Glutathione S-transferases (GSTs) are a crucial gene superfamily for plant stress adaptation. However, their evolutionary trajectories and genomic organizational principles across the plant kingdom remain poorly understood. Through a large-scale comparative genomic analysis of 74 plant species, we identified 4,355 GST genes and classified them into 16 subfamilies. Phylogenetic reconstruction revealed massive and lineage-specific expansion of the stress-responsive Tau and Phi subfamilies in land plants, in contrast to the high conservation of ancient subfamilies (e.g., Theta, Zeta). Structural analysis suggested clade-specific motifs in Tau members associated with functional diversification. In polyploid barnyardgrass, genome duplication led to a disproportionate increase in GST copies: Tau and Phi genes showed unbalanced retention and formed selective clusters on homeologous group 1 and 2 chromosomes, while ancient subfamilies maintained dosage stability. Our study elucidates divergent evolutionary dynamics within the GST family. The lineage-specific expansion and selective retention of clustered Tau/Phi genes during polyploidization suggest a potential genomic signature that may be associated with adaptive evolution in plants. This study provides a comprehensive genomic resource and framework for future functional studies of GSTs in plant stress biology.

Invasive alien plants seriously threaten native plant biodiversity and agricultural production. The development of environmentally friendly agriculture requires sustainable weed control techniques to manage these invasive alien weeds. This study evaluated the allelopathic effects of ethanol extract from Artemisia frigida against five invasive alien plants (Ageratum conyzoides, Bidens pilosa, Ipomoea purpurea, Eclipta prostrata, and Amaranthus retroflexus). The main components in the extract were identified using high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), and we assessed their allelopathic effects on seed germination of the five species. The results showed that the ethanol extract of A. frigida completely inhibited seed germination of all five invasive plants at 5 g·L-1. Thirteen components were identified, among which 4-ethyloctanoic acid, cis-jasmone, and p-anisic acid exhibited significant inhibitory effects. Notably, 4-ethyloctanoic acid demonstrated broad-spectrum herbicidal activity. At 50 mg·L-1, it completely inhibited B. pilosa growth and had the strongest inhibitory effects on A. conyzoides and E. prostrata. This compound disrupted redox homeostasis and induced oxidative stress by modulating antioxidant enzyme activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). These findings indicate that 4-ethyloctanoic acid is the main allelochemical with herbicidal potential in A. frigida, providing a theoretical basis for developing novel herbicides and environmentally friendly control techniques for invasive alien plants.

Rice (Oryza sativa) is a staple crop that is highly susceptible to heat stress (HS), which severely impairs growth and yield. In this study, we identified the rice Ovate Family Protein OsOFP3 as a novel negative regulator in response to heat. Our results demonstrate that the expression of OsOFP3 is suppressed at both the transcriptional and protein levels under HS. Overexpression of OsOFP3 significantly reduces the survival rate of rice seedlings under HS and exacerbates chlorophyll degradation, membrane damage, and the accumulation of reactive oxygen species (H2O2 and O2-). In contrast, OsOFP3 mutants exhibit enhanced heat tolerance. Moreover, OsOFP3-overexpressing plants display increased stomatal opening and decreased stomatal closure under HS. Molecular interaction analysis further reveals that OsOFP3 interacts with the C-terminal domain of OsHTAS, a known positive regulator of heat tolerance encoding an E3 ubiquitin ligase, and this interaction depends on the RING domain of OsHTAS. Taken together, our findings indicate that OsOFP3 negatively regulates rice heat tolerance by disrupting ROS homeostasis, inhibiting stomatal closure, and potentially antagonizing the OsHTAS-mediated signaling pathway. This research provides new insights into the molecular mechanisms underlying HS tolerance in rice.

