Search Results (619)

Arbuscular Mycorrhizal Fungi (AMF) can form symbiotic relationships with most plants. They can alleviate the toxic effects of heavy metals on plants. This study analyzed the effects of AMF (Diversispora versiformis, D.v.) on the physiological responses and root organic acid secretion of tomato (Solanum lycopersicum L.) under cadmium (Cd) stress, in order to elucidate how AMF enhance Cd tolerance. The results indicated that when the AMF inoculation rate of tomato seedlings ranged from 26.75% to 38.23%, the AMF treatment significantly promoted tomato growth. Cd significantly reduced the agronomic traits of tomato. However, AMF inoculation dramatically lowered the Cd level from 19.32 mg/kg to 11.54 mg/kg in tomato roots, and effectively reduced the negative effect of Cd toxicity on seedling growth. Cd stress also significantly reduced the chlorophyll fluorescence parameters, chlorophyll contents, and photosynthetic intensity parameters in seedling leaves, while the AMF treatment significantly increased these indicators. Under Cd stress, the AMF treatment significantly increased the activities of SOD, POD, and CAT, and reduced the levels of reactive oxygen species and the contents of osmotic regulatory substances in roots. Under Cd stress conditions, the AMF treatment also significantly increased the auxin level (57.24%) and reduced the abscisic acid level (18.19%), but had no significant effect on trans-zeatin riboside and gibberellin contents in roots. Cd stress markedly reduced the content of malic acid and succinic acid by 17.28% and 25.44%, respectively; however, after the AMF inoculation, these indicators only decreased by 2.47% and 2.63%, respectively. Under Cd stress, AMF could increase tomato roots’ antioxidant capacity to reduce ROS level, thereby alleviating the toxicity induced by ROS and maintaining reactive oxygen metabolism, enhancing the plant’s stress resistance. In summary, the AMF treatment enhances the osmotic regulation capacity and maintains the stability of cell membranes by reducing the levels of osmotic regulatory substances in roots. It also enhances the Cd tolerance of tomato plants by regulating the contents of root hormones and aerobic respiration metabolites, among other pathways. Therefore, inoculating plants with AMF is a prospective strategy for enhancing their adaptive capacity to Cd-polluted soils. Full article

Brassinosteroids (BRs) are essential regulators of plant development and stress responses, but the distinct contributions of BR biosynthesis and signaling to hormonal crosstalk remain poorly defined. Here, we investigated the effects of the BR biosynthesis inhibitor brassinazole (BRZ) and the BR-insensitive mutant bri1-6 on endogenous phytohormone profiles in Arabidopsis thaliana. Using multivariate analysis and targeted hormone quantification, we show that BRZ treatment and BRI1 disruption alter hormone balance through partially overlapping but mechanistically distinct pathways. Principal component analysis (PCA) and hierarchical clustering revealed that BRZ and the bri1-6 mutation do not phenocopy each other and that BRZ still alters hormone profiles even in the bri1-6 mutant, suggesting potential BRI1-independent effects. Both BRZ treatment and the bri1-6 mutation tend to influence cytokinins and auxin conjugates divergently. On the contrary, their effects on stress-related hormones converge: BRZ decreases salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in the WT leaves; similarly, bri1-6 mutants show reduced SA, JA, and ABA. These results indicate that BR biosynthesis and BRI1-mediated perception may contribute independently to hormonal reprogramming, with BRZ eliciting additional effects, possibly via metabolic feedback, compensatory signaling, or off-target action. Hormone correlation analyses revealed conserved co-regulation clusters that reflect underlying regulatory modules. Altogether, our findings provide evidence for a partial uncoupling of BR levels and BR signaling and illustrate how BR pathways intersect with broader hormone networks to coordinate growth and stress responses. Full article

