Search Results (1,014)

Extending the fruiting season of Annona squamosa L. requires overcoming autumn and winter flowering declines. This study investigates the efficacy of light-quality regulation technologies and their temperature dependence for floral induction. Field surveys initially identified temperature as the primary climatic factor governing flowering. Under suboptimal autumn temperatures, red light (R-660) night-break (NB) treatments significantly enhanced shoot growth and flowering compared to other light spectra. Transcriptomic analysis revealed 2027 upregulated and 341 downregulated transcripts consistently regulated by R-660, with significant enrichment in the plant hormone signal transduction pathway. Furthermore, R-660 upregulated cold response genes (e.g., CBFs, WRKYs, ERD7), which are associated with the maintenance of vegetative vigor under suboptimal autumn temperatures. However, mid-winter R-660 NB failed to induce flowering without supplemental greenhouse heating. Ultimately, warm ambient temperature is the absolute prerequisite for A. squamosa floral induction, with R-660 serving as a highly effective seasonal supplement to extend autumn flowering. Full article

Abiotic stresses caused by climate change pose a significant challenge to global food security, making it necessary to develop stress-resistant crops. Foxtail millet (Setaria italica (L.) P. Beauv.) is a drought-tolerant C₄ cereal and serves as a model crop for elucidating stress adaptation mechanisms and promoting climate-resilient agricultural solutions. This paper reviews the tolerance mechanisms of foxtail millet to abiotic stresses. Physiologically, the species exhibits excellent water-use efficiency, requiring 75% less irrigation than traditional cereals, achieved through enhanced osmotic adjustment via soluble substance accumulation and the maintenance of ion homeostasis. Morphological adaptations include reduced leaf area, adjusted stomatal density, well-developed root systems, and specialized anatomical features that optimize water conservation. At the molecular level, stress tolerance involves complex transcriptional networks mediated by multiple transcription factor family members, including those (NF-Y, DREB, NAC, WRKY, MYB) that coordinate stress-responsive gene expression, antioxidant defense systems, and osmotic adjustment pathways. Furthermore, this review summarizes multi-omics characteristics, including genomics (such as QTL mapping and GWAS), proteomics, transcriptomics, metabolomics, and regulatory networks, for foxtail millet under abiotic stress tolerance. Additionally, reproductive resilience is maintained through efficient mobilization of stem reserves to panicles, phenological plasticity in flowering timing, and preserved gametic viability under thermal stress. Combining advanced molecular breeding with the inherent tolerance of foxtail millet positions this crop as both a solution to climate change and a genetic resource for enhancing the stress resistance of other cereals. These findings establish foxtail millet as a valuable model for developing sustainable agricultural technologies essential for food security under projected climate scenarios. Full article

Soil salinization is one of the major abiotic stresses limiting agricultural production. As an economically important fruit tree worldwide, grapevine generally exhibits weak salt tolerance. Therefore, identifying key stress-tolerance genes is of great significance for improving stress resistance in grapevines. In this study, the transcription factor gene VvWRKY57, which is induced by salt stress, was cloned from the grape cultivar Vitis vinifera ‘Shine Muscat’. Its function under salt stress was systematically evaluated via heterologous overexpression in Arabidopsis thaliana. The full-length CDS of the VvWRKY57 gene is 915 bp, encoding a protein of 305 amino acids. The protein contains a typical WRKY conserved domain, belongs to group II of the WRKY family, and is localized in the nucleus and cytoplasm. Expression pattern analysis showed that VvWRKY57 was expressed in roots, stems, and leaves of grapevine. Based on this expression profile, transgenic Arabidopsis thaliana plants overexpressing VvWRKY57 were generated to further investigate its role in salt tolerance. Subsequent salt tolerance assays revealed that, compared with wild-type plants, the overexpression lines exhibited stronger resistance phenotypes under salt stress. This study demonstrates for the first time that grape-derived VvWRKY57 functions in enhancing salt tolerance in model plants, providing a novel genetic resource and theoretical basis for crop salt-tolerance molecular breeding using this gene. Full article