Rubber trees are crucial to the global industrial economy, but they are facing the threat of powdery mildew caused by Erysiphe quercicola. Effective management of this disease depends on early detection. However, traditional monitoring methods are labor-intensive and often inaccurate. This limitation underscores the need for more precise and efficient techniques. This study developed and validated an integrated molecular detection platform that combines quantitative PCR (qPCR), droplet digital PCR (ddPCR), and propidium monoazide (PMA) treatments. The platform demonstrated a robust detection range, accurately quantifying E. quercicola at concentrations as low as 10 spores/mL spore DNA and 10−5 ng/μL mycelial DNA. Additionally, the system distinguished viable from non-viable spores and detected E. quercicola mycelia in both asymptomatic leaves and aged lesions, significantly enhancing early-stage detection and disease monitoring. This technology also helps assess the efficacy of fungicides against powdery mildew, potentially reducing the use of chemicals and their environmental impact. By improving early diagnosis and disease management, this approach promises to reduce dependence on fungicides and mitigate economic and environmental impacts, highlighting the enormous potential of advanced molecular technologies in sustainable agricultural practices in rubber plantations.

Quinones are secondary metabolites widely produced by plants. They are sensed by the leucine-rich receptor kinase CANNOT RESPOND TO DMBQ 1 (CARD1) and play important roles in immunity and growth in nonparasitic plants. Quinone perception typically involves the posttranslational modification of proteins, particularly through cysteine oxidation. However, the relationship between quinone-induced cysteine modifications and the quinone-CARD1 signaling pathway remains unclear. Here, we performed a redox proteomics analysis to determine the extent of CARD1-mediated cysteine oxidation of proteins in Arabidopsis (Arabidopsis thaliana) seedlings following treatment with a quinone, 2,6-dimethoxy-1,4-benzoquinone (DMBQ). We found that GLUTAREDOXIN C1 (GRXC1) is a substrate protein of CARD1, whose oxidation is induced by DMBQ treatment. GRXC1 interacts with and is phosphorylated by CARD1, mediating Arabidopsis primary root growth. This work provides a molecular basis for understanding the DMBQ-induced redox signaling pathway and the DMBQ-CARD1-GRXC1 signaling pathway in response to redox alterations in Arabidopsis.

The yield and quality of rubber tree latex are affected by environmental stresses and plant hormone stimulation. Heat shock protein 90 (HSP90) is widely involved in various developmental processes and stress responses in plants, especially in drought stress. In this study, we cloned the HbHSP90.3 gene and characterized its expression pattern in different tissues and mechanical wounding treatments of the rubber tree and found that it is highly expressed in latex and responds to mechanical wounding treatment. To reveal the roles of plant hormones and HSP90.3 protein in the drought resistance process of rubber trees. Treatment with the specific HSP90 protein inhibitor geldanamycin (GDA) and yeast expression experiments demonstrated that HbHSP90.3 has a relieving effect on water deficit in rubber trees. The expression pattern showed that the HbHSP90.3 gene was closely related to hormone signaling, especially for Indole acid (IAA) and Zeatin (ZT) induction under different plant hormone treatments. Protein interaction analysis showed that HbHSP90.3 interacted with the suppressor of the G2 allele of skp1 (HbSGT1b). Taken together, HbHSP90.3 interacts with HbSGT1b in the nucleus and plays a key role in water deficit.

The rubber tree (Hevea brasiliensis Muell. Arg.) holds significant socio-economic value due to its contribution to the production of natural rubber (NR). However, prolonged sexual reproduction leads to nutrient depletion (N, P, K, Mg2+) in rubber trees, resulting in reduced latex yield and quality. Gibberellin (GA) regulates critical processes including plant growth and flowering time. To investigate the regulatory mechanism of GA on rubber tree flowering, inflorescences were sprayed with GA3 and the GA biosynthesis inhibitor chlormequat chloride (CCC). Both treatments inhibited flowering and reduced nutrient accumulation in inflorescences and leaves. Subsequent transcriptome sequencing of inflorescences sampled at multiple time points post-treatment identified differentially expressed genes (DEGs). Analysis of these DEGs, combined with endogenous hormone detection, revealed crosstalk between plant hormone signaling pathways. Specifically, differential expression was observed in genes associated with GA signal transduction, flowering regulation, and NR biosynthesis. These findings were confirmed by real-time quantitative PCR (RT-qPCR). This study provides novel insights into the mechanisms of underlying GA signaling-mediated inhibition of flowering in rubber trees and offers potential avenues for enhancing latex production within the rubber industry.

