Search Results (189)

Cereal crops including wheat, rice, maize, barley, and sorghum collectively supply most global caloric and protein requirements, yet their productivity is increasingly constrained by combined abiotic stresses that co-occur under field conditions. Simultaneous drought, heat, salinity, and cold impose yield losses that consistently exceed those caused by individual stresses and elicit molecular responses that are qualitatively distinct from single-stress reactions and cannot be inferred from them. Despite this agronomic reality, the molecular mechanisms governing combined stress responses in cereals remain poorly resolved, and no integrated framework connecting the transcriptional, epigenetic, and genome-editing dimensions of combined stress tolerance has previously been articulated for this crop group. This review proposes a three-tier integrated framework for understanding and engineering combined abiotic stress tolerance in major cereals. The first tier encompasses transcription factor networks, including bZIP, WRKY, NAC, AP2/ERF, DREB, MYB, and HSF families, that translate combined stress signals into transcriptional reprogramming through ABA-dependent and ABA-independent pathways, hormonal crosstalk, and osmoprotectant and antioxidant defence systems. The second tier addresses the epigenetic regulatory layer, encompassing DNA methylation, histone modifications, and non-coding RNA pathways that gate TF binding site accessibility and encode stress memory in cereals. The third tier examines CRISPR-based tools, including multiplexed Cas9 editing and dCas9-based epigenome editing, that engineer validated targets from both tiers, while confronting polyploid off-target effects, growth penalties, and a laboratory-to-field validation gap. The three tiers are mechanistically coupled, with TF activity shaping epigenetic landscapes, epigenetic states gating TF access, and both providing precision engineering targets. Critical gaps include the absence of combined-stress epigenomic datasets, limited characterisation in barley and sorghum, and early-stage combined-stress-specific strategies. Full article

Seed dormancy is a vital adaptive mechanism regulated by the DELAY OF GERMINATION (DOG) gene family. Here, we present the first systematic genome-wide identification and expression profiling of the DOG gene family (RsDOGs) in radish (Raphanus sativus). Comprehensive analysis of physicochemical properties, chromosomal distribution, and phylogeny revealed strong evolutionary conservation alongside functional divergence. Notably, several RsDOG proteins harbor natural fusions of the DOG1 domain with a bZIP domain, suggesting potential transcription factor activity and novel regulatory functions. Promoter analysis identified abundant ABA-responsive and abiotic stress-responsive cis-acting elements. Quantitative real-time PCR (qRT-PCR) profiling across contrasting cultivars—dormant variety Rs275 and non-dormant variety Rs100—at 4 h and 28 h post-imbibition revealed distinct differential expression patterns. In particular, TRs0x5c022182.1 exhibited high expression levels in dormant seeds, suggesting its potential involvement in seed dormancy regulation in radish. This study provides key insights into the structural evolution and expression dynamics of RsDOG genes, laying a solid foundation for molecular breeding aimed at optimizing seed germination traits. Full article

Salinity stress affects not only the survival and productivity of halophytic plants, but also the composition, structure and processability of their biomass. In Salicornia spp., salt-induced regulation of ion transport, osmotic adjustment, reactive oxygen species signaling, antioxidant defense, and cell wall remodeling can directly influence residual salinity, water retention, texture, extractability, drying behavior, and oxidative stability of plant biomass. However, most existing transcriptomic studies of Salicornia and related halophytes have focused mainly on salt tolerance mechanisms, whereas the connection between stress-regulated molecular networks and processing-related biomass traits remains insufficiently systematized. This review addresses this gap by proposing a mechanistic framework that links salinity perception, ROS-mediated signaling, ABA and MAPK pathways, antioxidant gene families, transcription factor networks and processing-oriented quality traits. Special attention is given to enzymatic antioxidant systems, including SOD, CAT, APX, POD and components of the ascorbate-glutathione cycle, as well as to non-enzymatic defense mechanisms involving ascorbate, glutathione, phenolic compounds, carotenoids, proline and glycine betaine. The review also discusses the regulatory roles of WRKY, DREB/CBF, NAC, bZIP and MYB transcription factor families as molecular control points connecting salinity stress responses with downstream metabolic and structural traits. Network-based approaches, including WGCNA, pathway signatures and transcript panels, are considered more informative than single-gene markers for predicting complex quality traits in Salicornia biomass. In addition, recent genomic and computational strategies, including CRISPR/Cas-mediated functional validation, GWAS, genomic selection, multi-omics integration and AI-assisted modeling, are discussed as emerging tools for candidate-gene prioritization and predictive assessment of stress-dependent biomass quality. Overall, this review shifts the interpretation of Salicornia transcriptomics from a descriptive salt-tolerance model toward a mechanistic and application-oriented framework for improving halophytic raw materials for food, feed and bioprocessing applications. Full article