Plant growth regulators Gibberellin A3 (GA₃) and N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) are widely used in ‘Shine Muscat’ cultivation to regulate berry shape and size. However, the molecular mechanisms underlying their regulation of berry shape remain poorly understood. This study was designed to elucidate the cytological processes and molecular basis through which GA₃ and CPPU modulate berry morphology in ‘Shine Muscat’. The results showed that spraying GA₃ or CPPU alone increases the hormone levels of endogenous auxin (IAA) and GA₃ and reduces the levels of endogenous 6-benzyladenine (6-BA). GA₃ treatment resulted in the number of cells per unit area being significantly reduced and the cell transverse and longitudinal diameters being significantly increased. CPPU treatment increases the number of cells per unit area, cell transverse and longitudinal diameters. In the results of CKvsG2 and CKvsC2 transcriptome sequencing, 2793 and 1082 differentially expressed genes (DEGs) were identified, respectively. These DEGs are significantly enriched in Gene Ontology (GO) terms related to plant hormones; the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the zeatin biosynthesis pathway (ko03030) is significantly enriched. The Arabidopsis response regulator (ARR) is down-regulated in response to GA₃ application and up-regulated in response to CPPU application. Transient overexpression of VvARR (OE-VvARR) in ‘Shine Muscat’ berry increased the number of berry cells and cell transverse and longitudinal diameters. Furthermore, virus-induced gene silencing of VvARR (VIGS-VvARR) reduced the number of berry cells but increased cell transverse and longitudinal diameters. The OE-VvARR grape hormone levels of endogenous GA₃, 6-BA, and IAA were significantly increased. In VIGS-VvARR grape, the levels of endogenous IAA and 6-BA are significantly increased, but there is no significant difference in endogenous GA₃. These findings offer novel insights into the molecular mechanisms by which GA₃ and CPPU govern berry development, corroborating the hypothesis that VvARR acts as a pivotal regulator mediating the effects of these plant growth regulators on berry cell morphology and, consequently, berry shape. Full article

Spinach is a dioecious vegetable and an excellent model for investigating plant sex differentiation. Exogenous gibberellin treatment induced sepal hypoplasia and sex reversal, converting 42% of stamens into pistils in male plants. Transcriptome analysis identified 112 male-biased genes enriched in stamen and pollen development, while hormone profiling revealed coordinated changes in GA, cytokinins, auxin, jasmonic acid, and abscisic acid. Functional assays demonstrated that silencing SpAMS or SpPGIP caused extensive carpelization, and in situ hybridization localized their expression to developing anthers. Dual-luciferase assays confirmed that SpAMS directly activates the B-class gene SpPI, and genomic mapping placed SpAMS in the pseudo-autosomal region of the Y chromosome. These results indicate that GA disrupts hormonal homeostasis and anther wall integrity, while the SpAMS–SpPI pathway regulates tapetal development to maintain male identity. Our findings identify SpAMS as a key male-promoting factor in spinach and provide a framework for elucidating sex determination mechanisms in dioecious plants. Full article

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article

Rice (Oryza sativa L.) is one of the major food crops. Yield and quality are affected by premature leaf senescence, a complex and tightly regulated developmental process. To elucidate the molecular regulatory mechanism controlling rice leaf senescence, the integrative transcriptome, metabolome and weighted gene co-expression network analysis (WGCNA) of flag leaves in five development stages (FL1–FL5) was performed. In this study, a total of 9412 differential expressed genes (DEGs) were identified. To further mine DEGs related to leaf senescence, a total of five stage-specific modules were characterized by WGCNA. Among them, two modules displayed continuous down-regulated and up-regulated trends from stages FL1 to FL5, which were considered to be highly negatively and positively correlated with the senescence trait, respectively. GO enrichment results showed that the genes clustered in stage-specific modules were significantly enriched in a vast number of senescence-associated biological processes. Furthermore, large numbers of senescence-related genes were identified, mainly participating in transcription regulation, hormone pathways, degradation of chlorophyll, ROS metabolism, senescence-associated genes (SAGs), and others. Most importantly, a total of 40 hub genes associated with leaf senescence were identified. In addition, the metabolome analysis showed that a total of 309 differential metabolites (DMs) were identified by WGCNA. The integrative transcriptome and metabolome analysis identified a key hub gene OsBELH4A based on the correlation analysis conducted between 40 hub genes and 309 DMs. The results of function validation showed that OsBELH4A overexpression lines displayed delayed leaf senescence, and significantly increased grain number per plant and grain number per panicle. By contrast, its knockout lines displayed premature leaf senescence and reduced grain yield. Exogenous hormone treatment showed that OsBELH4A significantly responded to SA and auxin. These findings provide novel insights into leaf senescence, and further contribute to providing genetic resources for the breeding of crops resistant to premature senescence. Full article