ATP synthase is a key enzyme in photophosphorylation in photosynthesis and oxidative phosphorylation in respiration, which can catalyze the synthesis of ATP and supply energy to organisms. ATP synthase has been well studied in many animal species but has been poorly characterized in plants. This research identified forty ATP synthase family members in the rubber tree, and the phylogenetic relationship, gene structure, cis-elements, and expression pattern were analyzed. These results indicated that the ATP synthase of mitochondria was divided into three subgroups and the ATP synthase of chloroplast was divided into two subgroups, respectively. ATP synthase in the same subgroup shared a similar gene structure. Evolutionary relationships were consistent with the introns and exons domains, which were highly conserved patterns. A large number of cis elements related to light, phytohormones and stress resistance were present in the promoters of ATP synthase genes in rubber trees, of which the light signal accounts for the most. Transcriptome and qRT-PCR analysis showed that HbATP synthases responded to cold stress and hormone stimulation, and the response to ethylene was most significant. HbMATPR3 was strongly induced by ethylene and salicylic acid, reaching 122-fold and 17-fold, respectively. HbMATP7-1 was 41 times higher than the control after induction by jasmonic acid. These results laid a foundation for further studies on the function of ATP synthase, especially in plant hormone signaling in rubber trees.

Submergence stress is a major constraint in direct-seeded rice production. This study investigated the effect and biochemical mechanism of sprouting, a traditional agronomic practice, on improving submergence tolerance in rice. Our findings demonstrate that sprouting is an effective seed treatment that significantly enhances the plant’s ability to withstand flooding. Specifically, 48 h sprouting increased shoot height and root length by 163% and 423%, respectively, in the YLYJ48 variety under 6-day submergence. Sprouting upregulated the activity of glutathione reductase (GR) and the expression of its related genes, thereby significantly promoting the biosynthesis of glutathione (GSH). GSH content in seeds increased from 64.86 µg g−1 FW (0 h) to 83.00 µg g−1 FW (48 h) in HZ, and from 82.14 to 92.52 µg g−1 FW in YLYJ48. This process provides critical antioxidant protection for seedlings to implement a rapid “escape strategy,” ultimately enhancing their submergence tolerance. Functional verification showed that seed soaking with exogenous GSH (0.1%) effectively improved submergence tolerance by increasing antioxidant reserves. Exogenous GSH treatment elevated shoot height by approximately 50% in both HZ and YLYJ48 varieties under submergence. Field trials further demonstrated that exogenous GSH application significantly enhanced seedling establishment rates by 30–35% and improved seedling growth traits under submergence tolerance stress across multiple rice varieties. This study reveals part of the mechanism by which sprouting enhances submergence tolerance by influencing glutathione metabolism, offering practical strategies for flood-resilient direct-seeded rice cultivation.

Dandelions possess a wide range of medicinal properties and demonstrate remarkable adaptability and tolerance to salinity and alkalinity. MYB genes in plants are implicated in growth, differentiation, metabolism, and responses to both biotic and abiotic stresses. The function of MYB genes in dandelions, particularly the R2R3-MYB gene family, requires further investigation. In this study, we identified a total of 130 members of the dandelion R2R3-MYB gene family at the genome-wide level, all of which were mapped to eight dandelion chromosomes. MEME analysis revealed that TmR2R3-MYB proteins contain three conserved motifs. Phylogenetic analysis categorized all TmR2R3-MYBs into 29 subfamilies. Transcriptomic studies in different tissues indicated that TmR2R3-MYBs exhibit distinct expression patterns in different tissues, indicating their diverse functions in dandelions. Notably, TmMYB44 from the S22 subfamily displayed the highest expression level in roots. Additionally, six representative TmR2R3-MYBs were selected from the S22 subfamily for expression profiling under salinity and alkalinity treatments. The results demonstrated that the TmR2R3-MYBs from the S22 subfamily are involved in the response to salinity and alkalinity stress. These findings provide a basis for further exploration of the functions of TmR2R3-MYBs in abiotic stress tolerance.

