Search Results (146)

Quinoa (Chenopodium quinoa), a stress-tolerant pseudocereal ideal for studying abiotic stress responses, was used to systematically identify optimal reference genes for qPCR normalization under gradient stresses: low temperatures (LT group: −2 °C to −10 °C), heat (HT group: 39° C to 45 °C), and drought (DR group: 7 to 13 days). Through multi-algorithm evaluation (GeNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder) of eleven candidates, condition-specific optimal genes were established as ACT16 (Actin), SAL92 (IT4 phosphatase-associated protein), SSU32 (Ssu72-like family protein), and TSB05 (Tryptophan synthase beta-subunit 2) for the LT group; ACT16 and NRP13 (Asparagine-rich protein) for the HT group; and ACT16, SKP27 (S-phase kinase), and NRP13 for the DR group, with ACT16, NRP13, WLIM96 (LIM domain-containing protein), SSU32, SKP27, SAL92, and UBC22 (ubiquitin-conjugating enzyme E2) demonstrating cross-stress stability (global group). DHDPS96 (dihydrodipicolinate synthase) and EF03 (translation elongation factor) showed minimal stability. Validation using stress-responsive markers—COR72 (LT), HSP44 (HT), COR413-PM (LT), and DREB12 (DR)—confirmed reliability; COR72 and COR413-PM exhibited oscillatory cold response patterns, HSP44 peaked at 43 °C before declining, and DREB12 showed progressive drought-induced upregulation. Crucially, normalization with unstable genes (DHDPS96 and EF03) distorted expression profiles. This work provides validated reference standards for quinoa transcriptomics under abiotic stresses. Full article

Low-temperature stress severely limits plant growth and reduces agricultural productivity. Calmodulin-like (CML) proteins are crucial calcium sensors in plant cold responses. Transcriptome analysis of cold-stressed Saussurea involucrata identified seven differentially expressed CML genes. qRT-PCR confirmed that SiCML6 was strongly induced at 4 °C and −2 °C. Bioinformatics analysis showed that SiCML6 encodes a transmembrane protein containing an EF-hand domain. This protein carries a signal peptide and shows the closest phylogenetic relationship to Helianthus annuus CML3. Its promoter contains ABA, methyl jasmonate (MeJA), and cold-response elements. Arabidopsis plants overexpressing SiCML6 showed significantly higher survival rates at −2 °C than wild-type plants. Under freezing stress, SiCML6-overexpressing lines exhibited reduced malondialdehyde content, relative electrolyte leakage, and ROS accumulation (H₂O₂ and O₂⁻), along with increased proline, soluble sugars, soluble proteins, and total antioxidant capacity (T-AOC). SiCML6 elevated the expression of cold-responsive genes CBF3 and COR15a under normal conditions and further upregulated CBF1/2/3 and COR15a at 4 °C. Thus, low temperatures induced SiCML6 expression, which was potentially regulated by ABA/MeJA. SiCML6 enhances freezing tolerance by mitigating oxidative damage through boosted T-AOC and osmoprotectant accumulation while activating the CBF-COR signaling pathway. This gene is a novel target for improving crop cold resistance. Full article

Asia minor bluegrass (Polypogon fugax), a widespread Poaceae weed, exhibits broad tolerance to abiotic stresses. Validated reference genes (RGs) for reliable RT-qPCR normalization in this ecologically and agriculturally significant species remain unidentified. This study identified eight candidate RGs using transcriptome data from seedling tissues. We assessed the expression stability of these eight RGs across various abiotic stresses and developmental stages using Delta Ct, BestKeeper, geNorm, and NormFinder algorithms. A comprehensive stability ranking was generated using RefFinder, with validation performed using the target genes COR413 and P5CS. Results identified EIF4A and TUB as the optimal RG combination for normalizing gene expression during heat stress, cold stress, and growth stages. EIF4A and ACT were most stable under drought stress, EIF4A and 28S under salt stress, and EIF4A and EF-1 under cadmium (Cd) stress. Furthermore, EIF4A and UBQ demonstrated optimal stability under herbicide stress. Additionally, application of validated RGs revealed higher acetyl-CoA carboxylase gene (ACCase) expression in one herbicide-resistant population, suggesting target-site gene overexpression contributes to resistance. This work presents the first systematic evaluation of RGs in P. fugax. The identified stable RGs provide essential tools for future gene expression studies on growth and abiotic stress responses in this species, facilitating deeper insights into the molecular basis of its weediness and adaptability. Full article

