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At least 19 recordsLinked to original sources

PubMed2026

Integrated phenotype, endogenous hormones and transcriptome analysis revealed the mechanism of response of Phoebe bournei seedlings to shade signals.

Understory tree seedlings are subjected to prolonged shading stress imposed by the canopy foliage, which significantly impedes their growth. A hallmark of shaded environments is a reduced red to far-red light ratio (R: FR). This study elucidates the physiological and molecular responses of the endangered tree species Phoebe bournei to shading signals. Seedlings were exposed to white light (control) and simulated shading environments with R: FR ratios of 1.5, 0.8, and 0.2. The findings reveal that an increase in the proportion of far-red light significantly enhances seedling height, root-collar diameter, internode length, petiole length, leaf surface area, and leaf biomass. Differentially expressed genes (DEGs) in each treatment group predominantly enrich pathways associated with hormone signaling, stress responses, and photosynthesis. Validation experiments demonstrate that shading promotes the activity of Rubisco and RCA enzymes, total chlorophyll (Chl) accumulation, and elevated levels of hormones including indole-3-acetic acid (IAA), gibberellic acid (GA3), salicylic acid (SA)/methyl salicylate (MeSA), cytokinins (CK), abscisic acid (ABA), and jasmonic acid (JA). Weighted Gene Co-expression Network Analysis (WGCNA) identifies seven hub genes linked to photosynthesis and plant hormone regulation: MYB, KSC, SUAR, CESA POD, CESA, and SAUR. Collectively, shading signals induce P. bournei seedlings to elongate their stems and petioles, enhance photosynthetic enzyme activity, and accumulate specific hormones, with pertinent genes actively participating in light signal transduction. This research sheds light on the shading response mechanism of P. bournei, providing a robust theoretical framework for the breeding of shade-tolerant trees and the conservation of endangered species.

Transcriptome↗

PubMed2026

A CqbZIP55-CqPIF3 regulatory module associated with light-responsive flavonoid biosynthesis during quinoa seedling de-etiolation.

Quinoa (Chenopodium quinoa) is an emerging leafy vegetable and microgreen crop rich in health-promoting flavonoids, yet the regulatory mechanisms linking light perception to early metabolic adaptation remain unclear. Here, we integrated phenotypic, transcriptomic, metabolomic, and molecular analyses to investigate early de-etiolation responses in quinoa seedlings. Short-term light exposure rapidly promoted seedling establishment and induced transcriptional programs associated with photosynthesis, carbon metabolism, hormone signaling, and flavonoid biosynthetic gene expression, whereas metabolite changes were more limited, indicating temporal uncoupling between transcriptional activation and metabolic accumulation. Genome-wide bZIP analysis identified CqbZIP55 as a light-responsive regulator that directly binds and activates the CqCHS promoter. CqPIF3 also bound the CqCHS promoter and showed stronger transactivation activity than CqbZIP55 in transient reporter assays. Protein interaction and dual-luciferase assays showed that CqbZIP55 physically interacts with CqPIF3 and modulates CqPIF3-associated promoter activity. Exogenous quercetin upregulated CqbZIP55 and prolonged CqCHS expression, suggesting a candidate metabolite-associated reinforcement mechanism. Together, these findings support functional interplay between CqbZIP55 and CqPIF3 in light-responsive regulation of flavonoid biosynthetic gene expression in quinoa seedlings, while further quinoa-based perturbation and in vivo promoter-occupancy assays are required to establish their physiological role in planta. This study provides a framework for further investigation of photoprotective metabolic regulation in quinoa.

Chenopodium quinoa↗

PubMed2026

Isolation and genomic characterization of Bacillus X32: a potent phosphate-solubilizing bacterium with growth-promoting effects on navel orange seedlings.