Macadamia integrifolia is a vital cash crop. The shells of its nuts serve multiple purposes in both agricultural practices and waste management initiatives. In this research, transcriptome analysis was carried out on three macadamia nut varieties with significantly different shell thicknesses, namely ‘A38’, ‘Guire No.1’ (‘GR1’), and HAES842 (‘842’), at the same stage of maturity. The results revealed remarkable differences in their gene expression profiles. A total of 4311 novel genes were identified, among which 1631 were functionally annotated. Analyses using Gene Ontology (GO), Clusters of Orthologous Groups (COGs), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the main categories of differentially expressed genes (DEGs) were associated with plant–pathogen interactions. Additionally, 10 members of the heat shock protein 90 (MiHSP90) family were identified and classified into subgroups A, B, and C by comparing them with the HSP90 gene family members of Arabidopsis and rice. Among these, the MiHSP90.1, MiHSP90.2, and MiHSP90.9 proteins were differentially highly expressed in the three macadamia nut varieties. These findings provide fundamental insights into the regulatory mechanisms underlying shell formation in macadamia nuts.

Hevea brasiliensis, the sole species within the Euphorbiaceae family capable of generating natural rubber (NR), holds considerable economic and industrial significance. A comprehensive analysis of the evolutionary model and functional roles of MYB genes related to NR biosynthesis is of vital importance for the genetic improvement of H. brasiliensis. The evolutionary patterns of MYB genes demonstrated an expansion of ancestral genes in the Crotonoideae subfamily, in contrast to the Euphorbioideae and Acalyphoideae subfamilies. H. brasiliensis possessed the largest number of MYB genes, with whole genome duplication (WGD) or segmental duplication identified as the primary mechanism facilitating expansion of MYB. The number of MYBs in the Euphorbiaceae family had lineage specificity. The gene structure of HbR2R3-MYBs was more conserved, while Hb1R-MYB sequences showed significant variations and more complex gene structures. 209 HbR2R3-MYBs were classified into 29 subfamilies, which encompasses the identification of four new subfamilies. HbMYB88 reached peak expression levels at 12 hours after ethephon treatment and was prominently expressed in latex and stems. Moreover, HbMYB88 displayed low differential expression in secondary laticifers. HbMYB88 was localized in the cell nucleus and belonged to the S25 subfamily, which was associated with cell differentiation. Based on phylogenetic relationships, gene expression patterns, and inter-gene regulatory relationships, it was hypothesized that HbMYB88 was involved in laticifer cell differentiation through the Jasmonic acid (JA) pathway (COI1-JAZMYC), thereby influencing the biosynthesis of NR. Yeast One-Hybrid further proved that HbMYB88 can specifically bind to the promoter of HbMYC-1.