Astragalus membranaceus is an important medicinal plant with considerable pharmacological and economic value; however, its growth and productivity are frequently threatened by drought stress. Basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses, yet a comprehensive investigation of the bZIP gene family in A. membranaceus remains unavailable. In this study, 74 bZIP genes (AmbZIPs) were identified in the A. membranaceus genome and classified into 12 subfamilies based on phylogenetic relationships with Arabidopsis thaliana. Analyses of gene structure, conserved motifs, chromosomal distribution, and duplication events revealed high conservation within subfamilies and indicated that segmental duplication was the major driver of AmbZIP family expansion. Codon usage analysis showed that AmbZIP genes exhibited relatively weak codon usage bias, with codon preference predominantly shaped by natural selection rather than mutation pressure. A total of 23 optimal codons were identified, of which 91.3% were A/T-ending codons. Codon adaptability analysis further demonstrated that tobacco possessed the highest codon compatibility among five tested hosts, whereas Escherichia coli exhibited the lowest adaptability, suggesting that plant expression systems may be more suitable for functional studies of AmbZIP genes. Promoter analysis identified numerous cis-acting elements associated with phytohormone signaling and abiotic stress responses, particularly those related to abscisic acid, methyl jasmonate, salicylic acid, and drought responsiveness. Transcriptome analysis and quantitative real-time polymerase chain reaction (qRT-PCR) validation revealed that several AmbZIP genes were significantly induced under drought stress. Among them, AmbZIP46 displayed strong drought-responsive expression, transcriptional activation activity, and exclusive nuclear localization. These findings provide the first comprehensive characterization of the bZIP gene family in A. membranaceus and establish a valuable foundation for elucidating drought-tolerance mechanisms and facilitating molecular breeding in this medicinal plant. Full article

HD-Zip III transcription factors are known to play roles in regulating shoot apical meristem (SAM) and axillary meristem (AM) development, exerting direct effects on plant architecture and branching. However, the HD-Zip III (BjuHDZ) gene family has not been systematically characterized in Brassica juncea L. (B. juncea). Therefore, in this study, we performed a comprehensive bioinformatics analysis of the BjuHDZ gene family and identified a total of 20 members. These genes were randomly and unevenly distributed across the 16 chromosomes of B. juncea, and their encoded proteins exhibited divergent physicochemical properties. Through phylogenetic analysis, the 20 BjuHDZ proteins were divided into five subgroups (REV, HB8, HB9, HB14, and HB15). Conserved exon–intron organization and motif profiles were observed within each BjuHDZ gene subgroup. Furthermore, their promoter sequences harbored a wide array of cis-elements implicated in light responsiveness, hormonal regulation, stress tolerance, and growth/development. The qRT-PCR analysis showed that the expression levels of BjuHDZ7, BjuHDZ13, and BjuHDZ15 were significantly upregulated in the middle and upper axillary buds of two pairs of multi-branching (Bj02 and, Bj08) accessions. Meanwhile, BjuHDZ17 was highly expressed in the upper, middle, and lower axillary buds as well as in the SAM of both multi-branching materials. Taken together, these findings lay a foundation for further investigation into the biological functions of BjuHDZ genes in B. juncea. Full article

Salt stress is a major abiotic stress that threatens citrus yield and quality. To elucidate the molecular mechanisms underlying differential salt tolerance in citrus rootstocks, we performed an integrative transcriptomic and metabolomic analysis of salt-sensitive trifoliate orange (Poncirus trifoliata) and salt-tolerant Goutoucheng (Citrus aurantium) under 60 mM NaCl treatment for 12 h and 24 h. Physiological observations confirmed that Goutoucheng exhibited less growth inhibition and leaf damage than trifoliate orange. Transcriptome sequencing identified 2081 and 1588 differentially expressed genes (DEGs) in trifoliate orange at 12 h and 24 h, respectively, compared with 1166 and 997 DEGs in Goutoucheng. Metabolome profiling revealed 217 and 173 differentially accumulated metabolites (DAMs) in trifoliate orange versus 162 and 239 DAMs in Goutoucheng at the two time points. KEGG pathway analysis showed that DEGs were mainly enriched in the Mitogen-activated protein kinase (MAPK) signaling pathway—plant, plant hormone signal transduction, and flavonoid biosynthesis—and DAMs were mainly enriched in flavonoid biosynthesis, starch and sucrose metabolism, and glutathione metabolism. Integrative nine-quadrant and two-way orthogonal partial least squares analyses further pinpointed flavonoid biosynthesis as a central hub in salt response. Notably, quercetin derivatives accumulated preferentially in the salt-tolerant rootstock Goutoucheng. Several transcription factor families—including HSF, MYB, NAC, HB-HD-ZIP, C2H2, bHLH, AP2/ERF, and Trihelix—may enhance antioxidant capacity under salt stress by regulating flavonoid accumulation. Collectively, these results indicated that coordinated regulation of flavonoids contributed critically to salt stress adaptation in citrus rootstocks. The identified DEGs, DAMs, and transcription factors provide candidate targets for genetic improvement of salt tolerance in citrus. Full article