Leymus chinensis (Trin.) Tzvel., a vital native forage grass in northern China for ecological restoration and livestock production, faces severe yield losses and grassland degradation due to rust (Puccinia spp.) infection. Current control strategies, reliant on chemical interventions, are limited by evolving resistance risks and environmental concerns, while rust-resistant breeding remains hindered by insufficient molecular insights. To address this, we systematically evaluated rust resistance in 24 L. chinensis germplasms from diverse geographic origins, identifying six highly resistant (HR) and five extremely susceptible (ES) genotypes. Integrating transcriptomics and metabolomics, we dissected molecular responses to Puccinia infection, focusing on contrasting HR (Lc71) and ES (Lc5) germplasms at 48 h post-inoculation. Transcriptomic analysis revealed 1012 differentially expressed genes (DEGs: 247 upregulated, 765 downregulated), with enrichment in cell wall biosynthesis and photosynthesis pathways but suppression of flavonoid synthesis. Metabolomic profiling identified 287 differentially accumulated metabolites (DAMs: 133 upregulated, 188 downregulated), showing significant downregulation of pterocarpans and flavonoids in HR germplasms, alongside upregulated cutin synthesis-related metabolites. Multi-omics integration uncovered 79 co-enriched pathways, pinpointing critical regulatory networks: (1) In the nucleotide metabolism pathway, genes Lc5Ns011910, Lc1Xm057211, and Lc4Xm043884 exhibited negative cor-relations with metabolites Deoxycytidine and Cytosine. (2) In flavonoid biosynthesis, Lc2Xm054924, Lc4Xm044161, novel.8850, Lc2Ns006303, and Lc7Ns021884 were linked to naringenin and naringenin-7-O-glucoside accumulation. These candidate genes likely orchestrate rust resistance mechanisms in L. chinensis. Our findings advance the molecular understanding of rust resistance and provide actionable targets for breeding resilient germplasms. Full article

Plants are frequently exposed to various abiotic stresses, among which low-temperature stress markedly impairs growth and physiological functions. WRKY transcription factors are key regulators in plant responses to abiotic stress. In this study, a novel WRKY transcription factor gene, TrWRKY79, was cloned from white clover. Functional characterization revealed that the full-length TrWRKY79 protein possesses typical features of transcription factors, including transcriptional activation activity located at its C-terminal domain. Heterologous expression of TrWRKY79 in Arabidopsis thaliana significantly enhanced cold tolerance under low-temperature stress. Physiological assays showed that the transgenic lines exhibited higher chlorophyll content and elevated activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) compared to wild-type plants. Furthermore, Protenix was employed to predict the potential target genes of TrWRKY transcription factors, and their expression profiles were analyzed to help elucidate the regulatory network underlying cold tolerance. qRT-PCR analysis confirmed that several cold-responsive genes, such as COR47 and ABI5, were significantly upregulated in the transgenic lines. Collectively, these findings indicate that TrWRKY79 plays a positive regulatory role in enhancing cold tolerance, providing valuable insights into the molecular mechanisms of cold resistance in white clover and offering promising candidate genes for improving stress resilience in forage crops. Full article

Background: Bambusaoldhamii is an important economic bamboo species. However, flowering occurred after its introduction and cultivation, resulting in damage to the economy of bamboo forests. Currently, the molecular mechanism of flowering induced by introduction stress is still unclear. This study systematically explored the key genes and regulatory pathways of flowering in Bambusaoldhamii under introduction stress through field experiments combined with transcriptome sequencing and weighted gene co-expression network analysis (WGCNA), with the aim of providing a basis for flower-resistant cultivation and molecular breeding of bamboo. Results: The study conducted transcriptome sequencing on flowering and non-flowering Bambusaoldhamii bamboo introduced from Youxi, Fujian Province for 2 years, constructed a reference transcriptome containing 213,747 Unigenes, and screened out 36,800–42,980 significantly differentially expressed genes (FDR < 0.05). The results indicated that the photosensitive gene CRY and the temperature response gene COR413-PM were significantly upregulated in the flowering group; the expression level of the heavy metal detoxification gene MT3 increased by 27.77 times, combined with the upregulation of the symbiotic signaling gene NIN. WGCNA analysis showed that the expression level of the flower meristem determination gene AP1/CAL/FUL in the flowering group was 90.38 times that of the control group. Moreover, its expression is regulated by the cascade synergy of CRY-HRE/RAP2-12-COR413-PM signals. Conclusions: This study clarifies for the first time that the stress of introducing Bambusaoldhamii species activates the triad pathways of photo-temperature signal perception (CRY/COR413-PM), heavy metal detoxification (MT3), and symbiotic regulation (NIN), collaboratively driving the AP1/CAL/FUL gene expression network and ultimately triggering the flowering process. Full article