Maize is one of the most successful crops in utilizing heterosis which significantly improves maize stresses resistance and yield. Drought is a destructive abiotic stress that significantly reduces crop yield, particularly in maize. Drought stress and re-watering frequently occur during the growth and development of maize; however, the molecular mechanisms of heterosis under drought stress and re-watering have rarely been systematically investigated. Zhengdan7137 and Zhengdan7153 are two maize hybrid varieties with robust heterosis, and separately belongs to the SS×NSS and Reid×Tangsipingtou heterotic groups. 54 transcriptomes of these two hybrids and their parental inbred lines were analyzed under well-watering (WW), water-deficit (WD), and re-watering (RW) conditions using RNA-Seq. In this study, we identified 3,411 conserved drought response genes (CDRGs) and 3,133 conserved re-watering response genes (CRRGs) between Zhengdan7137 and Zhengdan7153. When comparing CDRGs and CRRGs to overdominance and underdominance genes, we identified 303 and 252 conservative drought response overdominance genes (DODGs) and underdominance genes (DUDGs), respectively, and 165 and 267 conservative re-watering response overdominance genes (RODGs) and underdominance genes (RUDGs), respectively. DODGs are involved in stress response-related processes, such as L-phenylalanine metabolism, carbohydrate metabolism, and heat response, whereas DUDGs are associated with glucose metabolism, pentose-phosphate shunt, and starch metabolism. RODGs and RUDGs contribute to the recovery of hybrids from drought stress by upregulating cell propagation and photosynthesis processes, and repressing stress response processes, respectively. It indicated overdominant and underdominant genes conservatively contributed to hybrid heterosis under drought stress. These results deepen our understanding of the molecular mechanisms of drought resistance, uncover conservative molecular mechanisms of heterosis under drought stress and re-watering, and provide potential targets for improving drought resistance in maize.

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

Macadamia nuts are one of the most important economic food items in the world. Pericarp thickness and flavonoid composition are the key quality traits of Macadamia nuts, but the underlying mechanism of pericarp formation is still unknown. In this study, three varieties with significantly different pericarp thicknesses, namely, A38, Guire No.1, and HAES 900, at the same stage of maturity, were used for transcriptome analysis, and the results showed that there were significant differences in their gene expression profile. A total of 3837 new genes were discovered, of which 1532 were functionally annotated. The GO, COG, and KEGG analysis showed that the main categories in which there were significant differences were flavonoid biosynthesis, phenylpropanoid biosynthesis, and the cutin, suberine, and wax biosynthesis pathways. Furthermore, 63 MiMYB transcription factors were identified, and 56 R2R3-MYB transcription factors were clustered into different subgroups compared with those in Arabidopsis R2R3-MYB. Among them, the S4, S6, and S7 subgroups were involved in flavonoid biosynthesis and pericarp formation. A total of 14 MiMYBs’ gene expression were verified by RT-qPCR analysis. These results provide fundamental knowledge of the pericarp formation regulatory mechanism in macadamia nuts.

S-metolachlor is a selective pre-emergence herbicide used in dryland. However, it is challenging to employ in paddy fields due to its phytotoxic effects on rice. As a common phytohormone, Gibberellin-3 (GA3) is inferred to have the ability to alleviate herbicide phytotoxicity. This study first quantitatively verified the phytotoxicity of s-metolachlor to rice and then demonstrated the mitigative effect of GA3 on these adverse reactions. Furthermore, a transcriptome of rice seedlings subjected to different treatments was constructed to assemble the reference genes, followed by comparative metabolomics and proteomics analyses. Metabolomics revealed an enrichment of flavonoid metabolites in the group of adding GA3, and these flavonoids can eliminate ROS in plants. Proteomics analysis indicated that differential proteins were enriched in the phenylpropanoid biosynthesis pathway responsible for the synthesis of flavonoids and that the functions of most differential proteins are associated with peroxidase. The proteome, combined with the transcriptome, revealed that the expressions of proteins and genes was related to the POD activity in the group of adding GA3. It was speculated that the elimination of ROS is key to alleviating the stress of s-metolachlor on rice growth. It was inferred that the mechanism of GA3 in alleviating the phytotoxicity of the substance s-metolachlor is by increasing the activity of the POD and influencing the growth of rice seedlings through the restoration of flavonoid synthesis. In this study, we screened GA3 as a safener to alleviate the phytotoxicity of s-metolachlor on rice. On this basis, the mechanism of alleviating phytotoxicity was studied. The application range of s-metolachlor might be expanded, providing a new supplementary method for weed control and herbicide resistance management.