Understanding the genetic architecture of complex traits is crucial for crop improvement and molecular breeding. We developed a mutagenized soybean population using carbon ion beam irradiation and conducted genome-wide association studies (GWAS) to identify variants controlling key agronomic traits. Whole-genome resequencing of 199 M4 lines revealed 1.48 million SNPs, predominantly C→T transitions, with population structure analysis identifying three distinct genetic groups. GWAS across five traits revealed striking differences in genetic architecture: the podding habit showed extreme polygenic control with 87,029 significant associations of small effect, while pubescence color exhibited oligogenic inheritance with only 122 variants. Hundred-seed weight displayed moderate complexity (4637 associations) with the largest effect sizes (−3.74 to 5.03) and major QTLs on chromosomes 4, 7, and 15–20. Growth habit involved 12,136 SNPs, including a strong chromosome 3 association (−log₁₀(p-value) > 50). Flower color showed 2662 associations clustered on chromosome 15. Functional analysis of 18,542 candidate genes revealed trait-specific pathway enrichments: flavonoid biosynthesis for flower color, phloem transport for seed weight, auxin signaling for growth habit, and amino acid transport for podding habit. This study demonstrates how mutagenesis-induced variation, combined with association mapping, reveals evolutionary constraints that shape genetic architectures, providing insights for genetics-assisted breeding strategies. Full article

Soybean (Glycine max (L.) Merr.) is a vital crop for the global supply of protein and oil, with its growth and development being regulated by genetic, hormonal, and environmental factors, particularly light and hormone signaling. The Small Auxin-Up RNA (SAUR) gene family plays a crucial role in plant growth regulation; however, the molecular mechanisms by which GmSAUR46 integrates photosynthesis and hormonal networks in soybean remain unclear. In this study, we focused on GmSAUR46b (Glyma.19G182600.1) and employed CRISPR/Cas9-mediated knockout and 35S-driven overexpression lines, alongside wild-type soybean (cv. Williams 82), to investigate its function. RNA sequencing (RNA-Seq) was conducted on shoot apical meristems, stems, and leaves at three developmental stages (V1, V2, V3), followed by transcriptomic analyses, including differential gene expression (DEG) identification and functional enrichment (GO, KEGG, KOG). Anatomical studies using paraffin sectioning and scanning electron microscopy (SEM) assessed the leaf midrib thickness and stem trichome density under varying light conditions. The transcriptomic results revealed DEGs enriched in pathways related to cell wall metabolism, hormone response, and photosynthesis. Anatomical analyses demonstrated that GmSAUR46b specifically regulates the leaf midrib thickness and stem trichome density in a light-dependent manner: under shade, the overexpression lines exhibited increased midrib thickness and trichome density, whereas the knockout lines showed reduced trichome density. Additionally, novel transcripts associated with stress resistance, hormone metabolism, and photosynthesis were identified, expanding the known soybean gene repertoire. Collectively, GmSAUR46b functions as a central hub integrating light signals with hormone and cell wall pathways to modulate soybean growth, particularly leaf and stem traits. This study advances understanding of SAUR gene function in soybean and provides valuable insights for molecular breeding aimed at improving adaptability and yield under diverse environmental conditions. Full article

Achieving high yield while maintaining disease resistance is a crucial goal in rice breeding programs. In this research, two cultivated rice varieties, Jia58 and Runxiang3, were selected as parental lines. A new variety, designated as the new variety RXN2, was generated and identified through a breeding process that involved hybridization of the parental lines followed by irradiation-induced mutagenesis of the offspring. Compared with its parental lines, RXN2 shows increased plant height, higher yield, and stronger resistance to bacterial blight. Comprehensive transcriptomic and metabolic analyses indicate that pathways associated with growth, such as gibberellin and auxin signaling, are upregulated in RXN2. Meanwhile, defense-related pathways, especially those involving jasmonic acid and peroxidase metabolism, are significantly enhanced. These results provide new insights into the trade-offs between growth and defense and elucidate the genetic and metabolic underpinnings of the simultaneous improvement in grain yield and disease resistance in rice. Full article