Global climate change is leading to more frequent extreme cold events, underscoring the need to study citrus cold tolerance to support breeding and enable potential northward expansion of citrus cultivation. In this study, the ‘Miyagawa’ wild type and its cold-tolerant mutant were selected for systematic comparison across cold-resistant phenotypes, leaf tissue structure, physiological and biochemical characteristics, and Cor8 gene expression. The mutant exhibited 50% lower relative conductivity and malondialdehyde (MDA) content under −6 °C stress compared to the wild type, indicating reduced membrane damage. Antioxidant enzyme activities were significantly higher in the mutant: superoxide dismutase (SOD) activity increased by 10–30%, peroxidase (POD) by 28%, and catalase (CAT) by up to 2-fold. Proline content was 57% higher in the mutant at peak levels, supporting stronger osmotic regulation. Moreover, Cor8 gene expression in the mutant was up to 2.98 times higher than in the wild type during natural overwintering. These findings confirm that the ‘Miyagawa’ mutant possesses distinct physiological, anatomical, and molecular advantages for low-temperature adaptation and provides valuable germplasm for breeding cold-tolerant citrus varieties. Full article

Cold stress adversely impacts tomato (Solanum lycopersicum) production, particularly in temperate regions, by impairing growth, development, and yield. Abscisic acid (ABA), a key phytohormone, plays a central role in mediating tomato’s response to cold stress through a complex crosstalk network with other hormones and signaling molecules. This review examines ABA’s interactions with hormones such as ethylene, jasmonates, auxin, gibberellins, salicylic acid, brassinosteroids, and strigolactones, as well as signaling molecules like hydrogen peroxide, nitric oxide, hydrogen sulfide, and calcium. These interactions regulate various physiological processes, including osmolyte accumulation, membrane stability, and oxidative stress mitigation, and influence the expression of cold-responsive genes, such as CBFs, COR, and LEA. Critical knowledge gaps remain, particularly in understanding ABA’s context-specific interactions with other hormones and the integration of calcium signaling with ABA pathways under cold stress. By synthesizing current research, this review enhances our understanding of tomato’s cold stress response and provides insights for genetically improving cold tolerance, supporting sustainable tomato production amid climate challenges. Full article

The CorA/MRS2-type transporters represent a crucial family of magnesium ion transporters widely distributed in plants. Through comprehensive screening and alignment using the Phytozome database, we identified seven magnesium-related MdMRS2 Confirm the deletion of the “Chinese Province” column in the address. genes in apple (MdMRS2-1 to MdMRS2-7), which were distributed across seven distinct chromosomes. Phylogenetic analysis classified these genes into five distinct clades. Tissue-specific expression profiles revealed the differential expression patterns of MdMRS2 members in different tissues such as the apple roots, stems, leaves, seedlings, seeds, flowers, and fruits. Among them, the expression level of MdMRS2-5 was the highest in fruits, while that of MdMRS2-6 was the lowest in seeds. Analysis of cis-regulatory elements in MdMRS2 promoter regions identified numerous light-responsive elements, MYB binding sites, and hormone-responsive elements, suggesting their transcriptional regulation may be influenced by related metabolic pathways or signaling molecules. qRT-PCR results showed that the relative expression levels of all genes were significantly upregulated compared with CK under M3 treatment, while there were no significant differences in other treatments. Among them, the upregulation of MdMRS2-7 was the most significant, increasing by 142% compared with CK. Notably, all MdMRS2 genes were significantly upregulated under 4 mmol·L⁻¹ MgSO₄ treatment. Subcellular localization experiments conducted in tobacco leaves confirmed the membrane and cytoplasmic distribution of these transporters, consistent with bioinformatic predictions. These genes may become candidate genes for subsequent functional studies. This work will provide a basis for future research on the response mechanism and function of the MRS2 gene family in response to magnesium stress. Full article