Soybean rust caused by the fungus Phakopsora pachyrhizi threatens global soybean production, causing yield losses of up to 80%. Race-specific Rpp genes provide short-term resistance due to pathogen variability, whereas partial resistance (PR) offers durable, broad-spectrum protection, though its genetic basis remains unclear. This study aimed to identify genomic regions and candidate genes underlying PR using the Fixed and Random Model Circulating Probability Unification (FarmCPU) genome-wide association study (GWAS) and machine learning (ML) methods, Random Forest (RF) and Support Vector Regression (SVR). A panel of 312 soybean accessions was evaluated under natural infection across six Ugandan environments. Rust index (RI), derived from rust severity and sporulation level, was used to estimate heritability (H²) and rank genotypes through Best Linear Unbiased Predictions (BLUPs), while Best Linear Unbiased Estimators (BLUEs) supported GWAS input. After quality control, 8272 SNPs were analyzed within a ±60 kb linkage disequilibrium (LD) window. Multi-environmental Analysis (MEA) of RI showed significant genetic effects (p < 0.01); H² = 0.57–0.68. Sixty-one loci were detected: six by FarmCPU, 15 by RF, and 41 by SVR. Key genes included Glyma.01G128100 (a WRKY transcription factor) and Glyma. 13G228000, receptor-like kinase) and Glyma.20G173100 (WD40-domain regulator). Integrating ML with GWAS improved locus detection, confirming the polygenic nature of PR and supporting the use of genomic selection and locus pyramiding for durable rust resistance. Full article

Phellodendron amurense Rupr. is a native tree species in China, well known for its significant medicinal value. Its pharmacological activity mainly derives from the abundant isoquinoline alkaloids in its bark. Berberine serves as the key compound underlying the multiple pharmacological effects of P. amurense and exhibits organ-specific accumulation. However, the genetic mechanisms governing this organ-specific accumulation remain unclear. Genes encoding O-methyltransferase (OMT) and cytochrome P450 (CYP) may play an important role in this regulatory process. In this study, by integrating transcriptomic and metabolomic data from the leaves and stems of P. amurense plantlets, we identified core candidate genes and transcription factors (TFs) that regulate the differential biosynthesis of berberine between these two organs. The results showed that 37 metabolites were significantly upregulated in stems, including main medicinal components such as berberine and jatrorrhizine, while 8497 genes were differentially expressed between leaves and stems. Among these, downstream genes in the berberine biosynthesis pathway, including OMTs and CYPs, were predominantly highly expressed in stems. A co-expression regulatory network identified some TFs such as PaBES1, PaWRKY12/13, PaNAC5, and PaMYB12 as the key nodes regulating the differential biosynthesis of berberine. Phylogenetic analysis classified the 97 PaOMTs into four subgroups. Core candidate genes such as PaOMT7 and PaOMT9 were contained in subgroup IV, potentially contributing to the specific modification of characteristic alkaloids in P. amurense. This study reveals the transcriptional regulatory networks underlying the organ-specific accumulation of berberine in P. amurense plantlets, providing key targets and theoretical support for the targeted improvement and development of elite medicinal varieties. Full article

Cotton, as a globally significant economic crop, is intricately regulated in its growth and development by the key genes for SA (Salicylic acid) biosynthesis. In the present study, a systematic analysis of genes related to SA biosynthesis was conducted across four cotton species, leading to the identification of 70 genes. Specifically, the tetraploid species Gossypium hirsutum and G. barbadense were found to harbor 22 and 23 genes, respectively, representing a substantial expansion compared to the 12 and 13 genes identified in the diploid progenitors G. arboreum and G. raimondii. Comprehensive characterization of chromosomal localization, phylogeny, domain architecture, and promoter cis-elements revealed a uniform distribution of key genes involved in SA biosynthesis across A/D sub-genomes of tetraploids with extensive interspecific collinearity; whole-genome and segmental duplication act as the dominant drivers for the expansion of this gene family, while partial gene loss following polyploidization results in non-doubled gene copy numbers in tetraploids relative to diploids, which reflects the evolutionary selection for genomic dosage balance. The key genes for SA biosynthesis demonstrate a high degree of conservation in protein sequences, protein structures, and conserved motifs, which constitute the structural basis for the stable maintenance of their core functions in the SA biosynthesis pathway during plant evolution. This is closely related to their core function in the salicylic acid (SA) synthesis pathway and serves as the structural basis for the stable maintenance of gene functions during evolution. Analysis of cis-elements revealed that the expression of key genes involved in SA biosynthesis is governed by a complex interplay of phytohormones, stress signals, and transcription factors. Yeast one-hybrid (Y1H) assays confirmed the interaction between the GhPAL and GhICS gene and predicted candidate transcription factors, specifically the binding of GhWRKY21 to GhICS2-1 promoter and GhMYB12 to GhPAL1-2 promoter, thus elucidating their stage-specific regulatory mechanisms in cotton fiber development and reflecting their evolution. This study provides a fundamental basis for investigating the role of the SA signaling pathway in cotton development and offers support for cotton molecular breeding. Full article

