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Background The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown. Results This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways. Conclusion Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

Enhanced Disease Susceptibility 1 ( EDS1 ) genes are central regulators of plant innate immunity and have emerging roles in biotic stress adaptation. Although extensively characterized in dicots, a genome-wide investigation of the EDS1 gene family in barley ( Hordeum vulgare L.) remains unavailable. Thirteen HvEDS1 genes were systematically identified by integrated HMM and BLASTP approaches. These genes encode structurally distinct proteins that differ in length, charge, stability and subcellular localization, with several of them reported to occur in the nucleus, chloroplasts, mitochondria and cytoskeleton. Phylogenetic analyses subdivided the HvEDS1 proteins into three major clades, revealing both a diversification of monocots and conserved ancestors. Analyses of gene structure and conserved motifs revealed clade-specific exon–intron architectures and domain configurations, suggesting functional specialization. Analysis of the genome distribution showed that the spread of HvEDS1 is primarily due to scattered duplications, with purifying selection acting on the duplicated pairs. Analysis of the promoters identified numerous cis-regulatory elements that respond to hormones (ABA, JA), light (G-box) and abiotic influences (MBS), suggesting multi-layered transcriptional regulation. The predicted miRNA–mRNA interactions revealed that hvu-miR6192, a stress-responsive microRNA, targets receptor-like kinases involved in abiotic stress signaling, suggesting a post-transcriptional regulatory role in HvEDS1-mediated stress responses. KEGG enrichment linked HvEDS1 genes to lipid signaling pathways, including glycerophospholipid and α-linolenic acid metabolism, as well as ubiquitin-mediated proteolysis. Structural modelling indicated conservation of key EDS1 domains, but showed protein-specific variations in loop flexibility and secondary structure content, suggesting different functional dynamics. The overall transition from a specialized, low-redundancy network under normal conditions to a highly coordinated and overlapping network under fungal stress condition reflects the versatility of the HvEDS1 family in rewiring of signaling cascades stress responsive pathways during different physiological conditions. This first genome-wide characterization of the HvEDS1 gene family reveals its structural diversity, evolutionary development and potential role in immunity and abiotic stress signaling. The identified candidates provide valuable targets for functional validation and molecular breeding of stress-resistant barley cultivars.

The Eceriferum (CER) gene family plays a crucial role in mitigating non-stomatal water loss and enhancing plant resilience to abiotic stresses, particularly drought and salinity. A comprehensive understanding of CER gene composition and expression dynamics is thereby, fundamental for developing stress-resilient crop varieties. In this study, we identified 12 CER genes in the barley ( Hordeum vulgare L.) genome through an extensive genome-wide analysis. These genes were mapped across multiple chromosomes, and phylogenetic classification delineated them into distinct subgroups, reflecting their evolutionary divergence. Structural analyses, including exon-intron architecture, conserved motif composition, and protein domain organization, revealed a high degree of conservation within subfamilies. Collinearity analysis indicated a limited occurrence of gene duplication events, suggesting an evolutionary trajectory distinct from that observed in other species. Additionally, promoter region analysis uncovered diverse cis-regulatory elements associated with hormonal regulation and abiotic stress responses, providing insights into potential transcriptional regulatory mechanisms. Expression profiling across different stress conditions demonstrated stress-specific gene expression patterns and dynamic transcriptional responses to salinity and drought. Collectively, these findings offer valuable insights into the functional roles of CER genes in barley and identify promising candidates for genetic interventions aimed at improving stress tolerance in cereal crops.

Background Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. Results Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. Conclusions These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.

