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PubMed2025

Rice ETHYLENE RESPONSE FACTOR 101 increases leaf angle by upregulating BRASSINOSTEROID UPREGULATED 1.

The leaf angle (LA) is a critical component of plant architecture that directly influences photosynthetic efficiency and grain yield. In the present study, we found that ETHYLENE RESPONSE FACTOR 101 (OsERF101), an APETALA2/ethylene response factor, plays a role in LA formation. A null mutation in OsERF101 resulted in reduced LA, whereas transgenic plants overexpressing OsERF101 (OsERF101-OEs) exhibited increased LA. OsERF101 increased the development of the adaxial lamina joint (LJ). Transactivation assays and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis indicated that OsERF101 activated BRASSINOSTEROID UPREGULATED 1 (OsBU1) transcription by directly binding to its promoter. However, OsERF101 expression was suppressed by exogenous brassinosteroid (BR) treatment and elevated endogenous brassinolide (BL) levels during LJ development. Additionally, OsERF101 downregulated the expression of BR biosynthesis genes, including Brassinosteroid-deficient dwarf2 (OsBRD2) and CYP90B2/OsDWARF4, leading to reduced levels of endogenous BL, the most active BR, in OsERF101-OEs. These findings suggested that OsERF101 mediates a negative feedback loop that balances endogenous BR levels and signaling. Collectively, rice plants have evolved diverse regulatory mechanisms involving OsERF101 to tune LA formation and optimize plant architecture finely.

Oryza↗

PubMed2024

A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling.

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.

Zea mays↗

PubMed2026

Brassinosteroids as Central Regulators of Plant Growth, Stress Tolerance, and Agricultural Resilience.

Brassinosteroids (BRs) are essential steroidal phytohormones that regulate plant growth, development, and responses to environmental stresses. Recent studies have demonstrated the important roles of BRs in enhancing plant tolerance to abiotic stresses, including drought, salinity, temperature extremes, heavy metal toxicity, and oxidative stress, as well as biotic stresses caused by pathogens and herbivores. This review summarizes current advances in BR biosynthesis, metabolism, transport, and signaling pathways, focusing on key components that mediate stress adaptation. We discuss the physiological and molecular mechanisms through which BRs improve stress tolerance, including regulation of antioxidant defense, ion homeostasis, osmotic adjustment, and stress-responsive gene expression. Particular attention is given to the extensive cross talk between BRs and other phytohormones, such as abscisic acid, jasmonic acid, salicylic acid, ethylene, auxin, and gibberellins, which enables plants to balance growth and defense under adverse conditions. Furthermore, we highlighted the potential applications of BRs in crop improvement through exogenous treatments, genetic engineering, and genome-editing approaches. However, the effectiveness of BR-based strategies is highly dependent on crop species, developmental stage, stress type, BR concentration, application method, and environmental conditions. In addition, excessive BR accumulation or application may result in undesirable growth responses, and further multi-location field validation is required before widespread agricultural implementation. Finally, we discuss emerging research trends, current knowledge gaps, and future perspectives for exploring BR signaling to develop climate-resilient crops. Overall, BRs represent promising targets for improving crop stress resilience; however, optimizing BR-mediated strategies and validating their long-term performance under diverse field conditions will be essential for their successful application in sustainable agriculture.

abiotic stress↗

PubMed2026

Genome-wide characterization of BraABCB transporters reveals their potential roles in hormone responses in Brassica rapa var. parachinensis.

