The WRKY transcription factors (TFs) are key regulators of plant responses to biotic and abiotic stresses. However, their roles in Amaranthus palmeri remain unexplored. In this study, 32 ApWRKYs were identified through bioinformatics and gene expression analyses. Subcellular localization predictions placed ApWRKYs in the nucleus, and transient expression assays of ApWRKY2 and ApWRKY5 confirmed nuclear targeting, supporting their role as transcriptional regulators. ApWRKYs are distributed across 15 genomic scaffolds, and phylogenetic analysis grouped them into three subfamilies, with conserved motifs identified within specific clades. Interaction analysis suggested potential post-transcriptional regulation by miRNAs. Gene expression profiling of ApWRKYs under glufosinate ammonium, NaCl, and PEG-induced osmotic stress treatments revealed potential distinct regulatory roles. Furthermore, transient overexpression in Arabidopsis thaliana found that ApWRKY1, ApWRKY2, and ApWRKY5 potentially regulate chlorophyll fluorescence and photosynthetic efficiency under glufosinate treatment. These findings establish ApWRKYs as central regulators of stress adaptation in A. palmeri, provide novel insights into WRKY-mediated regulation, and lay a foundation for future functional investigations aimed at enhancing stress resilience and herbicide management in horticultural systems.

Fusarium head blight (FHB), caused by Fusarium graminearum, is a fungal disease that severely affects wheat. The mycotoxins it produces, such as deoxynivalenol (DON), pose serious risks to human and animal health. In this study, a biocontrol strain, LYH8, was isolated from local sources in Jingzhou, Hubei Province. Plate confrontation assays demonstrated that LYH8 effectively inhibited the mycelial growth of F. graminearum, with an inhibition rate of 43%, and induced morphological abnormalities such as hyphal swelling and shrinkage. Based on 16S rRNA and gyrB gene sequencing and phylogenetic analysis, LYH8 was identified as Bacillus velezensis. In vivo experiments showed that disease severity in wheat coleoptiles and spikes was significantly reduced by treatment with LYH8 by 75-85%, and the accumulation of DON and its deoxynivalenol-3-glucoside (D3G) in grains was decreased by 20-22%. Further transcriptome analysis revealed that it affects pathogen growth by regulating amino acid biosynthesis, ribosomal biosynthesis, carbon metabolism pathways, and the catalytic activities of related genes. In summary, LYH8 significantly controlled FHB through multiple mechanisms, including inhibiting mycelial growth, reducing infection, and blocking toxin synthesis, demonstrating strong biocontrol potential.

Glyoxalase I (GLYI) is the key regulatory enzyme in the glyoxalase pathway. This pathway enables plants to neutralize methylglyoxal (MG) using glutathione (GSH), a mechanism significant for their acclimation to environmental stress. While functionally significant, the specific functions of GLYI genes in Amaranthus palmeri remain unexplored. In this study, integrated bioinformatics and expression analysis was used to identify five GLYI genes in A. palmeri. The results indicate that ApGLYI proteins are hydrophilic and slightly acidic, localized to scaffolds 1, 11, 13, and 16 of the A. palmeri genome. Phylogenetic analysis grouped ApGLYIs with other plant GLYI proteins into three distinct clades, each exhibiting conserved motif patterns. Expression analyses demonstrate that ApGLYI genes participate in both early and late regulatory phases of MG detoxification and signaling, responding to diverse stimuli including high temperature, NaCl, osmotic stress, exogenous methylglyoxal, abscisic acid (ABA), and methyl jasmonate (MeJA). Conversely, glufosinate ammonium treatment appears to compromise this cellular detoxification system. These results offer the evolutionary trajectory and functional significance of the ApGLYI gene. They establish a foundation for subsequent studies toward managing A. palmeri infestation and using these genes to improve stress resilience in cultivated crops through breeding strategies.

