Search Results (1,281)

Cold stress severely impairs grapevine (Vitis vinifera L.) growth, development, and productivity, necessitating the identification of elite cold-resistance genes for breeding tolerant cultivars. Chinese wild grape germplasm, particularly the endemic Vitis yeshanensis ‘Yanshan’ ecotype, represents a valuable reservoir of stress-resistance alleles with exceptional cold hardiness. In this study, we isolated an R2R3-MYB transcription factor gene VyMYB24 from ‘Yanshan’ grape and systematically characterized its function in low-temperature responses. VyMYB24 expression was rapidly and strongly induced by cold stress, with transcript levels peaking at 12 h after treatment. Heterologous overexpression of VyMYB24 in transgenic tobacco (Nicotiana benthamiana) induced pronounced architectural changes. Transgenic plants exhibited a dwarf and compact stature with enhanced lateral branching, thickened stems, and robust root systems. In addition, anatomical analysis revealed markedly increased xylem and phloem thickness. Under cold stress, transgenic lines outperformed wild-type plants, with reduced wilting, lower water loss, and improved survival and recovery rates. Physiologically, VyMYB24 activated the antioxidant defense system, elevated the activities of key reactive oxygen species (ROS)-scavenging enzymes, suppressed H₂O₂ and superoxide accumulation, and reduced malondialdehyde content and electrolyte leakage, thereby preserving cellular homeostasis. This study provides functional evidence for the positive regulatory role of VyMYB24 in cold tolerance via heterologous expression, underscores the genetic value of ‘Yanshan’ grape germplasm, and lays a preliminary foundation for improving crop stress resistance through the utilization of native wild germplasm genes. 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

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

Soil salinization has become a major global abiotic threat restricting sustainable viticulture, especially in coastal and inland saline–alkali zones. Unlike cereal crops mainly suffering from sodium toxicity, grapevine (Vitis vinifera L.) is a typical chloride-sensitive woody perennial, subjected to superimposed damages of osmotic stress, ionic imbalance and secondary oxidative injury under saline conditions which severely suppress vegetative growth and degrade berry quality. This review systematically summarizes the multi-layered physiological adaptive mechanisms of grapevine against salt stress, including ion homeostasis maintained by salt overly sensitive (SOS), Na⁺/H⁺ exchanger (NHX) and chloride channel (CLC) transporter families, active accumulation of osmoprotectants, synergistic enzymatic and non-enzymatic antioxidant systems, and phytohormone crosstalk networks formed by endogenous phytohormones (abscisic acid, ABA; jasmonic acid, JA; salicylic acid, SA; brassinosteroid, BR) and small signaling molecules. We further elaborate comprehensive molecular regulatory cascades governing salt tolerance, covering core functional genes for ion transport, master transcription factor families WRKY, MYB, APETALA2/Ethylene Response Factor (AP2/ERF), NAC, basic helix–loop–helix (bHLH) and emerging epigenetic regulatory layers mediated by deoxyribonucleic acid (DNA) methylation, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). In addition, we integrate four categories of field mitigation strategies for saline vineyards: germplasm improvement via salt-tolerant rootstock grafting, rhizosphere soil basal amendment, exogenous biostimulant regulation, and precision agronomic optimization. Current experimental systems do not fully recapitulate complex field combined-stress conditions, as most studies rely on laboratory single-salt stress simulation. Meanwhile, multi-omics, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) gene editing and high-throughput phenotyping tools provide promising approaches to deepen our understanding of grape salt tolerance. This review constructs a comprehensive theoretical framework linking physiological responses, molecular regulatory networks and practical field technologies, offering systematic theoretical references and technical guidance for salt-tolerant germplasm innovation and environmentally sustainable viticulture on saline soils. Full article

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits. Full article

The flower color of Michelia odora, an important landscape tree plant, shows significant ornamental value, but its regulatory mechanisms remain to be further explored. The present work integrated metabolomic with transcriptomic analyses for elucidating the anthocyanin biosynthesis mechanisms in light pink and deep pink M. odora flowers. Our metabolomic analysis identified 13 differentially expressed anthocyanins, 11 of which, especially cyanidins, were significantly accumulated within deep pink petals versus light pink ones. As revealed by our transcriptomic analysis, 33 differential genes were related to flavonoid and anthocyanin biosynthesis. Further, transcription factor genes, encompassing three MoMYB alongside two MobHLH genes, were likely the hub genes that modulated anthocyanin biosynthesis. Quantitative real-time PCR validation indicated that certain genes, like MoPAL, MoC4H, Mo4CL, MoCHS, MoCHI, MoUGT75C1, MoMYB3, MobHLH1, and MobHLH3, displayed concurrent expression with anthocyanin accumulation within deep pink petals. Collectively, these results indicate the role of anthocyanin accumulation in deep pink color, and the effect of upregulated genes on increasing anthocyanin levels. Our results shed novel light on color change mechanisms underlying M. odora, and provide a theoretical basis for flower breeding. Full article

