer, and late autumn. The genetic diversity of plants between locations was checked using the random amplified polymorphic DNA (RAPD) markers. Sugar and proline content was assayed spectrophotometrically, and abscisic acid (ABA) with the ELISA immunomethod. It can be assumed that the accumulation of sugars in giant goldenrod rhizomes facilitated the process of plant adaptation to adverse environmental conditions (high temperature and/or water scarcity) caused by extreme weather in summer and autumn. The same was true for high levels of proline and ABA in summer. On the other hand, the lowering of proline and ABA in autumn did not confirm the previous assumptions about their synthesis in rhizomes during the acquisition of frost resistance by giant goldenrod. However, in the location with intensive sunlight and most extreme soil conditions, a constant amount of ABA in rhizomes was noticed as well as its exudation into the rhizosphere. This research indicates that soluble sugars, proline, and ABA alterations in rhizomes can participate in the mechanism of acclimation of S. gigantea to specific soil and meteorological conditions in the country of invasion irrespective of plant genetic variation.

Analysis of bZIP gene family in lotus (Nelumbo) and functional study of NnbZIP36 in regulating anthocyanin synthesis

BACKGROUND

The basic leucine zipper (bZIP) family is a predominant group of transcription factors in plants, involved in regulating plant growth, development, and response to stressors. Additionally, the bZIP gene family has a key role in anthocyanin production. Despite the significant role of bZIP genes in plants, their potential contribution in lotus remains understudied.

RESULTS

A total of 124 bZIP genes (59 NnbZIPs and 65 NlbZIPs) were identified from genomes of two lotus species. These genes were classified into 13 groups according to the grouping principle of the Arabidopsis bZIP gene family. Analysis of promoter cis-acting elements indicated that most bZIP gene family members in lotus are associated with response to abiotic stresses. The promoters of some bZIP genes contain MYB binding sites that regulate anthocyanin synthesis. We examined the anthocyanin content of the petals from three different colored lotus, combined with transcriptome data analysis and qRT-PCR results, showing that the expression trends of NnbZIP36 and the homologous gene NlbZIP38 were significantly correlated with the anthocyanin content in lotus petals. Furthermore, we found that overexpression of NnbZIP36 in Arabidopsis promoted anthocyanin accumulation by upregulating the expression of genes (4CL, CHI, CHS, F3H, F3'H, DFR, ANS and UF3GT) related to anthocyanin synthesis.

CONCLUSIONS

Our study enhances the understanding of the bZIP gene family in lotus and provides evidence for the role of NnbZIP36 in regulating anthocyanin synthesis. This study also sets the stage for future investigations into the mechanism by which the bZIP gene family regulates anthocyanin biosynthesis in lotus.

A pervasive phosphorylation cascade modulation of plant transcription factors in response to abiotic stress

MAIN CONCLUSION

Transcriptional regulation of stress-responsive genes is a crucial step in establishing the mechanisms behind plant abiotic stress tolerance. A sensitive method of regulating transcription factors activity, stability, protein interaction, and subcellular localization is through phosphorylation. This review highlights a widespread regulation mechanism that involves phosphorylation of plant TFs in response to abiotic stress. Abiotic stress is one of the main components limiting crop yield and sustainability on a global scale. It greatly reduces the land area that is planted and lowers crop production globally. In all living organisms, transcription factors (TFs) play a crucial role in regulating gene expression. They participate in cell signaling, cell cycle, development, and plant stress response. Plant resilience to diverse abiotic stressors is largely influenced by TFs. Transcription factors modulate gene expression by binding to their target gene's cis-elements, which are impacted by genomic characteristics, DNA structure, and TF interconnections. In this review, we focus on the six major TFs implicated in abiotic stress tolerance, namely, DREB, bZIP, WRKY, ABF, MYB, and NAC, and the cruciality of phosphorylation of these transcription factors in abiotic stress signaling, as protein phosphorylation has emerged as one of the key post-translational modifications, playing a critical role in cell signaling, DNA amplification, gene expression and differentiation, and modification of other biological configurations. These TFs have been discovered after extensive study as stress-responsive transcription factors which may be major targets for crop development and important contributors to stress tolerance and crop production.