Phosphorus is an essential element for plant growth. However, in nature, most phosphorus exists in the form of insoluble compounds that plants cannot directly absorb, leading to phosphorus deficiency in agricultural systems. With increasing demand for economic crops such as citrus and the decline in soil fertility due to current management practices, there is a growing need for environmentally friendly fertilizers to improve and restore soil conditions. In this study, a highly efficient phosphate‑solubilizing strain X32 was isolated from the rhizosphere soil of Gannan navel oranges. Systematic genomic analysis identified it as a putative novel species within the genus Bacillus, showing the closest phylogenetic relationship to Bacillus spizizenii. However, both the average nucleotide identity (ANI = 93.18%) and digital DNA‑DNA hybridization (dDDH = 50.4%) values fell below the established thresholds for species delineation, indicating significant genomic differentiation. Whole‑genome sequencing further revealed that strain X32 harbors multiple functional genes potentially related to phosphorus metabolism, including inorganic phosphate‑solubilizing genes (e.g., gdh and gltA), phosphate transport genes (e.g., glpT, pstA, pstB, pstC), and phosphorus mineralization genes (e.g., phoA, phoD). Pot experiment results demonstrated that inoculation with strain X32 significantly promoted the growth of navel orange seedlings, as evidenced by marked increases in both aboveground and belowground fresh and dry weights, as well as plant height. Additionally, strain X32 significantly enhanced the activities of antioxidant enzymes (SOD, CAT, POD) and regulated the content of chlorophyll b in seedling leaves, these changes suggest that strain X32 may enhance stress resistance in plants and influence photosynthetic pigment composition, though direct measurements of photosynthetic performance are needed for confirmation. This study provides a theoretical basis for developing microbial fertilizers with efficient phosphorus solubilization and plant growth-promoting functions, which may help reduce dependence on phosphorus fertilizers and promote sustainable agricultural development.

Phosphates↗

PubMed2026

Genomic and genetic dissection underlying seedling drought resilience in oats.

Drought threatens global crop yields, and common oat, a vital nutritional source for food and feed, is particularly constrained in the semi‑arid regions where it is widely cultivated. Here, we report two high-quality genome assemblies for drought-resilient (Borris37) and drought-sensitive (XymC06) oat accessions with distinct seedling survival rates and genome sizes of 10.92 Gb and 10.96 Gb, and construct comprehensive landscapes of insertion‑deletions (InDels) and structural variants (SVs). Integrating population-level genomic, transcriptomic and phenotypic (seedling survival rate), we demonstrate that InDels and SVs underpin divergent drought resilience and identify 52 candidate genes associated with drought resistance whose expression is significantly modulated by these variants. Borris37 accumulates 36 favorable alleles of these genes. An InDel in the AsNF-YB3 promoter enhances binding to AsARF1, upregulating AsNF‑YB3 under drought, and overexpression of AsNF‑YB3 reduces ROS accumulation. Our findings provide resources and targets for drought‑resistance breeding in oat, thereby supporting global food security.

Drought Resistance↗

PubMed2026

EST-SSR based genetic polymorphism among Lablab (Lablab purpureus L. Sweet) accessions contrasting for drought stress at seedling stage.

Lablab is a multipurpose and the most drought-tolerant (DT) crop compared with its relatives. Despite its potential, Lablab is still an underutilized crop with a lack of improved varieties in many countries. The DT (D349, D147, HA4, D363, D352, D359, D348, D311, D55 and D250) and drought-susceptible (DS) (D271, D66, D106, D6, D26, D255, D28, D186, D95, and D258) accessions were earlier identified according to their morphological and biochemical responses to moisture stress at the seedling stage. These accessions were used to establish genetic polymorphism among the accessions contrasting for drought stress based on the Expressed Sequence Tag-Simple Sequence Repeats (EST-SSR) markers. The CTAB protocol was employed for the genomic DNA extraction. After DNA quality and quantity verification, the PCR was conducted using 16 EST-SSR primer pairs specific to the Lablab. The products were separated through the horizontal polyacrylamide gel electrophoresis (hPAGE). Discriminating ability of the markers and primers' efficiency were evaluated based on various genetic parameters. Principal Coordinate Analysis (PCoA) was performed to estimate the distance matrix among the population and among the accessions. While cluster analysis was processed to trace the genetic relationship among the accessions, dendrogram was constructed to decipher their genetic relationship. Analysis of Molecular Variance (AMOVA) was finally computed to quantify the diversity level and genetic relationship among the population, and among the accessions. A low polymorphism (GD = 0.19) was observed between the DT and DS accessions, likely due to limited discriminatory power of the EST-SSR markers. However, the PCoA, cluster analysis and AMOVA identified DT (D147, HA4, and D349) and DS (D106, D95, and D271) accessions as strongly contrasting populations under drought stress, with D147, HA4, D349, D363, D359, D352, and D348 further recommended as DT accessions. Given the low polymorphism observed, further validation using more informative molecular markers and advanced genomic approaches is recommended to improve the identification of drought-tolerance genes and related QTLs to support Lablab breeding programs.