Lignin deposition in fruit trees represents a fundamental physiological trade-off: essential for structural integrity and stress adaptation, yet excessive or mistimed activation compromises fruit texture, palatability, and market value. This review synthesizes advances in lignin biosynthesis and its multilayered regulation in commercial fruit species. We describe how abiotic (drought, salinity, temperature extremes) and biotic (pathogens, pests) stresses trigger lignification through transcriptional, post-transcriptional, hormonal, and epigenetic mechanisms, centered on the conserved NAC-MYB cascade. This core module integrates WRKY/ERF transcription factors (TFs), microRNA networks, and hormone signaling. Transcriptional programs are further refined by microRNAs, alternative splicing, DNA methylation, histone acetylation, and phytohormone crosstalk (abscisic acid, ABA; jasmonic acid, JA; salicylic acid, SA; and brassinosteroids, BRs). We emphasize molecular crosstalk integrating abiotic and biotic stress signaling via shared TFs, reactive oxygen species (ROS), and epigenetic memory. We critically examine lignification’s dual nature during development and postharvest storage, contributing to desirable traits (stone formation and skin toughness) but also driving defects (stone cell gritty texture and chilling-induced wooliness). Finally, we propose a strategic framework leveraging molecular breeding, targeted gene editing, and precision horticulture to fine-tune lignification, enabling climate-resilient cultivars without compromising fruit quality. Full article

Vitis heyneana Roem. et Schult. var. adenoclada (Hand.-Mazz.) is an important wild grapevine resource with unique berry traits and wine quality characteristics; yet the molecular mechanisms governing its phenolic biosynthesis remain to be further elucidated compared with cultivated Vitis vinifera. This study aimed to systematically characterize the transcriptional and metabolic regulation of phenolic compound accumulation in V. heyneana var. adenoclada using integrated metabolomics and transcriptomics. At the metabolic level, V. heyneana var. adenoclada exhibited significantly higher contents of phenolic acids (caffeic and ferulic acids), resveratrol, flavonols (quercetin and myricetin), flavan-3-ols (catechin and epicatechin), and anthocyanin diglucosides compared with V. vinifera cv. Cabernet Sauvignon. The two tested V. heyneana varieties showed distinct developmental accumulation profiles: Guiheizhenzhu No. 6 accumulated more ferulic acid, resveratrol, myricetin, and anthocyanins at maturity, whereas Yeniang No. 2 showed higher quercetin and flavan-3-ols at the green stage. Integrated multi-omics correlation analyses revealed that the elevated phenolic content is driven by the coordinated upregulation of key structural genes mediated by a complex MYB regulatory network. Specifically, MYB12 (MYBF1) positively correlated with COMT, CHI, DFR, and LAR. MYB5, MYBS3, and MYB61 promoted quercetin synthesis by activating FLS. MYB06, MYB4, and MYB36 enhanced STS transcription to drive resveratrol biosynthesis, whereas MYB1 and MYB5 cooperatively regulated UFGT, 5GT, and GST4, facilitating efficient synthesis and transport of anthocyanin diglucosides. These findings provide comprehensive mechanistic insights into phenolic metabolism in V. heyneana var. adenoclada and establish a valuable theoretical foundation for improving the flavor quality and regional utilization of wild grape wines. Full article

Soil salinity severely limits grapevine (Vitis spp.) growth and productivity, yet the mechanisms distinguishing tolerant and sensitive rootstocks remain incompletely understood. We compared the salt-tolerant rootstock ‘SO4’ with the salt-sensitive ‘Beida’ under 100 mmol L⁻¹ NaCl for 0, 6, and 12 days. Salinity progressively reduced photosynthetic pigments in both genotypes, although ‘SO4’ retained higher levels. Salt treatment also increased hydrogen peroxide, malondialdehyde, soluble sugars, soluble proteins, proline, and antioxidant enzyme activities. Compared with ‘Beida’, ‘SO4’ showed stronger osmotic adjustment and greater activation of superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase. RNA-seq analysis revealed extensive genotype- and time-dependent transcriptional reprogramming, with differentially expressed genes mainly associated with hormone signalling, secondary metabolism, carbon fixation, protein processing, and lipid metabolism. Weighted gene co-expression network analysis identified the MEblack module as positively associated with salt tolerance in ‘SO4’ but negatively associated with ‘Beida’. Within this module, Vitvi01g00735/VvBCA2 and Vitvi07g02043/VvLCB1 were prioritized as candidate hubs based on high module membership, gene significance, and intramodular connectivity. Hub-centred networks linked VvBCA2 to redox regulation, protein homeostasis, defense, and osmotic signalling, whereas VvLCB1 was associated with cell-wall remodelling, methyl metabolism, membrane signalling, and lipid turnover. Transcription-factor families, including MYB, WRKY, AP2/ERF, bHLH, and HSF, were more strongly represented in ‘SO4’. Collectively, these findings identify coordinated physiological and transcriptional mechanisms underlying salt tolerance and provide candidate genes for grapevine improvement. Full article