Genome-Wide Identification of bZIP Transcription Factors in Faba Bean Based on Transcriptome Analysis and Investigation of Their Function in Drought Response

Faba bean is an important cool-season edible legume crop that is constantly threatened by abiotic stresses such as drought. The basic leucine zipper (bZIP) gene family is one of the most abundant and diverse families of transcription factors in plants. It regulates plant growth and development and plays an important role in the response to biotic and abiotic stresses. In this study, we identified 18 members of the faba bean bZIP transcription factor family at the genome-wide level based on previous faba bean drought stress transcriptome sequencing data. A phylogenetic tree was constructed to group the 18 VfbZIP proteins into eight clades. Analysis of cis-acting elements in the promoter region suggested that these 18 VfbZIPs may be involved in regulating abiotic stress responses such as drought. Transcriptome data showed high expression of seven genes (VfbZIP1, VfbZIP2, VfbZIP5, VfbZIP7, VfbZIP15, VfbZIP17, and VfbZIP18) in the drought-tolerant cultivar under drought stress, in which VfbZIP1, VfbZIP2, and VfbZIP5 were consistently expressed as detected by quantitative real-time polymerase chain reaction (qRT-PCR) compared to the transcriptome data. Ectopic overexpression of the three VfbZIPs in tobacco, based on the potato Virus X (PVX) vector, revealed that VfbZIP5 enhanced the drought tolerance. Overexpressed VfbZIP5 in plants showed lower levels of proline (PRO), malondialdehyde (MDA), and peroxidase (POD) compared to those overexpressing an empty vector under 10 days of drought stress. Protein-protein interaction (PPI) analysis showed that VfbZIP5 interacted with seven proteins in faba bean, including VfbZIP7 and VfbZIP10. The results depict the importance of VfbZIPs in response to drought stress, and they would be useful for the improvement of drought tolerance.

Salt stress responses and alleviation strategies in legumes: a review of the current knowledge

Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes' expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes' response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant's priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.

Genome-wide identification of bZIP transcription factor family in Artemisia annua, its transcriptional profiling and regulatory role in phenylpropanoid metabolism under different light conditions

The basic leucine zipper (bZIP) protein transcription factors are known to modulate development, plant growth, metabolic response, and resistance to several biotic and abiotic stressors and have been widely studied in the model plant Arabidopsis thaliana. However, no comprehensive information about the bZIP transcription factor family in Artemisia annua has been explored to date. In this genome-wide study, we identified 61 bZIP TFs after removing false positives and incomplete sequences from Artemisia annua. Seven highly expressed homolog AabZIP TF genes under UV-B and differential light conditions in different tissues were identified from the publicly available microarray dataset as having their cis-regulatory elements involved in, flavonoids biosynthesis, seed-specific gene regulation, stress responses, and metabolic regulation. In-silico analysis and electrophoretic mobility shift assay (EMSA) confirmed the interaction of AabZIP19 TF over the AaPAL1 promoter in order to regulate the phenolics and flavonoid biosynthesis via the phenylpropanoid pathway. Further, RT-PCR analysis has been carried out to validate the transcript levels of selected AabZIP genes under white light, red light, blue light (45 min), and UV-B exposure (12 and 24 h). These genes have their highest expression levels under UV-B and blue light exposure, in contrast with white light. Therefore, the detection of ROS through staining confirms the accumulation of superoxide radicals and H2O2, and in addition to reducing ROS accumulation under UV-B and blue light irradiation, total phenols and flavonoids are significantly enhanced. This study laid the groundwork for deciphering the possible role of AabZIP TFs under different light stress-responsive conditions and in the regulation of secondary metabolism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01338-0.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Genome-wide identification and expression profiling of the bZIP gene family in Betula platyphylla and the functional characterization of BpChr04G00610 under low-temperature stress