Chrysanthemum is one of the world’s four main cut flowers. However, postharvest drought stress severely disrupts water homeostasis, triggering reactive oxygen species burst and membrane lipid peroxidation, thereby reducing its ornamental quality and vase life. Melatonin serves as a multifunctional antioxidant and stress regulator. This study demonstrated that 200 μmol L⁻¹ melatonin effectively alleviated drought-induced leaf wilting, maintained relative water content, decreased the accumulation of MDA, H₂O₂, and O₂^•−, and enhanced the activities of SOD, CAT, POD, and APX. Concurrently, non-enzymatic antioxidants (proline, GSH, ASA) accumulated to high levels. RNA-seq analysis revealed that drought affects pathways closely related to the production of antioxidant and osmoprotectant metabolites, while melatonin initiated extensive transcriptional reprogramming and responded to drought stress through distinct pathways at the early (12 h) and late (24 h) treatment stages. Melatonin also modulated key transcription factor families, including bHLH, NAC, ERF, MYB, and bZIP. Collectively, exogenous MT mitigates drought damage in chrysanthemum cut flowers by coordinating antioxidant systems and complex transcriptional regulatory networks. This study provides a theoretical foundation for improving postharvest drought tolerance and prolonging the vase life of cut flowers. Full article

Gene duplication is a primary evolutionary driver of gene family expansion and functional diversification in plants, yet how different duplication processes reshape the evolutionary architecture of transcription factor repertoires remains poorly resolved in lineage-specific genomic contexts. Here, we performed a comprehensive evolutionary and transcriptomic analysis of the basic leucine zipper (bZIP) family across 17 representative species, with a focus on Pooideae. We identified 1878 bZIP genes and found that, although copy numbers were relatively conserved in most diploid grasses, polyploid Triticeae showed substantial expansion. Genome-wide and Ks analyses indicated that bZIP genes were preferentially retained after whole-genome/segmental duplication, with many copies tracing back to the ancient grass-specific ρ-WGD event, the most recent shared polyploidization event in Poaceae. Phylogenetic analyses and orthology inference further resolved four evolutionary models linking ancient duplication with lineage-specific retention and expansion. Transcriptome analyses revealed structured expression divergence across developmental and stress-related contexts, and wheat homoeologous triads exhibited widespread subgenome expression bias that was dynamically reconfigured under stress and hormone treatments. Differences in transposable element landscapes among duplication models and subgenomes further suggest a role for local genomic context in regulatory divergence. Together, these findings establish a unified framework linking ancient duplication, selective retention, and transcriptional diversification of the bZIP family in Pooideae. Full article

GRAS transcription factors are essential for plant growth and stress adaptation, yet they remain uncharacterized in the medicinal herb Coptis chinensis. To address this gap, we performed a genome-wide identification of the GRAS family and investigated its transcriptional responses to temperature and light stress, integrating comparative transcriptomics with promoter analysis to explore potential co-expression with bZIP factors. A total of 48 CcGRAS genes were identified and found to be unevenly distributed across nine chromosomes. Expression profiling revealed that CcGRAS genes are markedly more responsive to varying light intensities (476, 8340 lx) than to temperature stresses (15, 35 °C), relative to controls (2060 lx for light, 25 °C for temperature). Co-expression analysis uncovered an underground tissue-specific module in which CcbZIP16 is upregulated with four CcGRAS genes (CcGRAS11, CcGRAS12, CcGRAS43, CcGRAS48) that are coordinately upregulated specifically under low-light conditions. The promoters of these co-expressed genes are significantly enriched in canonical light-responsive cis-elements, providing correlative evidence for their coordinated transcriptional control. Together, these findings identify a tissue-specific GRAS-bZIP co-expressed gene set under light stress and suggest a candidate regulatory framework for dissecting light adaptation mechanisms. This work also provides a foundation for targeted genetic improvements in stress tolerance and alkaloid biosynthesis in this important medicinal plant. Full article