Powdery mildew and anthracnose are the main diseases of rubber trees. In recent years, there have been large outbreaks in the rubber-planting areas of Asia, seriously affecting the yield and quality of rubber latex. ZAR1 is a conserved and distinctive coiled-coil nucleotide-binding leucine-rich (CNL) repeat in the plant kingdom, playing a crucial role in disease-resistance processes. To elucidate the function of the HbZAR1 gene in rubber trees (Hevea brasiliensis), three candidate HbZAR1 genes were identified using bioinformatics methods and comprehensively analyzed. The results indicate that the HbZAR1 protein is conserved in different plant species. Examination of cis-regulatory element sequences of HbZAR1genes reveals that the HbZAR1 gene promoter exhibits a remarkable enrichment of stress, light, and hormone elements. An expression analysis shows that the expression levels of the three HbZAR1 genes are highest in the bark and lowest in latex. Three HbZAR1 genes can respond to both rubber tree Erysiphe quercicola and Colletotrichum siamense infection; especially, HbZAR1.1 and HbZAR1.2 show significant upregulation in expression levels during the early stages of infection. These findings suggest that the three HbZAR1 genes may be involved in rubber tree susceptibility to E. quercicola and C. siamense through different immune mechanisms. Subcellular localization results indicate that the HbZAR1 genes are expressed in the nucleus and plasma membrane. This study also shows that the three HbZAR1 genes and activated mutant HbZAR1.1D481V do not induce stable ROS production and cell death, suggesting possible gene degradation, functional redundancy, or acting as minor genes in disease resistance. This research provides valuable insights for further studying the function of HbZAR1 genes in rubber trees and the mechanisms of immune molecules.

The basic leucine zipper (bZIP) transcription factors (TFs) play important roles in many physiological processes of plant-pathogenic fungi, especially concerning fungal development, fungicide resistance, and pathogenicity. Colletotrichum siamense is the predominant species causing Colletotrichum leaf disease (CLD) in rubber trees. However, little is known about the bZIP genes in C. siamense. In this study, 25 bZIP genes were systematically identified in the genome of C. siamense, and molecular features were characterized. Evolutionarily, the CsbZIP genes were divided into 11 groups, with the members in the same group sharing similar gene structures and conserved protein motif organizations. Furthermore, protein-protein interaction (PPI) analysis revealed that 15 bZIP proteins had functional partners in common or interacted with other CsbZIP proteins. Additionally, the expression of 23 CsbZIP genes changed in response to the antifungal chemicals melatonin, prochloraz, and thymol, and the genes could be divided into three clusters based on their expression patterns. Finally, gene deletion mutants of CsbZIP01/09/17 were constructed and functional analysis indicated that these genes operated as important regulators of mycelial growth, fungicide resistance, ergosterol biosynthesis, and virulence in C. siamense. This study provided the foundations crucial for further investigation of the functions of CsbZIP TFs in fungicide resistance and virulence.

Receptor kinases play a pivotal role in detecting environmental signals, and consequently, gene pleiotropy is frequently observed within this family. However, the trade-off in trait expression resulting from gene pleiotropy poses a constraint on the utilization of such genes in agricultural breeding. In this study, we identified the receptor kinase gene FERONIA-Like Receptor 13 (FLR13) as a pleiotropic gene influencing plant height, tillering, grain yield, and disease resistance. Using promoter editing, we generated novel alleles (FLR13T5T6-1, FLR13T5T6-2) that confer resistance to rice blast and increase per-plant yield. The knockout of the T5T6 segment alleviates the inhibitory effects of two transcription factors, OsGBP1 and OsWRKY53, on FLR13 expression. In summary, our study presents a promising avenue for enhancing the pivotal attributes of receptor-like kinases through a promoter-editing strategy.