Quinoa (Chenopodium quinoa Willd.) has been widely grown as a cash crop. However, the molecular mechanism by which it responds to cold stress at the seed germination stage is still largely unknown. In this study, we performed a comparative transcriptomic analysis between the cold-tolerant cultivar XCq and cold-sensitive cultivar QCq in response to cold stress. A total number of 4552 and 4845 differentially expressed genes (DEGs) were identified in XCq and QCq upon the treatment of cold stress, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that the mitogen-activated protein kinase (MAPK) signaling pathway was identified only among the up-regulated DEGs in XCq.The expression of DEGs, which encoding transcription factors, such as AP2/ERF, bHLH, bZIP, MYB, ICEs, and CORs related to cold response, were higher in XCq than in QCq in response to cold stress. Weighted gene co-expression network analysis (WGCNA) showed that DEGs clustered in the co-expression modules positively correlated with the factors of quinoa variety and temperature were significantly enriched in the oxidative phosphorylation metabolic pathway. Further physiochemical analyses showed that the activities of superoxide dismutase and peroxidase as well as the contents of soluble protein and sugar, were significantly higher in XCq than in QCq. In summary, MAPK signaling and oxidative metabolism were the key pathways in quinoa upon cold stress. Our findings revealed that the enhanced activities of antioxidant enzymes alleviate the lipid peroxidation of membranes and promote the accumulation of osmotic adjustment substances, thereby enabling seeds to better resist oxidative damage under cold stress. Full article

The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis. Full article

The oat is a crop and forage species with rich nutritional value, capable of adapting to various harsh growing environments, including dry and poor soils. It plays an important role in agricultural production and sustainable development. However, the molecular mechanisms underlying the responses of oat to drought stress remain unclear, warranting further research. In this study, we conducted a pot experiment with the drought-resistant cultivar JiaYan 2 (JIA2) and water-sensitive cultivar BaYou 9 (BA9) during the booting stage under three water gradient treatment conditions: 30% field capacity (severe stress), 45% field capacity (moderate stress), and 70% field capacity (normal water supply). After 7 days of stress, root samples were collected for transcriptome and proteome analyses. Transcriptome analysis revealed that under moderate stress, JIA2 upregulated 1086 differential genes and downregulated 2919 differential genes, while under severe stress, it upregulated 1792 differential genes and downregulated 4729 differential genes. Under moderate stress, BA9 exhibited an upregulation of 395 differential genes, a downregulation of 669, and an upregulation of 886 differential genes, and it exhibited 439 downregulations under severe stress. Under drought stress, most of the differentially expressed genes (DEGs) specific to JIA2 were downregulated, mainly involving redox reactions, carbohydrate metabolism, plant hormone signal regulation, and secondary metabolism. Proteomic analysis revealed that in JIA2, under moderate stress, 489 differential proteins were upregulated and 394 were downregulated, while 493 differential proteins were upregulated and 701 were downregulated under severe stress. In BA9, 590 and 397 differential proteins were upregulated under moderate stress, with 126 and 75 upregulated differential proteins under severe stress. Correlation analysis between transcriptomics and proteomics demonstrated that compared with no drought stress, four types of differentially expressed proteins (DEPs) were identified in the JIA2 differential gene–protein interaction network analysis under severe stress. These included 13 key cor DEGs and DEPs related to plant hormone signal transduction, biosynthesis of secondary metabolites, carbohydrate metabolism processes, and metabolic pathways. The consistency of gene and protein expression was validated using qRT-PCR, indicating their key roles in the strong drought resistance of JIA2. Full article