Thirty-six BraABCB genes were identified in Brassica rapa var. parachinensis; expression and interaction analyses suggest BraABCB27 and BraABCB28 as hormone-responsive candidates associated with BRI1-related proteins. ABCB transporters are ATP-dependent membrane proteins that mediate the transport of diverse substrates, including phytohormones, and play important roles in plant development and environmental adaptation. Previous studies in Arabidopsis have shown that several ABCB proteins participate in phytohormone transport, including auxin and brassinosteroid transport, whereas the functions of their homologs in Brassica rapa var. parachinensis remain poorly understood. In this study, 36 BraABCB genes were identified and classified into four phylogenetic groups. Conserved domain analysis showed that BraABCB proteins contain typical nucleotide-binding domains and transmembrane domains. Chromosomal distribution, collinearity, and Ka/Ks analyses suggested that the BraABCB family is evolutionarily conserved and mainly subject to purifying constraints. Promoter analysis and RT-qPCR assays of selected Group IV BraABCB genes revealed diverse expression patterns and responses to drought, high temperature, brassinolide, and indole-3-acetic acid treatments. Subcellular localization assays showed that selected Group IV BraABCB proteins exhibited predominant plasma membrane localization. Notably, BraABCB27 and BraABCB28, two close AtABCB1/AtABCB19-related homologs, showed detectable physical associations with BRI1-related proteins in BiFC and split-ubiquitin yeast two-hybrid assays. Together, these results provide a genome-wide characterization of the BraABCB gene family and identify BraABCB27 and BraABCB28 as candidate genes for future studies of their possible associations with BR-related membrane processes and hormone-regulated growth responses in B. rapa var. parachinensis.

Plant Growth Regulators↗

PubMed2025

Genetic basis and role of exotic accessions in cultivated cotton fiber quality improvement.

Exotic Gossypium accessions still harbor QTL‑validated alleles that, combined with CRISPR pyramiding and genomic selection, can break the entrenched fiber length-strength trade‑off. Cotton's four independent domestications twice in diploids and twice in allotetraploids offer a natural experiment in fiber improvement. Synthesizing three decades of data, we chart how polyploidy, selection and modern breeding have repeatedly reshaped the Gossypium genome. More than 15,000 quantitative trait locus (QTL) and genome wide association mapping studies (GWAS) hits converge on a handful of chromosomal "hotspots"; new MAGIC, NAM, NIL and long-read resources now narrow these peaks to < 200 kb, resolving causal genes such as GhHOX3, GhZF14 and GhMYB7. Multi-omics evidence links auxin, ethylene, gibberellin, brassinosteroid and strigolactone signaling to HDZIP IV, MYB, bHLH/HLH and ERF networks that drive fiber initiation, extreme cell elongation and cellulose deposition. Population genomics shows that ~ 40% of favorable fiber alleles are fixed in elite Gossypium hirsutum, yet wild diploids and landraces still harbor variants that could break the length strength trade-off. We propose a three-step roadmap genomic selection, CRISPR gene pyramiding and accelerated introgression to expand cotton's genetic base and deliver fibers suited to sustainable textile demands.

Gossypium↗

PubMed2025

Genomics control of biostimulant-induced stress tolerance and crop yield enhancement.

Biostimulants are changing modern agriculture, as they have the potential to secure healthy and sustainable food production while preserving the environment. They have two main biological effects: growth promotion and stress protection. Both effects can lead to enhancement of the yield and improvement of the marketable grade of the produce in crops, without compromising crop quality. Their use increased exponentially in the past decade, as they are highly efficient, ecologically friendly (non-toxic, biodegradable), and applicable to all major crops. While exponential data on the physiological mechanisms of stress protection is accumulating in recent years, the information as to how biostimulants act at the molecular level is still rather limited. Here we review the growing evidence of the biostimulants role in stress protection and yield enhancement of crops, as well as the recent transcriptomic and metabolomic data, which indicate biostimulants' molecular mode of action. In particular, we outline the role of genes encoding signaling components, plant hormones (abscisic acid, brassinosteroids, and ethylene), genes encoding transcription factors from ERF, WRKY, NAC, and MYB families, and genes related to growth, photosynthesis, and stress response. Finally, we describe strategies to study the genetic and genomics control of biostimulants mode of action, with foci on stress tolerance and yield enhancement. In Arabidopsis, established systems for biostimulants-induced protection against drought and oxidative stress will allow both forward and reverse genetics approaches to identify key genes from the biostimulants network. Mutations in such genes compromise the stress-protective effect of biostimulants. In major crops such as pepper and tomato, large Genome Wide Association Studies (GWAS) panels can be utilized to study crops responses to biostimulants in terms of drought tolerance, fruit qualities, and yield in order to pinpoint genes controlling biostimulants-induced stress protection and yield enhancement. The combination of these approaches allows identification and verification of important genes involved in the pathways of biostimulant-induced stress protection and yield enhancement, as well as deciphering parts of the intricate biostimulant-signaling network.