Background Evolutionarily conserved in plants, the enzyme D-myo-inositol-3-phosphate synthase ( MIPS ; EC 5.5.1.4) regulates the initial, rate-limiting reaction in the phytic acid biosynthetic pathway. They are reported to be transcriptional regulators involved in various physiological functions in the plants, growth, and biotic/abiotic stress responses. Even though the genomes of most legumes are fully sequenced and available, an all-inclusive study of the MIPS family members in legumes is still ongoing. Results We found 24 MIPS genes in ten legumes: Arachis hypogea , Cicer arietinum , Cajanus cajan , Glycine max , Lablab purpureus , Medicago truncatula , Pisum sativum , Phaseolus vulgaris , Trifolium pratense and Vigna unguiculata . The total number of MIPS genes found in each species ranged from two to three. The MIPS genes were classified into five clades based on their evolutionary relationships with Arabidopsis genes. The structural patterns of intron/exon and the protein motifs that were conserved in each gene were highly group-specific. In legumes, MIPS genes were inconsistently distributed across their genomes. A comparison of genomes and gene sequences showed that this family was subjected to purifying selection and the gene expansion in MIPS family in legumes was mainly caused by segmental duplication. Through quantitative PCR, expression patterns of MIPS in response to various abiotic stresses, in the vegetative tissues of various legumes were studied. Expression pattern shows that MIPS genes control the development and differentiation of various organs, and have significant responses to salinity and drought stress. Conclusion The MIPS genes in the genomes of legumes have been identified, characterized and their expression was analysed. The findings pave way for understanding their molecular functions and evolution, and lead to identify the putative MIPS genes associated with different cell and tissue development.

Background The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum ( CER ) gene family is associated with wax production and stress resistance. Results In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum , G. barbadense , G. raimondii , and G. hirsutum . There were variations in the physicochemical characteristics of the Gossypium CER ( GCER ) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394 , ghr-miR414d , and ghr-miR414f , targeted GhCER09A , representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis -regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D , GhCER04A , GhCER06A , and GhCER12D , exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing ( VIGS ) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. Conclusions This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

Background Abscisic acid (ABA) plays a central role in regulating plant responses to abiotic stress. It orchestrates a complex regulatory network that facilitates the transition from growth to defense. Understanding the molecular mechanisms underlying this ABA-induced transition from growth to defense is essential for elucidating plant adaptive strategies under environmental stress conditions. Results In this study, we used a refined dynamic network biomarker (DNB) approach to quantitatively identify the critical transition signal (CTS) and characterize the regulated stochasticity during the ABA-induced transition from growth to defense in Arabidopsis thaliana . By integrating high-resolution time-series RNA-seq data with dynamic network analysis, we identified a set of DNB genes that serve as key molecular regulators of this transition. The critical transition phase was identified precisely at the ninth time point (6 h after treatment), which marks the crucial switch from a growth-dominated to a defense -oriented state. Gene Ontology (GO) enrichment analysis revealed a significant overrepresentation of defense-related biological processes, while STRING network analysis revealed strong functional interactions between DNB genes and differentially expressed genes (DEGs) and highlighted key regulatory hubs. In particular, key hub genes such as PIF4 , TPS8 , NIA1 , and HSP90 -5 were identified as potential master regulators of ABA-mediated defense activation, highlighting their importance for plant stress adaptation. Conclusions By integrating a network-driven transcriptomic analysis, this study provides new insights into the molecular basis of ABA-induced transitions from growth to defense. The identification of CTS provides a new perspective on regulated stochasticity in plant stress responses and provides a conceptual framework for improving crop stress resistance. In addition, the establishment of a comprehensive database of ABA-responsive defense genes represents a valuable resource for future research on plant adaptation and resilience.