The basic leucine zipper (bZIP) gene, which plays a significant role in the regulation of tolerance to biotic/abiotic stresses, has been characterized in many plant species. Betula platyphylla is a significant afforestation species. To elucidate the stress resistance mechanism of birch, previous studies identified some stress resistance genes. However, the genome-wide identification and characterization of bZIP gene family in the birch have not been reported. Here, the 56 BpbZIP genes were identified and classified into 13 groups in birch. Cis-element analysis showed that the promoters of 56 family genes contained 108 elements, of which 16 were shared by 13 groups. There were 8 pairs of fragment repeats and 1 pair of tandem repeats, indicating that duplication may be the major reason for the amplification of the BpbZIP gene family. Tissue-specific of BpbZIP genes showed 18 genes with the highest expression in roots, 15 in flowers, 11 in xylem and 9 in leaves. In addition, five differentially expressed bZIP genes were identified from the RNA-seq data of birch under low-temperature stress, and the co-expressed differentially expressed genes were further screened. The analysis of gene ontology (GO) enrichment of each co-expression regulatory network showed that they were related to membrane lipids and cell walls. Furthermore, the transient overexpression of BpChr04G00610 decreased the ROS scavenging ability of birch under low-temperature stress, suggesting that it may be more sensitive to low-temperature. In conclusion, this study provides a basis for the study of the function of BpbZIP genes.

The ABA-induced NAC transcription factor MdNAC1 interacts with a bZIP-type transcription factor to promote anthocyanin synthesis in red-fleshed apples

Anthocyanins are valuable compounds in red-fleshed apples. The MdMYB10 transcription factor is an important regulator of the anthocyanin synthesis pathway. However, other transcription factors are key components of the complex network controlling anthocyanin synthesis and should be more thoroughly characterized. In this study, we used a yeast-based screening technology to identify MdNAC1 as a transcription factor that positively regulates anthocyanin synthesis. The overexpression of MdNAC1 in apple fruits and calli significantly promoted the accumulation of anthocyanins. In binding experiments, we demonstrated that MdNAC1 combines with the bZIP-type transcription factor MdbZIP23 to activate the transcription of MdMYB10 and MdUFGT. Our analyses also indicated that the expression of MdNAC1 is strongly induced by ABA because of the presence of an ABRE cis-acting element in its promoter. Additionally, the accumulation of anthocyanins in apple calli co-transformed with MdNAC1 and MdbZIP23 increased in the presence of ABA. Therefore, we revealed a novel anthocyanin synthesis mechanism involving the ABA-induced transcription factor MdNAC1 in red-fleshed apples.

Role of bZIP Transcription Factors in Plant Salt Stress

Soil salinity has become an increasingly serious problem worldwide, greatly limiting crop development and yield, and posing a major challenge to plant breeding. Basic leucine zipper (bZIP) transcription factors are the most widely distributed and conserved transcription factors and are the main regulators controlling various plant response processes against external stimuli. The bZIP protein contains two domains: a highly conserved, DNA-binding alkaline region, and a diverse leucine zipper, which is one of the largest transcription factor families in plants. Plant bZIP is involved in many biological processes, such as flower development, seed maturation, dormancy, and senescence, and plays an important role in abiotic stresses such as salt damage, drought, cold damage, osmotic stress, mechanical damage, and ABA signal response. In addition, bZIP is involved in the regulation of plant response to biological stresses such as insect pests and pathogen infection through salicylic acid, jasmonic acid, and ABA signal transduction pathways. This review summarizes and discusses the structural characteristics and functional characterization of the bZIP transcription factor group, the bZIP transcription factor complex and its molecular regulation mechanisms related to salt stress resistance, and the regulation of transcription factors in plant salt stress resistance. This review provides a theoretical basis and research ideas for further exploration of the salt stress-related functions of bZIP transcription factors. It also provides a theoretical basis for crop genetic improvement and green production in agriculture.