Expressed Sequence Tags↗

PubMed2025

NAM and CUC3 boundary genes maintain shoot apical meristem viability and suppress the development of axillary shoot in rice seedlings.

Cell division and differentiation within the shoot apical meristem (SAM) are essential for the morphogenesis of aboveground plant organs. This study reveals that the boundary genes OsNAM and OsCUC3 collaboratively maintain SAM activity. Loss of function in both OsNAM and OsCUC3 during the fourth leaf stage reduced SAM size, with the osnam oscuc3 mutant exhibiting abnormal leaf number and morphology. Furthermore, OsNAM and OsCUC3 inhibited the growth of axillary shoots. In the osnam oscuc3 mutant, the number of new leaves decreased, while buds in the coleoptile and the axil of the first leaf developed into tillers. Since OsNAM and OsCUC3 are involved in regulating both SAM activity and the growth of lateral shoots, we examined their expression patterns at the base of the main shoot. β-Glucuronidase (GUS) reporter activity and GFP reporter lines demonstrated that OsNAM and OsCUC3 have distinct expression patterns. Specifically, OsNAM was expressed throughout the SAM, whereas OsCUC3 was expressed only at the base of the SAM, with its expression gradually decreasing as seedlings develop. RNA sequencing analysis showed that the expression of genes related to leaf epidermal cell development, cell wall components, and hormonal signal transduction was altered in response to the loss of function of OsNAM and OsCUC3. Therefore, the boundary genes OsNAM and OsCUC3 not only inhibit the growth of axillary shoots but also regulate the development of aboveground organs, including leaf morphology and number, by maintaining the SAM activity in the main shoot.

Meristem↗

PubMed2026

Experimental and genomic evidence clarifies the mycorrhizal helper role of a widespread bacterium in Bishop pine forests.

Whether a widespread bacterial strain of Paraburkholderia can enhance the physiological responses of ectomycorrhizal fungi (EcMF) and host Bishop pine seedling growth remains unclear. We developed a 'top-down meets bottom-up' approach that harmonized data from molecular field surveys, experimental forest soil manipulations, statistical interaction models, metabolomics studies, bacterial isolations, controlled growth chamber experiments, and comparative genomics analyses to test the direction and strength of Paraburkholderia-EcMF interactions on host seedling physiology and identify potential mechanisms that support these tripartite interactions. Paraburkholderia sp. D1E increased host root colonization of Suillus pungens - a keystone EcMF taxon for seedling establishment. Paraburkholderia-Suillus co-inoculations also often drove additive seedling growth responses (e.g. biomass and foliar chemistry) and generated nonadditive, positive effects on seedling shoot height. Genomic comparisons identified low chitin and high arabinitol utilization potential as distinguishing features of Paraburkholderia-EcMF symbioses. Our analyses provide experimental evidence, genomic resources, and cross-data validation that highlight potential mechanisms involved in a widespread bacteria-EcMF-tree interaction. Given the diversity of bacteria and fungi in the rhizosphere, however, this approach should continue to be applied to other species combinations to generalize interaction mechanisms among bacterial, fungal, and plant partners.

Paraburkholderia↗

PubMed2025

Balancing nutrient remobilization and photosynthesis: proteomic insights into the dual role of lupin cotyledons after germination.

Efficient nutrient mobilization from seed storage tissues is essential for seedling establishment, particularly in legumes such as Lupinus albus (white lupin), which thrive in nutrient-poor soils. This study investigates the role of cotyledons in nitrogen (N) and mineral remobilization after germination during their transition from storage organs to photosynthetically active tissues, including the metabolic challenges posed by the coexistence of these two functions in epigeal germination. We cultivated white lupin seedlings under nitrogen-deficient conditions, analyzing cotyledon composition and function over 28 days. Our results indicate that 60% of cotyledon-stored proteins are degraded within the first 8 days, with free amino acids transiently accumulating before being redistributed to support growth. The progressive depletion of cotyledon reserves was accompanied by structural and metabolic changes, including an increase in photosynthetic proteins. However, cotyledon photosynthetic capacity remained lower than that of true leaves, suggesting a transient role in energy metabolism. The loss of cotyledons before day 12 significantly impaired seedling development, emphasizing their critical contribution to nitrogen, phosphate, and micronutrient supply during early growth. Comparative proteomic analysis revealed dynamic shifts in nutrient transport, amino acid metabolism, and stress response pathways following cotyledon removal. These findings underscore the significance of cotyledon nutrient remobilization in legume adaptation to low-fertility soils and highlight potential targets for breeding strategies aimed at improving nutrient use efficiency. By optimizing cotyledon nutrient composition and function, future breeding efforts could enhance seedling vigor, reduce fertilizer dependency, and improve the nutritional value of lupin-based foods.