During metamorphic development from larva to adult, insect brains exhibit cell proliferation; however, the molecular mechanisms governing this process remain poorly understood. Employing the lepidopteran insect Helicoverpa armigera (cotton bollworm), an agricultural pest, as a model system, this study demonstrates that the steroid hormone 20-hydroxyecdysone (20E) regulates neural cell proliferation during imaginal brain development by upregulating the expression of SOX12 and DELTA via nuclear receptor EcRA. SOX12 exhibits significantly elevated expression and is localized in the brain during metamorphosis. Overexpression of SOX12-GFP in the H. armigera epidermal cell line (HaEpi) promotes cell proliferation. RNA interference (RNAi)-mediated knockdown of Sox12 in larvae leads to lethality, delayed pupation, impaired imaginal brain development, downregulation of cell proliferation-related genes, and reduced neural cell proliferation in the brain. CRISPR/Cas9 knockout of Sox12 can also impair imaginal brain development and reduce neural cell proliferation in the brain. Sox12 is upregulated by 20E through its nuclear receptor EcRA, which subsequently induces Delta expression to facilitate imaginal brain development during metamorphosis. Notably, Delta knockdown recapitulates the phenotypic effects observed on Sox12 silencing and knockout. Collectively, these findings establish that the steroid hormone 20E, acting through the EcRA-SOX12-DELTA regulatory axis, drives neural cell proliferation in the developing imaginal brain during insect metamorphosis.

Calmodulin-like proteins (CMLs) are essential calcium-binding proteins in plants that play a vital role in plant growth and development. However, the functions of CMLs in wheat are not well understood. This study identified and analyzed 133 wheat CMLs genes (TaCMLs) through comprehensive bioinformatics and gene expression techniques. The findings revealed that most TaCMLs are intron-less and are unevenly distributed across the 21 chromosomes of the wheat genome. Duplication analysis identified 46 duplicated TaCMLs, which exhibited purifying selection. Evolutionary analysis classified the TaCML proteins into six subgroups, with certain motifs being conserved within specific phylogenetic groups. The TaCML proteins were localized in several organelles, and a transient expression of TaCML22 and TaCML40 in Nicotiana benthamiana leaves confirmed their localization in the nucleus and chloroplast. Yeast 2-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and microscale thermophoresis (MST) assays found a direct interaction between TaCML22 and TaCML40. Gene expression analysis found the involvement of TaCMLs in both early and late responses to abscisic acid (ABA), hydrogen peroxide (H₂O₂), indole-3-acetic acid (IAA), and Fusarium graminearum infection. DNA methylation was found to potentially reduce the regulatory functions of TaCMLs during stress responses. BSMV-based VIGS gene silencing of TaCML22 and TaCML40 leads to a reduction of silenced-plant antioxidant enzymes such as SOD, CAT, and POD and an increase in MDA levels under F. graminearum infection. These results lay the groundwork for further exploration of the functions of TaCMLs and their potential applications in developing stress-resistant wheat cultivars.

Long intergenic non-coding RNAs (lincRNAs) have been recently indicated to play a crucial role in plant disease resistance. In this study, 550 lincRNAs candidates were identified by their shorter length and containing fewer exons than protein-coding genes, and found to evenly distribute across chromosomes. Gene expression analysis indicated that eight lincRNAs and lincRNA-mRNA pairs exhibit significantly different expressions. Network analysis revealed the interactions between these eight lincRNAs and five genes. Melting Curve Analysis (MCA), Microscale Thermophoresis (MST), and Spectral Shift (SPS) experiment confirmed that MSTRG.55194 binds strongly to TraesCS5A03G0814500 and TraesCS3D03G0188700. Silencing MSTRG.55194 reduced the relative expression levels of target genes and stress response genes in wheat, thereby reducing wheat resistance to F. pseudograminearum. Additionally, transient expression of MSTRG.55194 in Nicotiana benthamiana reduced infection of Phytophthora infestans. This study demonstrates an important role of lincRNA MSTRG.55194 in wheat resistance against F. pseudograminearum infection, which would provide insight into molecular mechanisms of lincRNAs in wheat resistance and contribute to crop disease control.

Seeds with the same genetic information from the different parts of the maize ear vary in seed vigor. However, little is known regarding the associated mechanisms. In the present study, we explored the mechanism of maize ear position effects on seed vigor on hormone level and epigenetic modification. The dimethylated histone H3 Lys9 (H3K9me2) level in the seeds at middle sections of the ear was lower at 24 h of imbibition, and decreased more significantly than that of top seeds. Treatments with fluoridone (Flu), an inhibitor of abscisic acid (ABA) synthesis, on seeds at 10 days or 14 days after pollination changed expression level of ABA synthesis- and catabolism-related genes, and ultimately increased the gibberellic acid 4 (GA4)/ABA ratio of seeds and influenced seed vigor. 37.5 μmol/L Flu and 75 μmol/L Flu treatments both significantly increased the level of H3K9me2 in seeds by improved expression of H3K9 methyltransferase genes, GRMZM2G300955 and GRMZM2G165011. This indicated that H3K9me2 plays an important role in seed vigor regulating. The present study contributes to understanding of the mechanisms underlying GA4/ABA ratio and H3K9me2 cooperatively regulating maize seed vigor.