Background/Objectives: Environmental conditions in natural and cultivation-managed habitats strongly influence plant physiology and medicinal quality. However, the molecular mechanisms underlying metabolic differentiation in Anoectochilus roxburghii remain poorly understood. This study aimed to elucidate the metabolic and transcriptional differences between wild and cultivated A. roxburghii and to identify the regulatory mechanisms driving habitat-associated variation in metabolite profiles. Methods: We applied integrated non-targeted metabolomics and transcriptomics to compare metabolic profiles and gene expression in the leaves and stems of 15-month-old wild and cultivated A. roxburghii plants. Gene–metabolite correlation analysis was performed to identify coordinated correlation networks associated with key biosynthetic pathways. Results: Our analyses revealed clear differences in metabolite composition and transcriptional patterns between habitat types, suggesting distinct strategies of metabolic resource allocation. Wild plants showed significant enrichment of amino acids and other primary metabolites, whereas cultivated plants accumulated higher levels of flavonoids. Gene–metabolite correlation analysis indicated that multiple flavonoid metabolites were closely associated with key structural genes, including F3H, C12RT1, and HHT1, forming a tightly connected correlation network. In addition, several transcription factor families, including MYB, bHLH, WRKY, and AP2/ERF, showed strong correlations with genes involved in the flavonoid pathway, suggesting that flavonoid accumulation in cultivated plants may be associated with coordinated transcriptional control. Conclusions: Taken together, these findings suggest that habitat conditions are associated with differences in metabolic networks and resource allocation in A. roxburghii. This work provides new insight into the metabolic plasticity of this medicinal plant and highlights potential factors associated with molecular mechanisms that may contribute to variation in medicinal quality. Full article

Seed aging is a critical biological process that leads to progressive loss of seed vigor, thereby constraining germplasm conservation and agricultural productivity. To elucidate the molecular mechanisms underlying this process in grass species, we performed transcriptomic analyses to characterize regulatory networks underlying seed aging in Elymus sibiricus, a dominant forage species on the Qinghai–Tibet Plateau. Seeds were subjected to artificial accelerated aging (45 °C, 80% relative humidity, 1–6 days), followed by physiological evaluation and RNA sequencing. Seed vigor and germination percentage declined markedly with aging, accompanied by extensive transcriptional reprogramming. Integrative analyses identified pyruvate metabolism, MAPK signaling, and peroxisome function as key processes associated with vigor loss during late-stage aging. WGCNA further revealed that genes encoding heat shock proteins and glutathione metabolism-related enzymes were co-localized within the same module, suggesting a possible synergistic role in preserving seed viability during aging. In addition, WRKY24, ARF9, and ARF19 were identified as candidate hub transcription factors. WRKY24 may contribute to aging by modulating antioxidant defense-related genes (e.g., TRX1 and NRPC1), while ARF9 and ARF19 may regulate ROS homeostasis through predicted downstream targets, including FQR1, PER2, MAO1B, ANN5, and MT2B. Together, these findings support a hypothetical regulatory model in which WRKY and ARF transcription factors coordinate redox homeostasis and hormone signaling to regulate seed longevity in E. sibiricus. This study provides a systems-level framework for understanding seed aging in perennial grasses and identifies potential genetic targets for improving seed storability, with implications for germplasm conservation and alpine grassland sustainability. Full article