The C-repeat binding factors (CBFs) gene is essential for plants’ cold response, which could not only be induced by the inducer of CBF expression (ICE) genes but also activated the expression of the cold-regulated (COR) gene, thereby participating in the ICE-CBF-COR cold response pathway. However, this gene family and its functions in Actinidia arguta remain unclear. In this study, whole-genome identification and functional analysis of CBF family members in A. arguta were performed. Eighteen CBF genes, which were located on four chromosomes and had five tandem repeats, were identified. The proteins encoded by the genes were predicted to be located in the nucleus and cytoplasm. The results of the promoter cis-acting element analysis revealed light response elements, low-temperature response elements, and hormone (methyl jasmonate, gibberellin, salicylic acid, etc.) response elements. We analyzed collinearity with other kiwifruit genomes, and, interestingly, the number of CBF family members differed across geographic locations of A. arguta. RT-qPCR revealed that the expression of the CBF gene family differed under low-temperature treatment; specifically, we observed differences in the expression of all the genes. Based on phylogenetic relationships and RT-qPCR analysis, the expression of AaCBF4.1 (AaCBF4) was found to be highly upregulated, and the function of this gene in cold resistance was further verified via overexpression in transgenic Arabidopsis. AaCBF4-overexpressing plants showed higher tolerance to cold stress, showing a higher germination rate, higher chlorophyll content and lower relative electrolyte leakage. In addition, compared with the wild-type Arabidopsis, the overexpressing plants exhibited significantly reduced oxidative damage due to the reduction in reactive oxygen species production under cold stress. Therefore, AaCBF4 plays an important role in improving the cold resistance of Actinidia arguta and can be further used to develop kiwifruit germplasm resources with strong cold resistance. Full article

Low-temperature stress, including chilling and freezing injuries, significantly impacts plant growth in tropical and temperate regions. Plants respond to cold stress by activating mechanisms that enhance freezing tolerance, such as regulating photosynthesis, metabolism, and protein pathways and producing osmotic regulators and antioxidants. Membrane stability is crucial, with cold-resistant plants exhibiting higher lipid unsaturation to maintain fluidity and normal metabolism. Low temperatures disrupt reactive oxygen species (ROS) metabolism, leading to oxidative damage, which is mitigated by antioxidant defenses. Hormonal regulation, involving ABA, auxin, gibberellins, and others, further supports cold adaptation. Plants also manage osmotic balance by accumulating osmotic regulators like proline and sugars. Through complex regulatory pathways, including the ICE1-CBF-COR cascade, plants optimize gene expression to survive cold stress, ensuring adaptability to freezing conditions. This study reviews the recent advancements in genetic engineering technologies aimed at enhancing the cold resistance of agricultural crops. The goal is to provide insights for further improving plant cold tolerance and developing new cold-tolerant varieties. Full article

Background: Phospholipase A (PLA) enzymes catalyze the hydrolysis of glycerophospholipids, releasing free fatty acids and lysophospholipids that play vital roles in plant growth, development, and stress responses. Methods: This study identified and analyzed SlPLA genes through bioinformatics and further explored the function of PLA genes under cold stress through virus-induced gene silencing (VIGS) experiments. Results: This study systematically characterized the SlPLA gene family in tomato, identifying 80 genes distributed across 12 chromosomes. Phylogenetic analysis categorized these genes into three groups: pPLA, PLA1, and PLA2. Conserved motifs and gene structure analysis revealed distinct patterns, with some genes lacking untranslated regions (UTRs), which suggests functional diversification. Promoter analysis indicated that SlPLA genes are regulated by light, hormones, and stress-related elements, particularly cold stress. RNA-seq data and qRT-PCR results indicated the differential expression of SlPLA genes across various tissues in tomato cultivars (Heinz and Micro-Tom). Under cold stress, certain SlPLA genes, especially SlPLA1-2, were up-regulated, suggesting their involvement in cold tolerance. Silencing SlPLA1-2 resulted in increased membrane damage, elevated malondialdehyde (MDA) levels, higher electrolyte leakage, and a lower expression of cold-responsive genes within the ICE1-CBF-COR pathway and jasmonic acid (JA) biosynthesis. Conclusions: This study discovered 80 SlPLA genes in tomato across 12 chromosomes, categorizing them into pPLA, PLA1, and PLA2 via phylogenetic analysis. The qRT-PCR analysis identified that SlPLA1-2 was strongly induced by cold stress, and further experiments regarding genetics and physiology revealed that SlPLA1-2 boosts the cold tolerance of tomato by affecting the CBF signaling pathway and JA biosynthesis, offering insights for future stress-resilience breeding. Full article