Long noncoding RNAs (lncRNAs) have been revealed in multiple biological processes; however, their physiological roles, as well as their regulatory mechanisms, are largely unknown in organisms, especially in disease-causing fungi such as Fusarium graminearum, which causes Fusarium head blight in cereal crops. Herein, FG-lncRNA06490 was identified as a key regulator for pathogenesis in F. graminearum. Knockout of FG-lncRNA06490 resulted in significantly reduced pathogenicity during the experiment, which was recovered through a complementation test and dramatically increased by overexpression of FG-lncRNA06490, although the growth and development of the genetic modified strains was not impaired. A significant reduction in the deoxynivalenol (DON) level was observed in the knockout mutant compared with control strain, and the expression levels of TRI5 and TRI6, which are essential for DON synthesis, were correspondingly downregulated. In addition, the transcripts of the genes located 10 kb upstream and downstream of FG-lncRNA06490 were quantified, and significantly increased expression of FGSG_05143, FGSG_05144, and FGSG_12691, as well as dramatically decreased expression of FGSG_05145, was found in the knockout line. Subsequent experiments confirmed the silencing efficiency of FG-lncRNA06490, further validating its significance in F. graminearum. Altogether, we demonstrated the role of FG-lncRNA06490 in modulating the transcription of the genes potentially involved in the generation of DON, as well as pathogenesis. These preliminary insights into FG-lncRNA06490 highlight the function and regulatory model of lncRNAs in plant-fungus interaction.

Barley leaf stripe, caused by Pyrenophora graminea (Pg), significantly reduces yields across various regions globally. Understanding the resistance mechanisms of barley to Pg is crucial for advancing disease resistance breeding efforts. In this study, two barley genotypes—highly susceptible Alexis and immune Ganpi2—were inoculated with the highly pathogenic Pg isolate QWC for 7, 14, and 18 days. The number of differentially expressed genes (DEGs) in Alexis was 1350, 1898, and 2055 at 7, 14, and 18 days, respectively, while Ganpi2 exhibited 1195, 1682, and 2225 DEGs at the same time points. Gene expression pattern analysis revealed that Alexis responded more slowly to Pg infection compared to Ganpi2. A comparative analysis identified 457 DEGs associated with Ganpi2’s immunity to Pg. Functional enrichment of these DEGs highlighted the involvement of genes related to plant-pathogen interactions and kinase activity in Pg immunity. Additionally, 20 resistance genes and 24 transcription factor genes were predicted from the 457 DEGs. Twelve candidate genes were selected for qRT-PCR verification, and the results showed that the transcriptomic data was reliable. We conducted cloning of the candidate Pg resistance gene HvLRR_8-1 by the barley cultivar Ganpi2, and the sequence analysis confirmed that the HvLRR_8-1 gene contains seven leucine-rich repeat (LRR) domains and an S_TKc domain. Subcellular localization in tobacco indicates that the HvLRR_8-1 is localized on the cell membrane. Through the functional analysis using virus-induced gene silencing, it was demonstrated that HvLRR_8-1 plays a critical role in regulating barley resistance to Pg. This study represents the first comparative transcriptome analysis of barley varieties with differing responses to Pg infection, providing that HvLRR_8-1 represents a promising candidate gene for improving durable resistance against Pg in cultivated barley.