Low temperatures severely restrict tea plant (Camellia sinensis) growth and yield stability, yet how brassinosteroid (BR) signaling modulates cold acclimation at a systems level remains insufficiently defined. Here, we integrated transcriptomic and UHPLC–MS metabolomic profiling of tea leaves under Control, 24-epibrassinolide (EBR), Cold, and Cold + EBR treatments to delineate BR-potentiated cold responses. Principal component analyses revealed clear treatment-specific separation and tight clustering of biological replicates at both omics levels. Quantitatively, cold stress induced extensive reprogramming (4075 differentially expressed genes (DEGs) and 298 differentially accumulated metabolites (DAMs)), whereas EBR alone exerted relatively modest effects (231 DEGs and 50 DAMs). Notably, EBR under cold conditions further reshaped cold-responsive networks (371 BR-modulated DEGs and 17 BR-modulated DAMs), consistent with a potentiating role for BR signaling. Functional enrichment analyses highlighted phenylpropanoid metabolism and hormone signal transduction as core responsive modules, with coordinated activation of key gateway genes (PAL, C4H, and 4CL) and concurrent engagement of lignin-, flavonoid-, and catechin-associated branches under Cold + EBR. Metabolomic analyses identified flavonoids as the dominant responsive metabolite class (49.31%), particularly anthocyanins and flavonol glycosides. Integrative TF–metabolite–gene correlation networks prioritized WRKY transcription factors (TEA001162, TEA027058) and a UDP-glycosyltransferase gene (TEA025792) as candidate hub genes linking hormone signaling to phenylpropanoid outputs. Collectively, this work provides a systems-level framework of co-regulated transcript–metabolite modules and candidate molecular targets, offering a foundation for functional validation and practical improvement of cold resilience in tea production. Full article

Glucosinolates (GSLs) are unique sulfur-containing secondary metabolites in Brassica crops that critically influence stress resistance, nutritional quality, and economic value. This review systematically summarizes the chemical classification, tissue-specific distribution, and conserved three-phase biosynthetic pathway of GSLs in Brassica species. We dissect the core MYB–MYC–WRKY transcriptional regulatory network, elucidate how whole-genome duplication-driven gene functional diversification shapes species-specific GSL accumulation patterns, and outline the multi-layered regulatory system integrating endogenous and exogenous signals. Furthermore, we consolidate recent advances in the genetic dissection of GSL traits and molecular breeding strategies for targeted trait improvement. Finally, we propose a three-tiered regulatory cascade model for GSL metabolism and highlight future research priorities to address current breeding bottlenecks. This work provides a systematic theoretical framework for functional research and precision breeding of GSL metabolism in Brassica crops. Full article

Shoot branching, as an important architectural trait, influences the number of flower heads and the pattern of flowering in sunflowers (Helianthus annuus L.). However, the main genetic factors leading to extensive branching throughout the plant were not clearly understood. In this study, we analyzed branching inheritance and identified a significant locus using an F₂ population (n = 660) from a cross between the non-branched line 150A and the highly branched line PT326. The branching phenotypes varied from having no branches to complete plant branching, with segregation fitting a 3:1 ratio (χ² = 2.916, p > 0.05), suggesting that a single major gene controls this trait, with the non-branched phenotype being dominant. Using bulked segregant analysis (BSA) and whole-genome resequencing, a strong and consistent signal was identified on chromosome 10 across three separate statistical analyses, pinpointing a primary candidate interval of approximately 3.40 Mb, named qBr10. Through the use of 10 developed Kompetitive Allele-Specific PCR (KASP) markers and recombinant screening, qBr10 was restricted to a 388.5 kb (Chr10:13,422,378–13,780,875). Analysis of this interval identified 21 genes, among which WRKY21 and MTB3 were prioritized as candidate genes for further functional validation. Our findings identified qBr10 as a strong candidate for cloning and offer closely associated markers to aid in marker-assisted improvement of branching and capitulum number in sunflower breeding. Full article

Leaf senescence, the final developmental stage of a leaf, is a highly regulated process that is vital for the recycling of nutrients and the maintenance of plant fitness. Its control operates at multiple levels, including chromatin remodeling, transcription, post-transcriptional regulation, translation, and post-translational modifications. This review summarizes recent advances in understanding the roles of key transcription factor (TF) families—WRKY, NAC, and MYB—in modulating leaf senescence in Arabidopsis thaliana. We detail how these TFs integrate internal and external signals to regulate senescence-associated genes (SAGs). In addition, we explore the pivotal role of microRNAs (miRNAs) in post-transcriptional control of senescence, focusing on their regulation of these TF families. In conjunction with the transcriptome data of Arabidopsis miRNAs under conditions of dark-induced senescence, we also highlight several novel senescence-associated miRNAs. Integrating transcriptional and post-transcriptional perspectives, this review presents an updated regulatory network for leaf senescence and discusses potential applications for manipulating senescence in crops to improve yield and quality. Full article