The root system is an important determinant affecting the growth, adaptivity and stress resistance of citrus plants. Currently, the genetic regulatory network underlying root growth and development in citrus remains largely unknown. We report that a PtrAUX/IAA-ARF complex mediates the growth and development of roots in citrus through regulating the transcription of PtrSAUR. The auxin signaling pathway plays an essential role in regulating the growth and development of roots. In this study, we found that in citrus Poncirus trifoliata, PtrIAA12, encoding a canonical Aux/IAA protein, was highly expressed in the meristem and elongation zone of the root. Functional characterization showed that overexpression and silence of PtrIAA12 significantly enhanced and suppressed the elongation of primary roots, respectively. Further analysis revealed that PtrIAA12 could interact with some members of PtrARFs, of which, PtrARF8 was identified to be the transcriptional factor of PtrSAUR17. Investigation of PtrSAUR17 transgenic plants verified that PtrSAUR17 is a key gene regulating the growth of roots in citrus. In conclusion, PtrIAA12 and PtrARF8 are the key members of the AUX/IAA-ARF complex in citrus controlling the growth and development of roots through regulating the transcription of PtrSAUR17. Full article

Grain shape is a critical determinant of rice yield, quality, and market value. Recent advances in molecular biology, genomics, and systems biology have revealed a complex regulatory network governing grain development, integrating genetic loci, plant hormone signaling, transcriptional regulation, protein ubiquitination, epigenetic modifications, and environmental cues. This review summarizes key genetic components such as QTLs, transcription factors, and hormone pathways—including auxin, cytokinin, gibberellin, brassinosteroids, and abscisic acid—that influence seed size through regulation of cell division, expansion, and nutrient allocation. The roles of the ubiquitin–proteasome system, miRNAs, lncRNAs, and chromatin remodeling are also discussed, highlighting their importance in fine-tuning grain development. Furthermore, we examine environmental factors that impact grain filling and size, including temperature, light, and nutrient availability. We also explore cutting-edge breeding strategies such as gene editing, functional marker development, and wild germplasm utilization, along with the integration of multi-omics platforms like RiceAtlas to enable intelligent and ecological zone-specific precision breeding. Finally, challenges such as pleiotropy and non-additive gene interactions are discussed, and future directions are proposed to enhance grain shape improvement for yield stability and food security. Full article

This study explored the regulatory effects of exogenous glucose (Glu) and sucrose (Suc) on the growth performance and physiological mechanisms of cucumber seedlings under salt stress. Using two cucumber cultivars as experimental materials, pot experiments demonstrated that salt stress significantly suppressed seedling growth, decreased chlorophyll content, and triggered oxidative damage. However, pretreatment with exogenous sugars effectively mitigated these adverse effects by maintaining photosynthetic efficiency, enhancing the activities of key antioxidant enzymes—superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX)—and reducing the accumulation of reactive oxygen species (ROS) and membrane lipid peroxidation. Transcriptomic analysis revealed that the two sugars differentially modulated antioxidant pathways and transcription factor networks to synergistically enhance salt tolerance. Specifically, sucrose preferentially activated POD, whereas glucose specifically induced APX and RbohD. Furthermore, glucose upregulated NAC and ERF family genes, while sucrose suppressed certain WRKY members. Both sugars contributed to the restoration of auxin and abscisic acid (ABA) signaling pathways. This study provides a theoretical foundation for the role of sugar signaling in enhancing crop resistance to abiotic stress. Full article