ABSTRACTHeat stress is a significant climatic hazard, intensified by rising global temperatures and frequent heatwaves, hindering wheat production. Heat stress damage wheat maturity resulting in morphophysiological changes, biochemical disturbances and a decline in genetic potential. Understanding the morpho–physio–biochemical responses of wheat to heat stress is essential for identifying tolerance mechanisms and developing effective strategies to protect wheat under changing climatic conditions. Plants have evolved various mechanisms to cope with heat stress, which include alterations in their morphological and growth responses, as well as adjustments in physiological and biochemical pathways, alongside modifications in enzymatic activities. Recent advancements in conventional, molecular breeding and transgenic methods have facilitated the development of heat‐tolerant wheat cultivars exhibiting adaptive responses to heat stress whilst maintaining quality and productivity. This review illuminated the morpho‐physiological, biochemical and molecular impacts of heat stress, the mechanisms of tolerance and adaptation strategies in wheat. Besides, we aimed to explore the integration of innovative use of heat priming and the application of smoke water treatment for stress mitigation, thus providing the basis for identifying and promoting effective management practices to mitigate the effects of heat stress in wheat.

Litchi is renowned for its distinctive appearance, flavor, and nutrient composition. This study investigated the potential of nocturnal white LED light exposure, applied from the pre-second physiological fruit drop stage to harvest, to enhance the quality of ‘Feizixiao’ litchi. We focused on understanding its effects on the physical-chemical properties, aromatic profile, and gene activity. Our results showed that LED treatment significantly improved internal fruit quality by increasing the sugar/organic acid ratio in the litchi pulp and delaying the postharvest loss of key aroma compounds like 2,4-nonadienal and rose oxide isomers. Metabolomic analysis of the pulp identified 254 differentially accumulated metabolites (DAMs), primarily associated with amino acid biosynthesis. Additionally, LED treatment altered the anthocyanin profile in the pericarp, significantly elevating the level of cyanidin-3-O-glucoside, a key contributor to red pigmentation, even as it reduced the overall content of procyanidins. Transcriptomic data indicated that this shift may be attributed to LED-induced regulation of flavonoid biosynthesis genes. This work demonstrates LED light profoundly shapes litchi quality, offering valuable insights for balancing flavor and appearance in horticultural practices.

Phosphorus (P), one of the three primary macronutrients essential for plant growth, predominantly exists in soil as unavailable forms for plant uptake. Rhizosphere bacteria can mobilize the unavailable P through two key processes: organic phosphorus mineralization and inorganic phosphorus solubilization. Despite their ecological significance, the diversity and community structure of P-mobilizing bacteria in plant rhizospheres remain insufficiently characterized. In this study, we employed culturomics to isolate bacteria from tobacco rhizosphere and systematically evaluated their P mobilization activities. The P mobilization mechanism was analyzed through whole genome sequence analyses, and the promotion effect was evaluated by greenhouse experiment. A total of 266 P mobilization bacteria were screened, representing 41.50 % of the total isolates. These bacteria were further classified as 49 genera in four phyla: Pseudomonadota (63.16 %), Bacillota (18.80 %), Bacteroidota (10.15 %), and Actinomycetota (7.89 %), with Pseudomonas (25.10 %) and Bacillus (16.47 %) as dominant genera (>10 %). The collection comprised 232 P-mineralization bacteria (PMB) (47 genera), 126 P-solubilizing bacteria (PSB) (33 genera), and 92 dual-functional (26 genera) strains. PMB strains exhibited higher α-diversity and greater numerical abundance across all sampling sites than PSB. Genomic analyses revealed that Pseudomonadota strains displayed exceptional genetic flexibility, harboring more P mobilization genes than other phyla strains. Greenhouse experiments demonstrated that PSB strains significantly enhanced tobacco seedling growth, including shoot and root biomass, stem diameter and leaf area, increased both plant P content and rhizosphere soil available P concentrations. Our study provides new insights into microbial-mediated mechanisms governing phosphorus mobilization and biogeochemical cycling within plant rhizosphere ecosystems.