Lycoris plants are known for their diverse flower colors, but the molecular mechanisms behind these variations remain unclear. In this study, we first used the CIELAB system to precisely measure flower color. We objectively defined the petals of Lycoris sprengeri as blue-purple (Bp) and compared them with the white petals of Lycoris longituba (W) and the red petals of Lycoris radiata var. pumila (R). Metabolomic analysis showed that specific kaempferol glycosides, including kaempferol-3-O-sophoroside and lonicerin, accumulated significantly in the blue-purple petals. Transcriptomic analysis revealed that genes related to flavonoid biosynthesis were generally more active in the colored petals (Bp and R). However, different expression patterns of key hydroxylase genes created a metabolic split. Specifically, the blue-purple petals showed high expression of LrF3′5′H (directing synthesis toward delphinidin) and LrFLS (promoting kaempferol accumulation), whereas the red petals mainly expressed LrF3′H (leading to cyanidin synthesis). Further investigation identified LrWRKY70 as a core transcription factor highly correlated with these flavonoid pathway genes. Crucially, we discovered a new long non-coding RNA, LncRNA401, located downstream of the LrWRKY70 antisense strand. It showed a strong positive correlation with LrWRKY70. Functional verification through transient overexpression demonstrated that LncRNA401 significantly increased the expression of LrWRKY70. This, in turn, broadly activated downstream flavonoid biosynthesis genes, including LrCHS, LrF3′5′H, LrFLS, and LrDFR. This cascade ultimately promoted the synthesis of anthocyanins and kaempferol derivatives, resulting in the unique blue-purple phenotype. Our results reveal a novel LncRNA401-LrWRKY70 regulatory module. This module plays a key role in metabolic reprogramming for flower color formation in Lycoris, providing important insights into plant secondary metabolism and valuable targets for breeding specific flower colors. Full article

Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve indispensable protective functions in terrestrial plants, underpinning their adaptive responses to abiotic stresses such as drought, ultraviolet (UV) radiation, and oxidative damage. Although the role of HCT/HQT in the core phenylpropanoid pathway has been extensively characterized, its precise functional contributions to the flavonoid biosynthetic branch—particularly with respect to substrate selectivity, kinetic regulation, and metabolic channeling—remain incompletely understood. This review systematically analyzes the structural features, spatial conformation, catalytic mechanism, and substrate promiscuity of HCT/HQT to clarify its molecular determinants of activity and specificity. Furthermore, it highlights regulatory factors influencing HCT/HQT gene expression, such as transcription factors (MYB, bHLH, WRKY), phytohormones (GA₃, Eth, MeJA, 6-BA, MT), and abiotic/biotic stressors (temperature, blue light, nitric oxide, nano-selenium). Collectively, these insights illuminate how plants dynamically fine-tune phenylpropanoid metabolism in coordination with developmental programs and environmental challenges. This work provides a foundation for further research on HCT/HQT and supports efforts to develop improved crop varieties through targeted regulation of this central metabolic node. Full article

Tomato (Solanum lycopersicum) is a widely consumed vegetable crop and an established model system for plant functional genomics and genetic research in dicotyledons. Salt stress is a major abiotic factor limiting tomato productivity worldwide. The WRKY transcription factor family, one of the largest and most conserved plant-specific transcription factor families, plays pivotal roles in stress responses. This review summarizes recent advances in understanding the functions of tomato WRKY genes under salt stress, focusing on the genomic basis and evolutionary characteristics of the WRKY family, the roles of core WRKY members under salt stress, and the multi-layered regulatory networks mediating WRKY-dependent salt and alkali tolerance. To date, approximately 10 core SlWRKY genes have been functionally validated to regulate tomato salt tolerance, mainly by maintaining ion homeostasis, regulating reactive oxygen species (ROS) balance, facilitating osmotic adjustment, and integrating hormone signaling pathways. Despite this progress, systemic regulatory hierarchies and epigenetic modulation remain poorly resolved. Furthermore, we discuss how specific WRKY members directly regulate downstream effector genes, such as SlSOS1 and SlNHX4. However, direct experimental evidence for the coordination between tomato WRKYs and mitogen-activated protein kinase (MAPK) cascades, as well as epigenetic modifiers under salt stress, is still scarce in current studies. This review provides a theoretical framework and outlines potential technical pathways for translating fundamental insights into tomato salt tolerance into practical applications for sustainable agriculture. Full article