Search Results (439)

The seeds of Polygonatum sibiricum exhibit dormancy, which poses a major challenge for its cultivation. To elucidate the regulatory mechanisms underlying dormancy release, we performed integrated transcriptomic and metabolomic analyses on seeds at 0, 5, 10, and 15 d after seed imbibition. Physiological assays revealed progressive declines in abscisic acid (ABA) and starch levels, alongside increases in gibberellin (GA) and soluble sugar contents, reflecting the metabolic changes accompanying the transition from dormancy to germination. Transcriptomic analysis identified 11,520 expressed genes, with 6753, 7775 and 9387 differentially expressed genes (DEGs) at T5, T10, and T15, respectively. KEGG enrichment highlighted starch and sucrose metabolism and plant hormone signal transduction as key pathways. Notably, the GA biosynthesis gene GA3ox was markedly upregulated, while the DELLA repressor (Isoform0012761) showed sustained downregulation, suggesting relieved GA signaling. In the ABA pathway, CYP707A catabolic genes exhibited biphasic expression, and ABA signaling components (PYL, PP2C, SnRK2) showed stage-specific remodeling. A total of 316, 412, and 479 differentially expressed transcription factors were identified across stages, with the GRAS family being the largest. Co-expression network analysis revealed 19 transcription factors integrating starch/sucrose metabolism with ABA and GA signaling, most of which were downregulated, except one C2H2 member showing sustained upregulation. These findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant. Full article

The plant epidermis, adorned with trichomes and root hairs, represents a critical interface where developmental programming and environmental responses converge. Although the genetic basis of epidermal patterning has been extensively characterized in model systems, how these pathways are modulated under abiotic stress remains incompletely understood. This review integrates recent advances in epidermal development and stress biology, focusing on MYB–bHLH–WD40 (MBW) complexes, GIS-family C2H2 zinc-finger proteins, and ROOT HAIR DEFECTIVE SIX-LIKE (RSL) transcription factors. These regulators participate in interconnected, organ-specific networks that coordinate trichome and root-hair development. Their activities are shaped by gibberellin–brassinosteroid interactions, ethylene–auxin coordination, jasmonate and abscisic acid signaling, and cytokinin- and nutrient-responsive pathways. We further discuss how reactive oxygen species and calcium oscillations translate transcriptional regulation into polarized cell growth. The resulting epidermal plasticity reflects trade-offs among growth, defense, resource acquisition, and conservation. By integrating single-cell transcriptomics, nutrient sensing, and evolutionary perspectives, this review provides a framework for understanding environmentally responsive epidermal development and identifies opportunities for improving crop resilience. The resulting framework identifies testable opportunities for crop improvement, while emphasizing that native network equivalence, pleiotropic effects, and field-level stress benefits remain to be established in crop species. Full article

Oligosaccharides are plant immune elicitors with recognized roles in seed germination, root development and stress regulation. However, most studies have focused on single oligosaccharides or the independent effects of rhizosphere microorganisms. The coordinated regulation of plant physiological networks and microbial communities by oligosaccharide-based seed coatings remains poorly understood, especially for xanthan oligosaccharides. Here, using wheat root transcriptomics, rhizosphere 16S rRNA sequencing, and physiological assays, we found that a xanthan oligosaccharide composite seed coating significantly improved germination potential, germination rate and seedling vigor. It promoted root and shoot growth under field conditions, optimized the balance of auxin, gibberellin and abscisic acid, activated endosperm hydrolytic enzymes and accelerated nutrient mobilization. Transcriptomics revealed stage-specific regulation of membrane lipid metabolism, hormone signaling, antioxidant defense, carbon/nitrogen metabolism and ABC transporters. Microbiome analysis showed selective enrichment of beneficial genera (Devosia, Paenarthrobacter, Citricoccus), which were positively associated with root nitrogen metabolism and MAPK signaling. Collectively, the coating promoted wheat growth and was associated with stress-related physiological and molecular responses; however, direct stress-challenge and functional-validation experiments are required to verify stress-tolerance mechanisms. Full article