Lupinus↗

PubMed2025

A PIF-regulated switch in cell axis growth drives cotyledon expansion through tissue-specific cell expansion and division.

Despite its crucial role during seedling deetiolation, cotyledon expansion has been largely overlooked, with hypocotyl elongation favored as the primary phenotypic readout in light signaling research. Here, we investigate how cotyledon expansion is regulated during seedling establishment and reveal that light-induced cotyledon expansion involves a rapid switch in growth direction - from longitudinal in darkness to transversal upon initial light exposure. Using PIFq- and phyA/phyB-deficient Arabidopsis mutants, we demonstrate that this switch is repressed by PIFs in the dark and promoted by phytochromes under red light. Notably, expansion is antagonistically regulated in the light by GUN1-mediated plastid retrograde signaling. Cotyledon expansion involves rapid epidermis cell expansion, transitioning from rectangular in darkness to characteristic lobed cells in light. Importantly, our findings show that mesophyll extension is driven not only by cell enlargement but also by palisade cell division, consistent with an enrichment of cell cycle-related genes that are antagonistically regulated by the PIF/phy system and retrograde signaling in the cotyledon. Finally, using mutant lines expressing PIF1 and phyB specifically in the epidermis, we establish that epidermal expansion can drive palisade cell growth, while mesophyll cell division is predominantly regulated by light at the tissue-specific level. This study provides a novel framework for investigating cotyledon expansion during seedling deetiolation, incorporating tissue-level regulation. We propose that cotyledons serve as an excellent model for studying morphogenesis and organ geometry, which in plants is governed by directional cell growth.

Cotyledon↗

PubMed2026

Exogenous gibberellin promotes lateral branch development in stumping Pinus yunnanensis by regulating endogenous hormones and TCP genes.

While plant stumping can break apical dominance, promote lateral branching, and thereby increase yield, a significant technical challenge remains in further enhancing the coppicing regrowth capacity after stumping. This study used one-year-old Pinus yunnanensis Franch seedlings as subjects. Through exogenous application of gibberellin 3 (GA3) and Paclobutrazol (PAC), it investigated the regulatory role of gibberellin (GA) in sprouting and identified TCP genes related to branching within the GA pathway. Results indicate that exogenous hormone treatments altered endogenous hormone levels in P. yunnanensis seedlings. Exogenous GA3 treatment significantly increased endogenous IPA, ABA, GA3, GA1, SA, and SAG content. Correlation analysis with sprout number revealed a positive relationship between endogenous hormones and sprout number, indicating that exogenous GA3 significantly influenced sprout number. After hormone application, the cumulative number of sprouts increased with seedling age across all treatments. Therefore, to further investigate whether changes in sprout number were caused by gene alterations in the GA signaling pathway, this study analyzed the GA signaling pathway and its associated transcription factors. Fifteen TCP family members were screened from the P. yunnanensis transcriptome, phylogenetically classified into Class I and Class II subfamilies. Conserved motif sites within the Class II family co-occurred, exhibiting high conservation. Genes from the Class II subfamily were cloned, and their differential expression across various tissues was analyzed via real-time quantitative PCR. Expression patterns under different hormone treatments were also examined. Our results reveal that PyTCP4, PyTCP6, and PyTCP20 are significantly upregulated by PAC (a GA synthesis inhibitor) and show strong negative correlations with sprouts number, while GA3 treatment partially alleviates this effect. These findings provide direct evidence that TCP transcription factors act as repressors of shoot branching, linking their hormone-responsive expression to the regulation of sprouts formation in P. yunnanensis. These results indicate that TCP transcription factors play a crucial role in shoot and root emergence, with their expression influenced by exogenous hormones, thereby affecting the growth and development of emerging shoots and roots. This provides a reference and basis for analyzing the expression patterns and functions of TCP genes in P. yunnanensis, facilitating further research into their functions.

Gibberellins↗

PubMed2026

Mulberry-derived endophytic Bacillus velezensis suppresses gray mold and promotes mulberry growth via reshaping the root metabolism and microbiome.