Ectopic expression of DnaJ type-I protein homolog of Vigna aconitifolia (VaDJI) confers ABA insensitivity and multiple stress tolerance in transgenic tobacco plants

Reduced crop productivity results from altered plant physiological processes caused by dysfunctional proteins due to environmental stressors. In this study, a novel DnaJ Type-I encoding gene, VaDJI having a zinc finger motif in its C-terminal domain was found to be induced early upon treatment with heat stress (within 5 min) in a heat tolerant genotype of Vigna aconitifolia RMO-40. VaDJI is induced by multiple stresses. In tobacco, ectopic expression of VaDJI reduced ABA sensitivity during seed germination and the early stages of seedling growth of transgenic tobacco plants. Concomitantly, it also improved the ability of transgenic tobacco plants to withstand drought stress by modulating the photosynthetic efficiency, with the transgenic plants having higher Fv/Fm ratios and reduced growth inhibition. Additionally, transgenic plants showed a reduced build-up of H2O2 and lower MDA levels and higher chlorophyll content during drought stress, which attenuated cell damage and reduced oxidative damage. An analysis using the qRT-PCR study demonstrated that VaDJI overexpression is associated with the expression of some ROS-detoxification-related genes and stress-marker genes that are often induced during drought stress responses. These findings suggest a hypothesis whereby VaDJI positively influences drought stress tolerance and ABA signalling in transgenic tobacco, and suggests that it is a potential gene for genetic improvement of drought and heat stress tolerance in crop plants.

FtbZIP85 Is Involved in the Accumulation of Proanthocyanidin by Regulating the Transcription of FtDFR in Tartary Buckwheat

As a drought-tolerant crop, Tartary buckwheat survives under adverse environmental conditions, including drought stress. Proanthocyanidins (PAs) and anthocyanins are flavonoid compounds, and they participate in the regulation of resistance to both biotic and abiotic stresses by triggering genes' biosynthesis of flavonoids. In this study, a basic leucine zipper, basic leucine zipper 85 (FtbZIP85), which was predominantly expressed in seeds, was isolated from Tartary buckwheat. Our study shows that the expressions of FtDFR, FtbZIP85 and FtSnRK2.6 were tissue-specific and located in both the nucleus and the cytosol. FtbZIP85 could positively regulate PA biosynthesis by binding to the ABA-responsive element (ABRE) in the promoter of dihydroflavonol 4-reductase (FtDFR), which is a key enzyme in the phenylpropanoid biosynthetic pathway. Additionally, FtbZIP85 was also involved in the regulation of PA biosynthesis via interactions with FtSnRK2.6 but not with FtSnRK2.2/2.3. This study reveals that FtbZIP85 is a positive regulator of PA biosynthesis in TB.

Overexpression of cotton Trihelix transcription factor GhGT-3b_A04 enhances resistance to Verticillium dahliae and affects plant growth in Arabidopsis thaliana

Verticillium wilt is a soil-borne fungal disease that severely affects cotton fiber yield and quality. Herein, a cotton Trihelix family gene, GhGT-3b_A04, was strongly induced by the fungal pathogen Verticillium dahliae. Overexpression of the gene in Arabidopsis thaliana enhanced the plant's resistance to Verticillium wilt but inhibited the growth of rosette leaves. In addition, the primary root length, root hair number, and root hair length increased in GhGT-3b_A04-overexpressing plants. The density and length of trichomes on the rosette leaves also increased. GhGT-3b_A04 localized to the nucleus, and transcriptome analysis revealed that it induced gene expression for salicylic acid synthesis and signal transduction and activated gene expression for disease resistance. The gene expression for auxin signal transduction and trichome development was reduced in GhGT-3b_A04-overexpressing plants. Our results highlight important regulatory genes for Verticillium wilt resistance and cotton fiber quality improvement. The identification of GhGT-3b_A04 and other important regulatory genes can provide crucial reference information for future research on transgenic cotton breeding.

GmGSTU23 Encoding a Tau Class Glutathione S-Transferase Protein Enhances the Salt Tolerance of Soybean (Glycine max L.)