Understanding whether long-term vascular cambium vitality in ancient trees reflects progressive decline or adaptive reprogramming is central to grasping woody plant longevity. We performed an integrative analysis of functional traits, transcriptome profiles, and metabolomic landscapes of cambial zone enriched from 80-, 500-, and 1000-year-old Styphnolobium japonicum trees. With increasing tree age, the vascular cambium showed fewer cell layers, reduced thickness, and lower auxin, gibberellin, and IAA/ABA ratios, whereas bark thickness, malondialdehyde, abscisic acid, jasmonic acid, and salicylic acid contents increased. Transcriptomic and metabolomic analyses revealed that differentially expressed genes and metabolites were primarily enriched in the cell cycle, phytohormone signaling, and phenylpropanoid biosynthesis pathways. Specifically, genes associated with cell division were down-regulated in millennial trees, whereas phenolic acids, flavonoids, and lignin-related metabolites significantly accumulated. Piecewise structural equation modeling suggested associations among tree age, transcription factors, structural genes, metabolites, and cambial functional traits. These results indicate that cambial senescence is not a simple linear decay but a highly coordinated remodeling process, providing crucial evidence for delayed senescence in long-lived woody species. Full article

Camellia oleifera is a significant woody oil tree species native solely to China. The bud–seedling grafting technique has been widely applied to this tree due to its significant advantages in improving propagation efficiency and shortening the growth cycle. However, the healing process and its underlying molecular regulatory mechanisms during interspecific heterografting in Camellia remain poorly understood. In this study, we established both homografting and heterografting systems using C. oleifera bud seedlings as rootstocks, grafted with scions from C. oleifera, C. meiocarpa, and C. weiningensis. We systematically investigated the response patterns and differences in metabolites and gene expression before and after grafting healing through endogenous hormone detection, LC-MS untargeted metabolomics, and transcriptomic sequencing. The results showed that the grafting survival rates between C. oleifera and the other species were high (>88%), indicating strong compatibility. Metabolomic analysis revealed that differential metabolites, such as Gibberellin A53, Sophoramine, and Morellin, accumulated significantly with prolonged grafting time, and interspecific grafting combinations exhibited specific highly expressed metabolite profiles. We integrated multi-dimensional data comprising hormone levels, differential metabolites, and DEGs. A “hormone-gene” interaction network was constructed using WGCNA. The analysis revealed that key hub genes, including CYP73A, F3H, CHS, LHCA1, and LHCB5, were significantly correlated with flavonoid biosynthesis and elevated iPR content. We hypothesize that these genes enhance graft healing capacity by regulating secondary metabolism and hormone signaling pathways. The identified candidate genes, phytohormones, and metabolites provide potential molecular markers and regulatory targets for evaluating graft compatibility, selecting suitable rootstock–scion combinations, and optimizing grafting and propagation practices in C. oleifera, providing a crucial theoretical basis for superior cultivar breeding and the investigation of graft compatibility mechanisms. Full article

Protein hydrolysates (PHs) have emerged as a pivotal category of plant biostimulants in sustainable agriculture. They are derived from the enzymatic, chemical, or thermal hydrolysis of agro-industrial by-products of animal or plant origin. These complex mixtures of free amino acids, oligopeptides, and polypeptides enhance crop productivity, nutrient use efficiency, and abiotic stress resilience. This review examines and compares the production methods, chemical composition, agronomic performance, physiological mechanism, and safety profiles of animal-derived (A-PHs) and vegetal-derived (V-PHs) protein hydrolysates, with particular emphasis on hydrolyzed collagen (HC) as an emerging biostimulant. Furthermore, the specific physiological roles of proline in mediating plant stress tolerance and hydroxyproline-rich glycoproteins in maintaining cell wall integrity are evaluated. Animal-derived sources, including collagen, keratin, and fish by-products, are characterized by elevated glycine, proline, and hydroxyproline concentrations, amino acids with established roles in root architecture promotion, reactive oxygen species (ROS) scavenging, and osmotic adjustment under stress. Conversely, V-PH exhibit richer bioactive peptide profiles and superior environmental sustainability indices. Underlying mechanisms encompass hormone-like activities mimicking auxin and gibberellin signaling, transcriptional reprogramming of nitrogen assimilation pathways, antioxidant enzyme modulation, and rhizosphere microbiota stimulation. Full article

Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome shooting in staple food bamboos remain largely unknown. Here, we performed integrated metabolomic and transcriptomic analyses of Fargesia rufa rhizomes collected along an elevational gradient (1000 m, 1500 m, and 2000 m), with a critical paired comparison at 2000 m between a non-shooting cold gully-edge site (16.4 °C) and a shooting warm gully-center site (21.1 °C), where soil temperature is elevated by approximately 4 °C due to prolonged solar exposure. Our results demonstrate that soil temperature, rather than elevation per se, acts as the primary driver of rhizome shooting, with an apparent threshold near 20 °C. A core shooting metabolome (CSM) comprising 843 metabolites was consistently accumulated across all shooting conditions, which featured gibberellin/auxin precursors, TCA cycle intermediates, and phenylpropanoid compounds. Correspondingly, a core shooting transcriptome (Rh_shooting) of 10,970 genes was identified, which resolved into three functionally distinct temporal clusters: “shooting-on” (activated upon threshold crossing, enriched in hormone signaling and cell wall metabolism), “temperature-dose” (progressively upregulated with rising temperature, enriched in energy metabolism and defense), and “microenvironment-enhanced” (specifically upregulated in the high-elevation warm gully, enriched in photosynthesis and antioxidant pathways). Integrative network analysis further revealed zeatin riboside and multiple hub genes as central coordinators linking hormone signaling, energy metabolism, and cell wall remodeling. Collectively, these findings establish a molecular framework linking altitudinal temperature variation to bamboo rhizome regeneration—a process that directly determines the spatiotemporal availability of bamboo shoots for giant pandas. This work provides mechanistic insights into giant panda foraging ecology and has direct implications for predicting habitat quality under climate change and informing evidence-based conservation strategies for this flagship species and its critical food resource. Full article

As a crucial component of plant architecture, shoot branching significantly enhances photosynthetic efficiency and optimizes the source-sink allocation of photosynthetic products, which directly impacts crop productivity. The formation of lateral branches is co-regulated by various internal and external factors, including genetic factors, phytohormones, metabolic, and environmental factors. In this review, we provide a mechanistic overview of the key regulatory events involved in axillary meristem (AM) formation and lateral branch development, emphasizing the significant regulatory roles of phytohormones (such as auxins, cytokinins, strigolactones, brassinosteroids, gibberellins, abscisic acid, and other phytohormones) in this process. Furthermore, we highlight the transcription factors SHOOT MERISTEM-LESS (STM) and BRANCHED1 (BRC1) as central hubs that integrate multiple hormonal signals to control AM initiation and lateral branch development, respectively. By elucidating the regulatory mechanisms of these key nodes, we propose future research directions that can provide a foundation for shaping ideal crop plant architecture through genetic engineering and breeding strategies. Full article

Class I KNOX1 (KNOTTED1-like homeobox 1) transcription factors integrate gibberellin (GA), cytokinin (CK), and auxin (IAA) signaling to maintain shoot apical meristem identity and coordinate plant organogenesis. This review examines the structural conservation, evolutionary dynamics, and regulatory architecture of KNOX1 genes across horticultural crops, drawing essential mechanistic context from model species. We synthesize KNOX1 functions in six agronomic domains, including plant architecture and branching, leaf morphogenesis and ornamental traits, floral development and sex determination, fruit formation and quality, storage organ specification, and abiotic stress resilience. Particular attention is given to recent breakthroughs in cucurbit inferior ovary development, tomato chloroplast patterning, and potato tuber morphogenesis. We identify critical bottlenecks constraining translation, including fragmented regulatory networks, recalcitrant transformation systems in woody perennials, uneven taxonomic coverage favoring annual vegetables over ornamentals and medicinal species, and a near-complete absence of multi-environment field validation. We propose four strategic priorities to bridge this gap: (i) construction of spatiotemporal expression atlases using single-cell and spatial transcriptomics; (ii) tissue-specific and promoter-engineered CRISPR/Cas9 editing to circumvent pleiotropic penalties; (iii) cross-species comparative evo–devo analysis of lineage-specific innovations (compound leaves, inferior ovaries, tubers); and (iv) integrated field trials assessing genotype-by-environment interactions and trait stability. This framework aims to accelerate KNOX1-directed molecular design breeding in horticultural crops. Full article