INTRODUCTION: Gray mold is an important fungal disease caused by Botrytis cinerea which threatens global agriculture. As chemical control faces limitations, biological control using Bacillus has gained attention for its environmental friendliness and growth promotion. However, their ecological basis and application potential in mulberry gray mold control remain insufficiently understood. OBJECTIVE: This study aimed to evaluate the biocontrol efficacy of the mulberry derived endophytic strain Bacillus velezensis ZJU_268 and to investigate its associated effects on plant growth, root-associated microbiomes, and metabolic profiles. METHODS: Greenhouse assays were combined with genomic and comparative genomic analyses, amplicon sequencing, non-targeted metabolomics, and functional validation of isolated microbes and metabolites to assess the effects of ZJU_268 and its cell free supernatant (CFS) on mulberry seedlings. RESULTS: This study isolated a mulberry derived endophytic bacterium, B. velezensis ZJU_268, which exhibits strong antifungal activity and reduces the incidence of gray mold in mulberry seedlings. Whole-genome sequencing and comparative genomic analyses revealed strain-specific regions and genes associated with root colonization, stress adaptation, and antimicrobial biosynthesis. Both live cells and CFS significantly promoted seed germination, seedling growth, and biomass accumulation in a dose dependent manner. Amplicon sequencing showed that ZJU_268 and its supernatant reshaped the mulberry root microbiome, enriching beneficial bacterial and fungal taxa while reducing potentially pathogenic members. Cultivable members of the enriched microbiota displayed strong antifungal activity against B. cinerea and promoted mulberry growth. Metabolomic profiling further showed that ZJU_268 and its supernatant were associated with marked metabolic shifts in mulberry roots, accompanied by the accumulation of selected metabolites that supported the growth of representative enriched isolates. CONCLUSIONS: This study demonstrates that ZJU_268 suppresses gray mold and promotes mulberry growth in association with direct antagonistic activity, microbiome restructuring, and holobiont-level metabolic shifts, providing a promising biological strategy for sustainable mulberry disease management.

Bacillusvelezensis↗

PubMed2026

Pathogenicity of Cadophora luteo-olivacea on Quercus robur and multi-omics characterization of antagonism by Trichoderma atroviride.

Pedunculate oak (Quercus robur L.) is a foundation tree species in European forests and reforestation programs, but nursery propagated seedlings can harbor cryptic trunk diseases pathogens. Cadophora luteo-olivacea, known from grapevine trunk diseases, has been detected in oak nurseries, yet its pathogenicity on oak and interactions with antagonistic fungi remain unclear. We fulfilled Koch's postulates for C. luteo-olivacea isolate CZ_395 on Q. robur seedlings under experimental inoculation conditions and quantified growth reduction of C. luteo-olivacea by Trichoderma atroviride isolate CZ_180 in dual culture. Proteomic and metabolomic profiling of the contact zone was performed at two post contact sampling points, 4 and 8 dpi, to identify candidate molecular signatures associated with the interaction. Inoculated seedlings developed extensive stem lesions (mean 11.9 cm), whereas controls showed minimal wound response (mean 0.9 cm; p < 0.001). In dual culture, T. atroviride reduced the visible colony development and radial growth of C. luteo-olivacea under the tested in vitro conditions. Contact zone proteomics revealed 257 differentially abundant proteins at 8 days, including cell wall targeting hydrolases, secreted proteases, oxidoreductases (44 upregulated), and transporters. Metabolomics detected contact specific changes in amino acids, central carbon intermediates, and lipid-associated features, including reduced ergosterol. This study demonstrates that C. luteo-olivacea can induce necrotic lesions in Q. robur under experimental inoculation conditions and identifies proteomic and metabolomic signatures associated with the interaction between T. atroviride and C. luteo-olivacea, providing a basis for nursery risk assessment and future evaluation of biocontrol potential.

Quercus↗

PubMed2026

Phenotypic, physiological and transcriptomic analysis of graded salt stress responses in Pyrus betulifolia Bunge and functional characterization of the hub gene PbSTY46.