Crops, Agricultural↗

PubMed2026

Phytohormones in fungi: inter-kingdom modulators or fungal self-controlling elements?

SUMMARYLeveraging data from innovative experimental approaches, omics technologies, and bioinformatics, we offer new insights into how fungi communicate with and perceive their environment to achieve ecological success. By integrating comparative data from both the fungal and plant kingdoms, we critically reassessed the evolutionary, biochemical, and functional landscape of phytohormones in fungi, challenging the conventional notion that these molecules serve exclusively as plant regulators or as means of communication with them. Our analysis demonstrates that fungi not only synthesize a diverse array of phytohormones-including auxins, cytokinins, gibberellins, abscisic acid, ethylene, brassinosteroids, salicylic acid, and oxylipins-but also possess hormone-sensing and signal transduction mechanisms architecturally distinct from those of plants. Employing genomics, phylogenetics, and structural analyses, the review uncovers that many hormone biosynthetic and sensing pathways in fungi are evolutionarily ancient, sometimes predating their roles in plant-fungus interactions, and that some pathways show convergence rather than direct gene homology. Fungal phytohormones regulate development, growth, and metabolism, thereby playing key functions in their ecological context. The review emphasizes that, while biosynthetic pathways tend to be highly conserved, perception and signaling mechanisms in fungi are more varied and often remain poorly understood. We conclude that fungi have an intrinsic and autonomous hormonal physiology that underpins their ecological adaptability and success. Collectively, this analysis reframes fungal biology, highlighting the need for deeper investigation into the signaling and regulatory roles of phytohormones in fungi beyond their interactions with plants.

cell signaling↗

PubMed2026

Genome-wide identification and functional analysis of the BES1-like (VfBES1) gene family in Vernicia fordii reveals its role in floral development.

BACKGROUND: Vernicia fordii Hemsl (also known as Tung tree), an significant commercial oil-producing tree species, is a monoecious and diclinous species with male and female flowers on the same inflorescence; however, the molecular mechanisms governing its floral sex determination remain elusive, particularly the genetic basis underlying the skewed female-to-male flower ratio and the evolutionary dynamics of sex-related gene families, which severely restrict targeted breeding for yield enhancement. In the model plant Arabidopsis, the BRI1 EMS SUPPRESSOR 1 (BES1) transcription factor family plays a crucial role in Brassinosteroid (BR) signaling and reproductive development. However, its function remains largely unexplored in woody perennials. RESULTS: In this study, we introduce the genome-wide identification and functional characterization of the BES1-like (VfBES1) gene family in the Tung tree for the first time. Integrative multi-omics approaches reveal seven VfBES1 genes that are clustered into three phylogenetically distinct clades, each characterized by clade-specific motifs and structural simplicity. Segmental duplication events (VfBES1-1/VfBES1-5 and VfBES1-4/VfBES1-7) and promoter cis-element enrichment (hormone-responsive and abiotic stress-related motifs) highlight evolutionary innovation and functional diversification. Spatiotemporal expression profiling reveals VfBES1 genes' tissue- and stage-specific roles. VfBES1-1 predominantly expresses in female flowers and fruits, suggesting its possible roles in late-stage sex maintenance or ovule and fruit development. VfBES1-2 and VfBES1-6 exhibit male flower-specific and early floral developmental activation, respectively. Nuclear-localized VfBES1-6 displays co-expression with VfMYB35-1 gene, which is a regulator of male structure degeneration. CONCLUSIONS: Findings in this study shed light on the regulatory roles of VfBES1 genes in the floral development of the Tung tree, providing a reference for its precision breeding to enhance flowering synchrony and seed productivity. This study also provides a comparative framework for understanding the functional diversity of BES1-like genes in non-model woody plants.