Basic leucine zipper (bZIP) transcription factors are widely involved in plant growth, development, environmental adaptation, and secondary metabolism. However, the bZIP gene family in Taxus yunnanensis has not been systematically characterized, and its potential involvement in shading-responsive regulation of paclitaxel biosynthesis remains unclear. In this study, a genome-wide analysis was performed to identify and characterize the bZIP family in T. yunnanensis. Phylogenetic analysis, conserved motif and domain identification, promoter cis-element analysis, chromosomal localization, and expression profiling were conducted to investigate their structural features and regulatory potential. A total of 18 TyubZIP genes were identified and classified into 10 subfamilies. These genes exhibited variation in physicochemical properties but showed conserved structural features and nuclear localization. Promoter analysis revealed abundant light-responsive, hormone-related, and stress-related cis-elements. Expression profiling indicated tissue-specific expression patterns and diverse responses to shading treatment. WGCNA further identified candidate TyubZIP genes potentially associated with paclitaxel biosynthesis. Among them, TyuHY5 was selected for functional analysis. Subcellular localization and transcriptional assays demonstrated that TyuHY5 can bind to the promoter of TyuDBTNBT and positively regulate its activity. These findings provide the first genome-wide characterization of the bZIP family in T. yunnanensis and identify TyuHY5 as a shading-responsive candidate regulator of paclitaxel biosynthesis, providing insights that may inform the genetic improvement and cultivation strategies of Taxus for enhanced paclitaxel production. Full article

Low-temperature stress significantly limits plant growth, development, and productivity, posing a major environmental constraint. The potato (Solanum tuberosum L.) is particularly vulnerable to low temperatures, underscoring the crucial need to enhance cold tolerance in potato breeding efforts for sustainable production. Basic leucine zipper (bZIP) transcription factors serve as central regulators of plant developmental processes and stress responses; however, their functional role in cold tolerance in tetraploid potato remains poorly understood. Here, we report a systematic characterization of the bZIP gene family in tetraploid potato and provide preliminary evidence that StbZIP104 enhances plant cold tolerance. A total of 191 StbZIP genes were identified and classified into 11 subfamilies, exhibiting uneven chromosomal distribution and expansion primarily driven by whole-genome and segmental duplication. Promoter cis-element analysis, together with GO and KEGG enrichment analyses, indicated that StbZIP genes are broadly associated with hormone signaling, stress responses, signal transduction, and environmental adaptation. Expression profiling under low-temperature treatment revealed eight cold-inducible StbZIP genes (log₂FC ≥ 1 and FDR < 0.05), among which StbZIP104 was strongly induced (log₂FC ≥ 2) and showed 5.36-fold higher expression in highly cold-resistant cultivars than in cold-sensitive cultivars. Subcellular localization confirmed that StbZIP104 is a nuclear-localized protein. Functional validation confirmed that overexpressing StbZIP104 notably improved cold tolerance in transgenic Samsun NN tobacco (Nicotiana tabacum cv. Samsun NN). This was supported by heightened superoxide dismutase and peroxidase activities, increased levels of soluble protein and soluble sugars, and decreased malondialdehyde content compared to the wild type under cold stress. This study establishes a basis for the functional characterization of the bZIP gene family in tetraploid potato and serves as a theoretical reference for understanding the mechanisms that govern cold tolerance in this species. Full article

Drought stress critically impacts plant growth and productivity. The bZIP transcription factor family is crucial for abiotic stress responses, yet its role in larch drought tolerance remains unclear. This study identified 19 bZIP genes in Larix kaempferi (Lamb.) Carr. and characterized LkbZIP4. Bioinformatics analysis classified it into the A subgroup. Subcellular localization and yeast two-hybrid assays confirmed that it is a nucleus-localized transactivator. Expression pattern analysis revealed that LkbZIP4 was highly specifically expressed in roots and was significantly induced by drought stress. A series of transgenic overexpression lines was successfully established through Agrobacterium tumefaciens-mediated method, using embryogenic callus of hybrid larch (L. kaempferi × L. gmelinii). Under 7% PEG-induced drought stress, LkbZIP4-overexpressing transgenic calli displayed enhanced drought tolerance relative to wild-type. This was evidenced by better growth, higher biomass, and reduced membrane damage, indicated by lower malondialdehyde content and relative electrolyte leakage. Meanwhile, these transgenic calli accumulated higher levels of osmoregulatory substances, including proline and soluble sugars, along with enhanced activities of antioxidant enzymes including superoxide dismutase and peroxidase. Our results indicate that LkbZIP4 functions to promote drought tolerance in larch, likely through the enhancement of osmotic adjustment and oxidative defense mechanisms. Full article