Iron (Fe) is an essential micronutrient for plants. However, both iron deficiency and excess can severely inhibit plant growth and productivity. Arbuscular mycorrhizal (AM) fungi have been shown to improve plant mineral nutrition and stress tolerance, yet the integrated physiological and molecular mechanisms underlying AM-mediated iron homeostasis regulation, particularly in woody tree species, remain poorly understood. In this study, we investigated the effects of inoculating Eucalyptus grandis seedlings with the AM fungus Rhizophagus irregularis on their growth, photosynthetic performance, antioxidant defense, and transcriptional responses under varying Fe supply levels (5, 25, and 200 µM). Our results demonstrated that AM symbiosis significantly alleviated the growth inhibition induced by both low-Fe (5 µM) and high-Fe (200 µM) stress, enhanced photosynthetic capacity, as evidenced by increased net photosynthetic rate (Pn), stomatal conductance (Gs), and PSII photochemical efficiency; under low-Fe, Pn, Gs, and Fv/Fm increased by 33.7%, 42.4%, and 25.2%, respectively. AM symbiosis also significantly enhanced the activities of antioxidant enzymes (POD, SOD, and CAT) under high-iron stress, accompanied by reduced accumulation of reactive oxygen species and lipid peroxidation; specifically, POD, SOD, and CAT activities increased by 79.3%, 88.7%, and 87.0%, respectively. Transcriptomic analysis identified 44 MYB transcription factors that were differentially induced by AM symbiosis under iron stress, among which six genes (EgMYB-2, EgMYB-3, EgMYB315-1, EgMYB315-2, EgMYB61, and EgMYB306) were significantly upregulated by AM under both low- and high-iron conditions, as verified by qRT-PCR. Correlation analysis revealed strong positive associations between the expression of these EgMYB genes and antioxidant enzyme activities as well as photosynthetic parameters, suggesting their potential involvement in coordinating iron stress responses. Overall, our findings indicate that AM fungus enhances iron stress tolerance in E. grandis through a multilevel strategy that includes photosynthetic protection, antioxidant defense activation, and transcriptional reprogramming involving MYB transcription factors as potential regulators. This study provides integrated physiological-molecular analysis and novel insights into AM-mediated Fe homeostasis regulation in the woody tree species E. grandis. Full article

Waterlogging-induced hypoxic stress severely impairs vegetative growth and crop yield of melon (Cucumis melo L.). The formation of adventitious roots represents a critical morphological adaptive strategy for melon seedlings to alleviate hypoxic damage and maintain viability under waterlogging conditions. Nevertheless, the synergistic molecular regulatory mechanisms governing waterlogging-triggered adventitious root development in melon remain largely uncharacterized at the proteomic and metabolomic layers. In this study, the waterlogging-tolerant melon line ‘L8’ with superior adventitious root production capacity was exposed to waterlogging treatment, and hypocotyl tissues were harvested at 0, 24, 48 and 72 h post-waterlogging for untargeted metabolomic and proteomic analyses. A total of 1337 differentially accumulated metabolites (DAMs) and 2898 differentially expressed proteins (DEPs) were identified across the pairwise comparisons. Functional enrichment analyses of DAMs and DEPs indicated that pathways related to linoleic acid metabolism, α-linolenic acid metabolism, phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and glutathione metabolism were centrally implicated in adventitious rooting induced by waterlogging. At the protein level, pivotal functional proteins associated with anaerobic respiration (pyruvate decarboxylase, alcohol dehydrogenase), ethylene biosynthesis (1-aminocyclopropane-1-carboxylate oxidase), cell wall remodeling and antioxidant defense were significantly up-regulated throughout adventitious root development. In addition, three transcription factors, namely the GRAS family protein MELO3C025904.1, MYB-related protein MELO3C007640.1, and ZF-HD protein MELO3C022921.1, exhibited differential expression across different time points compared to the control. Moreover, metabolomic profiling identified three prominent metabolites with regulatory functions, encompassing the terpenoid acorusnol, the piperidine alkaloid 1,4′-bipiperidine-1′-carboxylic acid, and the flavonoid 4′,7-dihydroxy-2′-methoxy-3′-prenylisoflavan. Omics correlation analysis revealed extensive concordance between metabolomic and proteomic profiles. Nine core DAMs, including N-methylserotonin, Val-Val and glyuranolide, were tightly correlated with hundreds of DEPs and key transcription factors, constructing a complex regulatory network governing waterlogging stress acclimation and adventitious root morphogenesis. This study systematically characterizes the coordinated proteomic and metabolomic reprogramming underlying waterlogging-induced adventitious root formation in melon. These findings deepen our understanding of the molecular mechanism of waterlogging tolerance and provide valuable candidate genes and metabolic targets for genetic improvement of waterlogging resistance in melon. Full article