Pyrus betulifolia Bunge is a salt‑tolerant rootstock for pear, but its salt‑tolerance mechanisms remain largely unknown. In this study, P. betulifolia seedlings were subjected to graded NaCl stress at concentrations of 0 (CK), 50 (T1), 100 (T2), and 200 (T3) mM. We integrated phenotypic observation, physiological assessment, transcriptomic profiling, and functional gene validation to systematically elucidate its salt tolerance mechanisms. Salt stress inhibited seedling growth and root traits in a concentration-dependent manner, and T3 caused the most severe damage. Osmotic solutes responded differentially: soluble sugars peaked under T2, while proline peaked under T3. Antioxidant enzymes showed tissue-specific biphasic responses and declined after prolonged T3 stress. Meanwhile, chlorophyll and photosynthesis decreased, whereas anthocyanin increased, indicating a metabolic shift from photosynthesis to photoprotection. Transcriptome analysis revealed distinct responses depending on stress intensity: mild stress induced membrane lipid remodeling, moderate stress activated circadian rhythm and hormone signaling, and severe stress enhanced phenylpropanoid biosynthesis and thiamine metabolism. Gene Set Enrichment Analysis (GSEA) further highlighted progressive enrichment of phenylpropanoid biosynthesis, heme binding, and oxidoreductase activity. Weighted Gene Co‑expression Network Analysis (WGCNA) identified a blue module significantly positively correlated with root traits, from which the hub gene PbSTY46 was identified. Functional validation via overexpression, loss‑of‑function mutants, and pharmacological interventions (MeJA/DIECA) confirmed that PbSTY46 acts through JA signaling to enhance antioxidant enzyme activities and thereby confer salt tolerance. Collectively, P. betulifolia adopts a "survival‑first" strategy that coordinates growth arrest, osmotic homeostasis, and ROS scavenging. These findings establish PbSTY46 as a key regulator that links JA signaling to antioxidant defense. Thus, PbSTY46 represents a promising candidate for marker‑assisted breeding of salt‑tolerant pear cultivars.

Salt Stress↗

PubMed2025

Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.).

Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions.

Eleusine↗

PubMed2025

The SlWRKY39-SlZF61 module synergistically regulates SlGSTU42 to enhance low-temperature tolerance in tomato.

Low-temperature stress affects plant growth, and WRKY transcription factors alleviate such damage by regulating downstream genes. This study found that tomato SlWRKY39 significantly responds to low temperatures: its overexpression enhances seedling low-temperature tolerance by promoting ROS scavenging, while knockout exacerbates ROS accumulation and increases sensitivity to low temperatures. Transcriptome analysis indicated induction of glutathione metabolic pathway genes in slwrky39 plants under low-temperature stress. Y1H, EMSA, and Dual-LUC experiments confirmed that SlWRKY39 specifically binds to and activates the SlGSTU42 promoter; silencing SlGSTU42 attenuated the low-temperature tolerance conferred by SlWRKY39 overexpression, verifying that SlWRKY39 improves low-temperature tolerance via direct regulation of SlGSTU42. Additionally, SlZF61 interacts with SlWRKY39, enhancing its regulatory effect on SlGSTU42. SlZF61 overexpression strengthens low-temperature tolerance, while knockout increases sensitivity to low temperatures. In summary, under low-temperature stress, SlWRKY39 and SlZF61 are upregulated expression in tomato; SlWRKY39 binds to the SlGSTU42 promoter, and SlZF61 interacts with SlWRKY39 to form a protein complex, enhancing this binding. They synergistically activate SlGSTU42 transcription, thereby improving seedling low-temperature tolerance by scavenging ROS. This coordinated regulatory mechanism provides a new theoretical basis and practical insights for enhancing tomato low-temperature tolerance and ensuring stable production under low-temperature stress conditions.

Solanum lycopersicum↗

PubMed2026

Physiological and transcriptomic responses of sunflower to combined saline-alkali stress.