Soil moisture plays a crucial regulatory role in determining the size and quality of citrus fruits. This study analyzed the fruit size and quality of citrus under different soil moisture conditions, including severe drought (SD), moderate drought (MD), and control (CK). Under drought stress, the fruit weight, longitudinal diameter, and transverse diameter of citrus fruits were significantly lower than those of the control. The content of soluble solids and titratable acid in fruits under drought stress was significantly higher than that of the control. Transcriptome sequencing revealed that compared with CK, there were 1186 differentially expressed genes in MD, including 414 up-regulated genes and 772 down-regulated genes; and 2315 differentially expressed genes in SD, including 1143 up-regulated genes and 1172 down-regulated genes. The differentially expressed genes were significantly enriched in cellular processes, metabolic processes, and plant hormone signal transduction. The down-regulated expression of auxin and gibberellin biosynthesis genes (YUC10, GA20_OX1, GA2_OX1, and GA20_OX2) and signal transduction-related genes (AUX/IAA13, SAUR32, GH3.1, and ARRs), and the up-regulated expression of cytokinin decomposition gene (CKX5) may be associated with reduced fruit size under drought conditions. The up-regulated expression of citric acid synthesis genes (PEPC2 and PEPCK1) and vacuolar transporters (PH1, PH4, PH8, and VHA-c3) may be associated with pronounced accumulation of citric acid in citrus under drought stress. In conclusion, water control regulated fruit size and acidity by modulating phytohormone metabolism and signaling, along with the synthesis and transport of citric acid. Full article

Pre-harvest sprouting (PHS), the premature germination of grains on the mother plant, causes substantial yield loss and grain-quality deterioration in rice under humid conditions. Although seed dormancy and germination are largely controlled by hormonal balance, the transcriptional mechanisms linking hormone signaling with metabolic adaptation during PHS remain unclear. In this study, we investigated the roles of two ethylene-responsive factor transcription factors, OsERF1 and OsERF94, in rice PHS regulation using CRISPR/Cas9-mediated knockout lines, together with physiological, gene-expression, and metabolite analyses. The oserf1-KO mutant showed reduced seed dormancy and increased germination under PHS-inducing conditions, accompanied by altered expression of abscisic acid- and gibberellin-related genes. In contrast, the oserf94-KO mutant exhibited enhanced dormancy and reduced germination, with decreased expression of hypoxia-responsive fermentation genes and impaired carbohydrate mobilization, as indicated by reduced soluble sugar and ethanol accumulation and increased starch content. These results suggest that OsERF1 contributes primarily to hormone-mediated dormancy maintenance, whereas OsERF94 supports metabolic activation required for germination under high-moisture conditions. Collectively, this study proposes a dual regulatory framework in which hormonal control and hypoxia-associated carbon metabolism coordinately determine rice PHS susceptibility. Full article

Bolting time is a pivotal agronomic trait that determines the yield and commercial quality of Brassica rapa ssp. chinensis var. utilis. To investigate the molecular basis of early bolting, an early-bolting line ‘m662’ and a late-bolting line ‘t151’ were used in this study. Phenotypic evaluation combined with shoot apical meristem (SAM) observation showed that 10 days of low-temperature vernalization markedly accelerated bolting in ‘t151’. Subsequently, SAM samples from ‘m662’, non-vernalized ‘t151’, and 10-day vernalized ‘V10-t151’ were collected at five developmental stages (7, 10, 13, 16, and 19 d after transplanting) for transcriptome sequencing. Weighted gene co-expression network analysis revealed that key module genes related to gibberellin signaling were specifically enriched in ‘m662’ before bolting, whereas those in the middle and late bolting stages were enriched in hormone response, cell cycle regulation, and floral organ development. In ‘t151’, hub genes detected at 7–13 d included three paralogs of the floral integrator gene SOC1 and BraA06.FPF1. BrSOC1 (BraA03g024230.4C) was significantly upregulated in response to vernalization. DEGs identified during the late developmental stage (16–19 d) included genes involved in transmembrane transport processes, flower development, reproductive shoot system development. Expression analysis across the three materials showed that vernalization accelerated bolting in ‘t151’ by repressing BrFLC expression and promoting BrSOC1 expression. This study elucidates the dynamic transcriptomic network underlying early bolting in non-heading Chinese cabbage, providing key functional genes and mechanistic insights for bolting regulation and molecular breeding. Full article