Flowers↗

PubMed2026

Dual regulation of the receptor-like kinase BIR1 involves site-directed transcript cleavage and 5'-leader-mediated translational control.

In Arabidopsis, BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASE 1 (BIR1) is a negative regulator of plant immunity and cell death. BIR1 was earlier described as a target of epigenetic and post-transcriptional degradation. During virus infections, degradome analysis of BIR1 transcripts mapped predominant mRNA cleavage sites at the 5'-untranslated leader region (site A) and the protein-coding sequence (sites B and C). Here, we identified another virus-associated cleavage site (D) within the BIR1 coding region and investigated the contribution of site-directed mRNA cleavage to BIR1 regulation. Mutations at B, C, and D sites enhanced mRNA stability by impairing transcript cleavage, resulting in increased BIR1 mRNA and protein accumulation. This regulation is disrupted in RNA silencing mutants, supporting a model of cis-directed small interfering RNA (siRNA)-mediated degradation. We next demonstrate that virus infection reduces BIR1 translation in Arabidopsis. Furthermore, our data reveal a repressive role for the 5'-leader in regulating BIR1 translation, potentially mediated by upstream open reading frames (uORFs) and a virus-responsive long non-coding RNA (lncRNA) derived from the natural antisense At4g39838 locus. Together, these findings reveal a multilayered regulatory mechanism that integrates sRNA-mediated cleavage with translational control, with broader implications for the fine-tuning of stress-responsive gene expression during infection.

Arabidopsis↗

PubMed2026

Genome-Wide Analysis of Triticum aestivum Root Meristem Growth Factor (RGF) Gene Family Highlights TaRGF5 as a Putative Component of Root-Associated Signaling.

Wheat (Triticum aestivum), a key global crop, faces rising drought stress that limits root growth and water uptake. Root meristem growth factors (RGFs) are small peptides that regulate root stem cell maintenance, meristem activity, and lateral root formation in model plants, yet the RGF gene family remains unexplored in wheat. Here, we performed a comprehensive genome-wide analysis of the TaRGF gene family, identifying 15 genes distributed across the A, B, and D subgenomes and classified into five homeologous groups (TaRGF1-TaRGF5), predominantly located on chromosomes 2 and 6. All TaRGFs contained a characteristic RGF motif, with dibasic cleavage sites and Asp-Tyr motifs indicating conserved maturation mechanisms. Based on the phylogenetic analysis, the TaRGF5 homeologs showed the highest similarity to Arabidopsis thaliana RGF5. Tested RNA-seq data revealed predominantly root-enriched expression for all TaRGF genes, with TaRGF5 exhibiting the most root-preferential and downregulation under drought stress. Quantitative real-time PCR (qRT-PCR) confirmed that drought stress suppressed the expression of TaRGF5A, TaRGF5B, and TaRGF5D in roots of wheat cultivar Sids-13 across all time points, unlike the higher accumulation seen in controls. Promoter analysis predicted a unique BES1 transcription factor binding site exclusively in TaRGF5B, linking brassinosteroid signaling to peptide-mediated root regulation. Structural modeling and molecular docking predicted an interaction between wheat TaRGF5 homeologs and root growth factor-insensitive receptor kinase (TaRGI3), characterized by conserved sulfotyrosine-mediated binding and favorable interaction energetics. Based on this characterization of the wheat RGF gene family, particularly the potential role of TaRGF5 in root development and drought-adaptation signaling, we propose targeting this gene for functional analysis to improve wheat resilience under water-limited conditions.

Triticum↗