BACKGROUND: Sunflower (Helianthus annuus L.), an important oilseed crop, is often used as a pioneer species for improving saline-alkali soils. However, the molecular mechanisms underlying sunflower seedling responses to combined saline-alkali stress remain unclear. This study aimed to elucidate the molecular basis of saline-alkali tolerance at the seedling stage by comparing physiological and transcriptomic responses between tolerant and sensitive sunflower hybrids. The saline-alkali tolerant hybrid K-27 and the sensitive hybrid K-7 were used as experimental materials. Root samples were collected at 0, 3, 12, 24, 48, and 96 h after exposure to combined saline-alkali stress (0.5% NaCl + Na2CO3, adjusted to pH 9.0). Physiological parameters, including antioxidant enzyme activities, osmolyte contents, ion concentrations, membrane damage levels, and cell wall components, were measured, followed by transcriptome sequencing analysis. RESULTS: Phenotypic analysis showed that the root length inhibition rate and fresh weight loss rate of K-27 were significantly lower than those of K-7, indicating stronger tolerance. Physiological analysis revealed that K-27 exhibited an inducible antioxidant enzyme response pattern. In addition, K-27 achieved osmotic adjustment through sustained proline accumulation (peaking at 12 h and remaining significantly higher than that of K-7 at 96 h) and exhibited higher basal levels of lignin and hemicellulose. Transcriptome analysis showed that the number of upregulated genes in K-27 was consistently higher than in K-7 at all time points, with 5,283 genes upregulated as early as 3 h after stress exposure. Venn analysis identified 44 core differentially expressed genes (cDEGs) shared between the two genotypes, which were mainly enriched in auxin biosynthesis regulation, phenylpropanoid biosynthesis, and glutathione metabolism. Among them, the benzoic acid carboxyl methyltransferase gene (BAMT) was continuously upregulated in K-27 but persistently downregulated in K-7. In addition, five other genes (encoding fatty aldehyde dehydrogenase, pectin methylesterase inhibitor, glutathione S-transferase, INPP5E, and HXXXD-type acyltransferase) exhibited significantly higher expression levels in K-27. CONCLUSION: K-27 tolerates combined saline-alkali stress through coordinated multi-layered response mechanisms, including inducible antioxidant defense, maintenance of ion homeostasis, sustained osmotic adjustment, and activation of the phenylpropanoid metabolic pathway. Candidate genes such as BAMT may provide potential targets for molecular breeding of saline-alkali tolerant sunflower, although their functions require further experimental validation.

Helianthus↗

PubMed2026

Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid.

BACKGROUND: Intraspecific hybridization in allopolyploid plants can generate additive and nonadditive changes in gene expression through interactions between divergent parental genomes. However, how it simultaneously affects gene expression and the relative expression of homoeologs in higher-order polyploids is less well understood. To study this, we sequenced seedling leaf transcriptomes and profiled gene body methylation in two hexaploid wheat (Triticum aestivum L.) cultivars and their F₁ hybrids. RESULTS: Although only 4.3% of genes differed in expression between the parents, 22.3% deviated from mid-parent expression in the hybrids, with many showing transgressive expression. 32.1% of triads contained at least one homoeolog that deviated from mid-parent expression, and all three homoeologs deviated in 11% of triads, substantially more than expected by chance. Triads in which all three homoeologs were overexpressed also showed reduced differences in expression among homoeologs. Greater parental divergence in relative homoeolog expression was associated with nonadditive expression. Genes lacking gene body methylation were also more likely to show dominant or transgressive expression, whereas gene body methylation was associated with more balanced homoeolog expression and additive or conserved expression. CONCLUSIONS: Intraspecific hybridization in hexaploid wheat, even without a change in ploidy, was associated with widespread nonadditive gene expression and altered relative homoeolog expression within triads. These responses were associated with parental differences in homoeolog expression and the absence of gene body methylation. Although our findings are limited to seedling leaves from a single intraspecific cross, they provide a basis for testing the generality of these patterns across tissues, developmental stages, and genetic backgrounds.

Triticum↗

PubMed2025

Construction of cDNA library of Dalbergia odorifera induced by low temperature stress and screening of low temperature tolerant genes.

To systematically analyze the gene function of Dalbergia odorifera, the seedlings of D. odorifera were treated with low-temperature stress for 6 h. Total RNA was extracted from a mixture of seedling roots, stems, and leaves, and a low-temperature-induced D. odorifera yeast cDNA expression library was constructed. The library volume was 1.032 × 108 CFU, and the PCR (Polymerase Chain Reaction) identification of the library bacterial fluid showed that the amplification was around 1000 bp, with a single randomly distributed band, indicating that the library had been recombinantly inserted into the pYES2 vector. The GO (Gene Ontology) analysis showed that the library genes were mainly involved in metabolic and stress signaling pathways. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis showed that the genes were primarily related to energy and metabolic pathways. Twenty-one genes were screened or obtained at -20°C for low-temperature tolerance. In addition, the organ expression profiles of the candidate genes were analyzed based on RNA-seq data, and the expression profiles of the candidate genes under low-temperature stress were also examined. The construction of the yeast library provides genetic resources for the analysis of the mechanism of low-temperature tolerance of D. odorifera, which is important for comprehending and utilizing the genetic resources of D. odorifera.

Gene Library↗