Background Proteins containing domains of unknown function (DUFs) play a crucial role in plant growth, development and stress adaptation, but many of them are still uncharacterized. The DUF789 family is one of the least studied of these, especially in economically significant crops like cotton ( Gossypium spp.), whose possible function in fibre production and abiotic stress response is yet unknown. Results In a comprehensive genome-wide analysis, a total of 91 DUF789 genes were identified in four Gossypium species: G. arboreum , G. barbadense , G. raimondii and G. hirsutum . Evolutionary and phylogenetic analyses placed the GhDUF789 proteins into different clades, with purifying selection identified as the major evolutionary force. Analyses of gene structure and conserved motifs revealed considerable structural diversity, with closely related genes showing similar exon–intron patterns and motif compositions. Synteny and duplication analyses showed that segmental and tandem duplications contributed to the DUF789 family expansion in cotton. Analysis of cis-regulatory elements revealed that the GhDUF789 promoters are enriched in motifs responsive to hormonal, developmental, light-induced and abiotic stresses. GO enrichment analyses, prediction of protein–protein interaction and secondary and tertiary structure modelling, indicated that GhDUF789 proteins are involved in clathrin-mediated vesicle trafficking and membrane trafficking. The miRNA target prediction revealed regulatory interactions with conserved miRNAs from cotton, in particular ghr-miR414 and ghr-miR396. Expression profiling based on transcriptome analysis, supported by validation using qRT-PCR, revealed that several GhDUF789 genes are differentially expressed during fibre development and respond strongly to drought, heat, salinity and cold stress, especially in drought-tolerant genotypes. Conclusions This study provides the first comprehensive characterization of the DUF789 gene family in cotton and offers new insights into its evolutionary dynamics, structural features and potential role in fibre development and adaptation to abiotic stress. The results provide a solid foundation for future functional studies and identify candidate GhDUF789 genes for targeted genetic improvement of stress resistance and fibre quality in cotton.

Background Enhanced Disease Susceptibility 1 (EDS1) genes are central regulators of plant immunity and abiotic stress responses. Although well studied in model species, their genome-wide characterisation in cotton ( Gossypium spp.) remains lacking. Results We identified 268 putative EDS1 genes across four Gossypium species ( G. hirsutum , G. barbadense , G. arboreum , and G. raimondii ) using HMMER-based domain searches. Phylogenetic analysis grouped the genes into five subfamilies, reflecting both conserved ancestry and subgenome-specific diversification. Chromosomal mapping, collinearity, and Ka/Ks analyses revealed that segmental and whole-genome duplications were the primary drivers of expansion, with most duplicates under purifying selection. Promoter analysis using PlantCARE uncovered cis-regulatory elements responsive to abscisic acid, jasmonic acid, drought (MBS), and light signals (G-box). miRNA target prediction via psRNATarget revealed ghr-miR414 as a key regulator targeting multiple GhEDS1 transcripts. Functional enrichment indicated roles in lipid metabolism and ubiquitin-mediated proteolysis. Finally, RNA-seq data and qRT-PCR confirmed that GhEDS1A-13 , GhEDS1D-57 , and GhEDS1D-48 were significantly upregulated under PEG-induced drought stress, implicating them in ABA-linked stress adaptation. Conclusions This study provides the first comprehensive characterisation of the EDS1 gene family in cotton, highlighting its evolutionary dynamics, regulatory complexity, and potential in improving drought tolerance through molecular breeding.

Background Puccinia arachidis fungus causes rust disease in the peanut plants ( Arachis hypogaea L.), which leads to high yield loss. Metabolomic profiling of Arachis hypogaea was performed to identify the pathogen-induced production of metabolites involved in the defense mechanism of peanut plants. In this study, two peanut genotypes, one susceptible (JL-24) and one resistant (GPBD-4) were inoculated with Puccinia arachidis fungal pathogen. The metabolic response was assessed at the control stage (0 day without inoculation), 2 DAI (Day after inoculation), 4 DAI and 6 DAI by Gas Chromatography-Mass Spectrometry (GC-MS). Results About 61 metabolites were identified by NIST library, comprising sugars, phenols, fatty acids, carboxylic acids and sugar alcohols. Sugars and fatty acids were predominant in leaf extracts compared to other metabolites. Concentration of different metabolites such as salicylic acid, mannitol, flavonoid, 9,12-octadecadienoic acid, linolenic acid and glucopyranoside were higher in resistant genotype than in susceptible genotype during infection. Systemic acquired resistance (SAR) and hypersensitive reaction (HR) components such as oxalic acid was elevated in resistant genotype during pathogen infection. Partial least square-discriminant analysis (PLS-DA) was applied to GC-MS data for revealing metabolites profile between resistant and susceptible genotype during infection. Conclusion The phenol content and oxidative enzyme activity i.e. catalase, peroxidase and polyphenol oxidase were found to be very high at 4 DAI in resistant genotype (p-value < 0.01). This metabolic approach provides information about bioactive plant metabolites and their application in crop protection and marker-assisted plant breeding.