We investigated the effect of Agrobacterium rhizogenes-mediated transformation mof rolB on adventitious root development and endogenous hormones in ‘duli’ (Pyrus betulaefolia) via transcriptomic analysis of wild-type (WT) and rolB-transformed plants. The formation of root primordia occurred earlier in transgenic ‘duli’ than in the WT plants. At seven days, 57% of the transgenic seedlings had formed root primordia, whereas root primordia first appeared at seven days in WT ‘duli’. The rooting rate of transgenic ‘duli’ and WT plants was 90% and 77.14%, respectively. rolB significantly promoted the formation of secondary roots. Within 20 days, auxin (IAA), gibberellic acid (GA₃), and zeatin riboside (ZR) were higher and abscisic acid (ABA) was lower in transgenic ‘duli’ than in WT plants. Gene Ontology analysis revealed high enrichment in signaling pathways and ADP binding, and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that several differentially expressed genes were enriched in flavonoid and carotenoid-related pathways and plant hormone signal transduction. rolB induced changes in the expression patterns of several genes involved in hormone biosynthesis, metabolism, and signal transduction pathways in ‘duli’. Weighted gene co-expression network analysis identified the DEGs associated with endogenous hormone levels and indicated that the central genes of modules most strongly correlated with ABA, ZR, IAA, and GA₃ regulate protein synthesis, signaling, and root tissue meristem activity. Protein–protein interaction analysis yielded a co-expression network of physiological and transcriptomic data during rooting and identified key genes at the network core. These findings provide valuable insights into the regulatory mechanisms of rolB and its influence on root development in ‘duli’. Full article

The increasing demand for sustainable alternatives to synthetic agrochemicals underscores the need for novel, naturally derived plant growth regulators (PGRs) with high specificity and minimal environmental impact. In this study, we propose agavenin (AG), a steroidal saponin from Agave species, as a promising candidate and evaluate its potential role in plant growth regulation through a comprehensive in silico approach. Using molecular docking, molecular dynamics simulations, ADME profiling, and FTIR spectroscopy, we analyzed the interaction of AG with three key protein receptors (KPRs) that regulate major hormonal pathways: GA3Ox2 (gibberellin), IAA7 (auxin), and BRI1 (brassinosteroid). AG showed strong and stable binding to GA3Ox2 and IAA7, with affinities comparable to their endogenous ligands, while exhibiting low interaction with BRI1—suggesting receptor selectivity. Molecular dynamics confirmed the stability of AG–GA3Ox2 and AG–IAA7 complexes over 100 ns, and ADME profiling highlighted favorable properties for bioavailability and transport. Collectively, these findings indicate that AG could function as a selective, receptor-targeted modulator of gibberellin and auxin signaling pathways. Beyond demonstrating the molecular basis of AG’s bioactivity, this work establishes a computational foundation for its future experimental validation and potential development as a sustainable, naturally derived growth regulator for plant biotechnology and agriculture. Full article

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles in rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, we developed a robust pipeline (“RiceLncRNA”) for the accurate identification of rice lncRNAs. Using strand-specific RNA-sequencing (ssRNA-seq) data from the resistant (IR25), susceptible (LTH), and Nipponbare (NPB) varieties under M. oryzae infection, we identified 9003 high-confidence lncRNAs, significantly improving identification accuracy over traditional methods. Among the differentially expressed lncRNAs (DELs), those unique to IR25 were enriched in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, which suggests that they are associated with the production of salicylic acid (SA) and auxin (IAA) precursors, which may be involved in defense responses. Conversely, DELs specific to LTH primarily clustered within carbon metabolism pathways, indicating a metabolic reprogramming mechanism. Notably, 21 DELs responded concurrently in both IR25 and LTH at 12 h and 24 h post-inoculation, indicating a synergistic regulation of jasmonic acid (JA) and ethylene (ET) signaling while partially suppressing IAA pathways. Weighted gene co-expression network analysis (WGCNA) and competing endogenous RNA (ceRNA) network analysis revealed that key lncRNAs (e.g., LncRNA.9497.1) may function as miRNA “sponges”, potentially influencing the expression of receptor-like kinases (RLKs), resistance (R) proteins, and hormone signaling pathways. The reliability of these findings was confirmed through qRT-PCR and cloning experiments. In summary, our study provides an optimized rice lncRNA annotation framework and reveals the mechanism by which lncRNAs enhance rice blast resistance through the regulation of hormone signaling pathways. These findings offer an important molecular basis for rice disease-resistant breeding. Full article