Background: Di19 (drought-induced 19)proteins belong to the C2H2-type zinc-finger family and play a crucial role in regulating plant growth, developmental processes, hormone signal transduction, and abiotic stress adaptation. However, research on the Di19 gene family in sweet potato and its diploid relatives remains relatively limited. Methods: At the whole-genome level, members of the Di19 gene family in sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30) were systematically identified, and multi-dimensional bioinformatics analyses were carried out. Results: Seven Di19 genes were identified per species, with the family’s overall evolutionary characteristics conserved. Some IbDi19s showed species-specific structural variations, mainly manifested as an increase in the number of exons, loss or substitution of conserved motifs. The expression patterns of Di19s of two diploid relatives are highly conserved. IbDi19s are mainly expressed in leaves and roots. Most members respond significantly to JA treatment, but hardly respond to IAA. The expression of IbDi19-1 was significantly up-regulated by 336-fold and 68-fold under GA3 and cold treatments, respectively. Based on bioinformatics and expression data, a hypothesis was proposed that IbDi19-1 may be involved in the regulation of low-temperature response and gibberellin signaling pathways. Conclusions: This study provides candidate genes and a theoretical basis for evolutionary analysis, stress-resistant molecular breeding of the Di19 gene family in sweet potato and its two diploid relatives. Full article

Plants must continuously balance the trade-offs between growth and defense, a constraint that is exacerbated by biotic and abiotic stresses, particularly when they occur together. Ethylene (ET) serves as a central, integrative regulatory node controlling this by linking developmental programs to stress-responsive signaling networks. Advances at the molecular and systems levels have revealed that ET mediates the redistribution of metabolic resources via coordinated regulation of its synthesis, perception, and downstream signaling. The ETR (Ethylene Receptor)-CTR1 (Constitutive Triple Response 1)-EIN2 (Ethylene Insensitive 2)-EIN3(Ethylene Insensitive 3) signaling module lies at the core of this network, integrating multiple hormonal pathways. Through dynamic crosstalk with jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), auxin (AUX), and gibberellins (GA), ET enables the fine-tuned coordination of growth inhibition, immune activation, and stress acclimation in response to environmental fluctuations. Processes such as induced systemic resistance, programmed cell death, and architectural plasticity further reinforce this regulatory framework, with ethylene-responsive transcription factors, including ERFs (ethylene responsive factor gene family) and WRKYs, acting as critical convergence points. Emerging insights into ACC (1-aminocyclopropane-1-carboxylic acid)-dependent signaling, chromatin remodeling, and tissue-specific regulation expand the functional scope of ET beyond traditional hormone paradigms. At the same time, the ability of pathogens to manipulate ET signaling underscores its dual role in both promoting immunity and facilitating susceptibility. By integrating molecular, physiological, and ecological perspectives, this review highlights ET as a central coordinator of plant stress resilience and growth optimization, providing a unifying framework for understanding how plants adapt to complex and dynamic environments. Full article

JAZ (Jasmonate ZIM-Domain) proteins are key negative regulators of the jasmonic acid (JA) signaling pathway and are involved in various plant growth, development, and stress regulation. However, the functions of the JAZ gene family in Camellia nitidissima remain poorly understood. Here, ten CnJAZ genes were identified at the genome-wide level, encoding 134–398 amino acids and unevenly distributed across eight chromosomes. All CnJAZs were predicted to localize to the nucleus. Based on phylogenetic and structural analyses, the ten CnJAZs were classified into five subfamilies, with members of the same subfamily sharing similar exon–intron structures. Collinearity analysis with Arabidopsis thaliana and Malus domestica suggests that the JAZ gene family shares a common ancestor. Promoter analysis revealed cis-acting elements responsive to light, methyl jasmonate (MeJA), and anaerobic stress. Transcriptome profiling showed that most CnJAZs exhibit tissue- and development-specific expression, particularly during flower development and organ formation. RT-qPCR confirmed that MeJA and gibberellin (GA₃) significantly induced the expression of CnJAZ, whereas ethylene (ETH) treatment up-regulated CnJAZ3 and CnJAZ5 by 80-fold after three hours. These findings highlight their important roles in growth, development, and hormonal regulation in C. nitidissima, laying a foundation for functional studies. Full article