Salt stress has a detrimental impact on crop yield, quality, and profitability. The tau-like glutathione transferases (GSTs) represent a significant group of enzymes that play a crucial role in plant stress responses, including salt stress. In this study, we identified a tau-like glutathione transferase family gene from soybean named GmGSTU23. Expression pattern analysis revealed that GmGSTU23 was predominantly expressed in the roots and flowers and exhibited a concentration–time-specific pattern in response to salt stress. Transgenic lines were generated and subjected to phenotypic characterization under salt stress. The transgenic lines exhibited increased salt tolerance, root length, and fresh weight compared to the wild type. Antioxidant enzyme activity and malondialdehyde content were subsequently measured, and the data revealed no significant differences between the transgenic and wild-type plants in the absence of salt stress. However, under salt stress, the wild-type plants exhibited significantly lower activities of SOD, POD, and CAT than the three transgenic lines, whereas the activity of APX and the content of MDA showed the opposite trend. We identified changes in glutathione pools and associated enzyme activity to gain insights into the underlying mechanisms of the observed phenotypic differences. Notably, under salt stress, the transgenic Arabidopsis’s GST activity, GR activity, and GSH content were significantly higher than those of the wild type. In summary, our findings suggest that GmGSTU23 mediates the scavenging of reactive oxygen species and glutathione by enhancing the activity of glutathione transferase, thereby conferring enhanced tolerance to salt stress in plants.

Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean

Abiotic stress is one of the most important factors reducing soybean yield. It is essential to identify regulatory factors contributing to stress responses. A previous study found that the tandem CCCH zinc-finger protein GmZF351 is an oil level regulator. In this study, we discovered that the GmZF351 gene is induced by stress and that the overexpression of GmZF351 confers stress tolerance to transgenic soybean. GmZF351 directly regulates the expression of GmCIPK9 and GmSnRK, leading to stomata closing, by binding to their promoter regions, which carry two CT(G/C)(T/A)AA elements. Stress induction of GmZF351 is mediated through reduction in the H3K27me3 level at the GmZF351 locus. Two JMJ30-demethylase-like genes, GmJMJ30-1 and GmJMJ30-2, are involved in this demethylation process. Overexpression of GmJMJ30-1/2 in transgenic hairy roots enhances GmZF351 expression mediated by histone demethylation and confers stress tolerance to soybean. Yield-related agronomic traits were evaluated in stable GmZF351-transgenic plants under mild drought stress conditions. Our study reveals a new mode of GmJMJ30-GmZF351 action in stress tolerance, in addition to that of GmZF351 in oil accumulation. Manipulation of the components in this pathway is expected to improve soybean traits and adaptation under unfavorable environments.

Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs

Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.

Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress

The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.

Genome-wide characterization of Alfin-like (AL) genes in apple and functional identification of MdAL4 in response to drought stress

Eleven Alfin-like (AL) genes were obtained from apple and MdAL4 was selected for improving drought stress tolerance of transgenic apple callus and Arabidopsis. Drought is an important environmental factor affecting plant growth all over the world. Alfin-like (AL) have well-documented functions in abiotic stress response, but their drought stress tolerance in apple (Malus domestica) are poorly understood. According to the transcriptome data, 11 MdAL genes containing conserved Alfin and PHD-finger domain were identified in apple and divided into three subgroups with a total of 35 members from different species. Subsequently, gene structures, conserved amino acid sequences, promoter cis-acting elements, and gene evolution events were analyzed. Based on differential expression of MdALs in response to abiotic stresses, MdAL4, which was highly expressed under drought, was further cloned and investigated. MdAL4 encoding nuclear-localized protein conferred enhanced drought tolerance in overexpressing transgenic calli of apple 'Orin'. Moreover, the ectopic expression of MdAL4 improved the drought tolerance of transgenic Arabidopsis, as judged from remarkably decreased malonaldehyde (MDA) content and electrolyte leakage in MdAL4 overexpressing plants relative to WT. Furthermore, MdAL4 possibly could bind to promoter regions of ROS-scavenging and stress-related genes to improve drought tolerance. Additionally, we found in silico evidence that three proteins containing the WD40 domain that interact with MdAL4. Based on these results, MdAL4 was identified as a positive regulator for improving drought stress of apple.