Background: Focal segmental glomerulosclerosis (FSGS) is a leading cause of renal disease presenting with steroid-resistant nephrotic syndrome (SNRS) and variable stages of chronic kidney disease (CKD). Monogenic etiologies for FSGS are increasingly recognized, particularly in pediatric and familial cases. Missense variants in the MAF BZIP Transcription Factor B (MAFB) gene cause a dominantly inherited condition with variable phenotype, ranging from isolated ocular or renal manifestations to syndromic FSGS. Methods: Detailed clinical and genetic investigations were conducted in an extended family presenting with a spectrum of renal and extra-renal manifestations. Results: Using Exome Sequencing (ES), a heterozygous variant, c.797T>C; p.(Leu266Pro) in the MAFB gene was identified in multiple affected family members. Variant segregation confirmed its presence in additional family members. The proband exhibited CKD accompanied by congenital auricular anomalies, hearing loss, and neurodevelopmental delay. An affected sibling presented with nephrotic-range proteinuria, Duane retraction syndrome (DRS) and neurodevelopmental involvement, while another family member had an isolated renal phenotype. Several of these features have not been previously associated with MAFB. Tools for structural modeling and stability predictions supported the functional impact of this variant. Conclusions: Our findings expand the phenotypic spectrum of MAFB-associated disease and further emphasize its variability. Full article

Salt stress is a major environmental constraint affecting plant growth and productivity. Crop wild relatives provide valuable genetic resources for stress tolerance, yet transcriptomic information for forest-derived wild species remains limited. In this study, we analyzed transcriptional responses of V. hirsuta, a crop wild relative (CWR) of legumes, after seven days of salt stress using de novo transcriptome sequencing. Seedlings were exposed to salt stress, and differentially expressed genes (DEGs) were identified between control (Vh_S0) and salt-treated (Vh_S7) plants using an FDR-adjusted threshold (q < 0.05). Gene Ontology and KEGG enrichment analyses revealed that salt-responsive DEGs were mainly involved in regulatory signaling, metabolic adjustment, redox-related processes, and macromolecular organization. Up- and down-regulated DEGs showed distinct yet overlapping enrichment patterns, indicating complex transcriptional reprogramming under salt stress. Transcription factor analysis identified bHLH, MYB, bZIP, NAC, and WRKY families as major regulators, with many families containing both up- and down-regulated members. Notably, genes associated with Na⁺/K⁺ homeostasis were consistently up-regulated and validated by qRT-PCR. These results suggest that continuous seven days salt stress adaptation in V. hirsuta involves coordinated regulation of signaling pathways, transcriptional networks, and transporter-mediated ion homeostasis, providing a valuable transcriptomic resource for crop wild relatives. Full article

Starch biosynthesis is a fundamental process influencing yield and fruit quality in banana, with ADP-glucose pyrophosphorylase (AGPase) serving as the rate-limiting enzyme catalyzing sucrose conversion into starch. However, the mechanisms underlying functional differentiation of AGPase family genes following polyploidization remain largely unexplored. In this study, eight AGPase genes, including large (MaAPL) and small subunit (MaAPS) members, were identified from the banana (Musa acuminata) genome, all harboring the conserved ADP-glucose pyrophosphorylase domain. Phylogenetic analysis traced their evolutionary origin to the ancient moss Physcomitrella patens, with polyploidization identified as the primary driver of gene family expansion. These genes exhibit conserved codon usage bias and have undergone strong purifying selection. Among them, MaAPS1 displayed distinct functional differentiation, increased intron number, enriched promoter cis-elements, and significantly elevated expression—features likely contributing to its adaptation for enhanced starch accumulation in fruit. Furthermore, the MaAPS1 protein was predominately localized in the chloroplast. Functional validation supported its regulatory involvement: transient silencing in banana fruit reduced starch content, while transient overexpression in banana fruit increased starch levels. Co-expression and molecular docking analyses revealed that transcription factors ERF1, C3H1, bZIP1, and bZIP3 may interact with the MaAPS1 promoter, indicating a multifactorial regulatory network. Overall, this study provides insights into polyploidy-driven functional innovation and transcriptional regulation of MaAPS1 in banana starch biosynthesis, providing valuable molecular targets for genetic improvement of yield and fruit quality. Full article