Atmospheric CO2 concentration is elevated globally, which has "CO2 fertilization effects" and potentially improves plant photosynthesis, yield, and productivity. Despite the beneficial effect of CO2 fertilization being modulated by vapor pressure deficit (VPD), the underlying mechanism is highly uncertain. In the present study, the potential roles of hormones in determining CO2 fertilization effects under contrasting high and low VPD conditions were investigated by integrated physiological and transcriptomic analyses. Beneficial CO2 fertilization effects were offset under high VPD conditions and were constrained by plant water stress and photosynthetic CO2 utilization. High VPD induced a large passive water driving force, which disrupted the water balance and consequently caused plant water deficit. Leaf water potential, turgor pressure, and hydraulic conductance declined under high VPD stress. The physiological evidence combined with transcriptomic analyses demonstrated that abscisic acid (ABA) and jasmonic acid (JA) potentially acted as drought-signaling molecules in response to high VPD stress. Increased foliar ABA and JA content triggered stomatal closure to prevent excessive water loss under high VPD stress, which simultaneously increased the diffusion resistance for CO2 uptake from atmosphere to leaf intercellular space. High VPD also significantly increased mesophyll resistance for CO2 transport from stomatal cavity to fixation site inside chloroplast. The chloroplast "sink" CO2 availability was constrained by stomatal and mesophyll resistance under high VPD stress, despite the atmospheric "source" CO2 concentration being elevated. Thus, ABA- and JA-mediated drought-resistant mechanisms potentially modified the beneficial effect of CO2 fertilization on photosynthesis, plant growth, and yield productivity. This study provides valuable information for improving the utilization efficiency of CO2 fertilization and a better understanding of the physiological processes.

The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.

Fusarium head blight (FHB) is a serious disease of wheat that threatens wheat production worldwide. In this study, high-throughput sequencing technology was used to analyze the rhizosphere soil microbial metagenomes of 4 wheat cultivars with different levels of resistance to FHB. The results showed that there were differences in the diversity, structure, and composition of rhizosphere microorganisms between resistant and sensitive varieties. The rhizosphere soil bacterial diversity of the resistant wheat varieties Su Mai 3 and Yang Mai 16 was higher than that of the susceptible wheat varieties Zheng Mai 9023 and Zhou Mai 20. The diversity of rhizosphere fungi in resistant varieties was lower than that in susceptible varieties, but the abundance was higher than that in susceptible varieties. Variety was found to alter the community structure of wheat rhizosphere microorganisms. Resistant varieties SM3 and YM16 and moderately susceptible variety ZM9023 had similar microbial community structure, while highly susceptible variety ZM20 was significantly different from other varieties. The study is aimed at analyzing the effects of wheat varieties of different resistance to FHB on the composition and abundance of rhizosphere soil microbial community to screen out bacteria or fungi that can be used to control FHB, providing the theoretical basis for FHB biological control.

Although nitrogen application and cutting frequency (CF) are two important factors affecting forage productivity and quality, their effects on alfalfa (Medicago sativa L.), particularly in humid areas, remain less understood. Here, we investigated the fertilization and cutting regimes for seasonal alfalfa cultivation in humid areas in southern China. Treatments performed over a 2-year period were of a split-plot design with four N application rates (60, 120, 180, and 240 kg N ha−1) and three CFs (five, four, and three times.). After cutting, forage components, yield, and quality were measured. In both 2-year cutting cycles, the effects of N application × CF interactions on forage yield and quality were non-significant. N application and CFs influenced plant height, mass shoot−1, leaf area shoot−1, and shoots plant−1. CF had remarkable effects on forage quality under different N applications, with forage cut five times having the best nutritive value and quality. However, neutral and acid detergent fiber contents were lower than when cutting three times, and produced the lowest yields. Forage cut four times had the highest in vitro digestible dry matter. In conclusion, to obtain high yields and desirable quality, the application of 180 kg N ha−1 and cutting three to four times in spring could be a suitable strategy for alfalfa forage production during seasonal cultivation in humid areas of southern China.

Anthocyanins are the main pigments that affect the color and quality of purple-fruited sweet pepper (Capsicum annuum). Our previous study indicated that blue light can induce anthocyanin accumulation in purple pepper. In view of its underlying mechanism that is unclear, here, anthocyanin content was determined, and transcriptome analysis was performed on pepper fruits harvested from different light treatments. As a result, among the identified anthocyanin metabolites, the levels of delphinidin (Dp) glycosides, including Dp-3-O-rhamnoside, Dp-3-O-rutinoside, and Dp-3-O-glucoside, were highly accumulated in blue-light–treated fruit, which are mainly responsible for the appearance color of purple pepper. Correlation between anthocyanin content and transcriptomic analysis indicated a total of 1,619 upregulated genes were found, of which six structural and 12 transcription factor (TF) genes were involved in the anthocyanin biosynthetic pathway. Structural gene, for instance, CaUFGT as well as TFs such as CaMYC2-like and CaERF113, which were highly expressed under blue light and presented similar expression patterns consistent with Dp glycoside accumulation, may be candidate genes for anthocyanin synthesis in response to blue-light signal.