Soil salinity severely restricts grapevine growth and development. Here, we integrated whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate DNA methylation changes and their relationship with gene expression under salt stress in Vitis vinifera L. ‘Shine Muscat’ grapevine. Salt stress altered genome-wide DNA methylation patterns, reducing methylation levels in CG, CHG, and CHH contexts following NaCl treatment. We identified 8606 differentially methylated regions (DMRs) and 3106 DMR-associated genes (DMGs) under salt stress. RNA-seq analysis revealed 2691 differentially expressed genes (DEGs), including multiple stress-related transcription factors (e.g., MYB, NAC, WRKY) and hormone-related genes strongly induced by salinity. Integrative analysis identified 171 genes that were both differentially methylated and differentially expressed, primarily enriched in metabolic pathways, fructose and mannose metabolism, and fatty acid biosynthesis. Notably, several key stress-responsive genes (e.g., VvNAC72, VvBAK1, VvMYBS3) showed coordinated changes between methylation status and transcript abundance. Collectively, this study provides a comprehensive integrative analysis of DNA methylation and transcriptome reprogramming in ‘Shine Muscat’ grapevine under salt stress, revealing potential epigenetic mechanisms involved in transcriptional regulation and salt adaptation. The identified candidate genes provide valuable targets for further functional validation and genetic improvement of grapevine salt tolerance. Full article

Efficient rooting is essential for the propagation of grape rootstocks. This study aimed to identify an effective rooting formulation for hardwood cuttings and to investigate its underlying physiological and molecular mechanisms. Seven grape rootstocks were treated with indole-3-butyric acid (IBA) combined with melatonin (MLT) or citric acid (CA), with IBA plus naphthaleneacetic acid (NAA) and water serving as controls. Rooting performance was comprehensively evaluated using morphological traits, physiological characteristics, endogenous hormone contents, and transcriptome analysis. Among all treatments, 400 mg/L IBA combined with 1.2 mM MLT exhibited the best rooting performance. This treatment significantly enhanced root activity, soluble sugar, and soluble protein contents. It also increased IAA and GA₃ levels and improved the IAA/ABA and GA₃/ABA ratios compared with the controls. Transcriptome analysis of ‘110R’ revealed that MLT-responsive genes were mainly enriched in plant–pathogen interaction, hormone signal transduction, and MAPK signaling pathways. Transcription factor families including MYB, ERF, and NAC were identified as potential regulators. Collectively, these findings demonstrate that IBA–MLT combined application promotes rooting by regulating physiological metabolism, hormone balance, and gene expression, providing a theoretical basis for improving grape propagation efficiency. Full article

Safflower (Carthamus tinctorius L.) is an economically important crop, and heat stress has become a major environmental constraint that limits its growth and development under global climate change. However, the molecular mechanisms underlying its response to heat stress remain poorly understood. Here, transcriptome sequencing was performed on safflower leaves exposed to heat stress (42 °C) for 0, 1, 2, 4, 8, and 12 h, with three biological replicates per time point. Compared with the control (0 h), a total of 12,964 differentially expressed genes (DEGs) were identified across the five time points (1, 2, 4, 8, and 12 h) using criteria of |log₂ (fold change)| ≥ 1 and false discovery rate (FDR) < 0.05, of which 1097 were common to all comparisons. KEGG enrichment analysis of these DEGs across all five comparison groups consistently showed significant enrichment in plant hormone signal transduction and the MAPK signaling pathway. Furthermore, a total of 750 transcription factors (TFs) were identified as differentially expressed across the five comparison groups, of which 99 were common to all comparisons, with the bHLH, MYB, WRKY, and HSF families being the most abundant. Weighted Gene Co-expression Network Analysis (WGCNA) identified five modules that were significantly associated with different heat stress time points. Furthermore, 13 hub genes were identified as potential targets for future functional studies on heat tolerance in safflower. The reliability of the RNA-seq data was confirmed by qRT-PCR validation of selected hub genes. Notably, a non-specific serine/threonine protein kinase (CtAH03G0292100) from the MEred module, which is also involved in plant hormone signal transduction, emerged as a promising candidate gene for heat tolerance. Collectively, these findings provide candidate genes for future functional studies aimed at further elucidating the mechanisms of heat tolerance in safflower. 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