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PubMed2026

Auxin-induced ARF transcription factor degradation defines tissue boundaries.

How organs partition themselves into discrete domains with distinct functions is a fundamental question in biology. The gynoecium of flowering plants provides an excellent system to address this question. Here, we show that the boundary between the stigma and style at the gynoecium apex is established by the complementary distribution of the phytohormone auxin and the Auxin Response Factor (ARF), ETTIN (ETT). Mechanistically, auxin induces ETT protein destabilization via the ubiquitin-proteasome pathway. A short sequence motif within an intrinsically disordered region is required for this auxin-triggered degradation. Disruption of this motif leads to ectopic ETT accumulation at the gynoecium apex and consequently abolishes stigma-style boundary development. We further demonstrate that this previously unrecognized mode of auxin-induced ARF instability is evolutionarily conserved among ETT orthologs across angiosperms. In summary, this study reveals how graded auxin distribution affects ARF transcription factor activity, contributing to the establishment of the stigma-style boundary, ensuring correct gynoecium formation and reproductive success in flowering plants.

Indoleacetic Acids↗
PubMed2026

Genome-Wide Identification of the LdARF Gene Family in Lilium davidii var. unicolor and Transient Functional Analysis of LdARF17 in Bulblet Regeneration.

Auxin response factors (ARFs) are key transcriptional regulators of the auxin signaling pathway and play important roles in plant organogenesis and regeneration. However, the functions of ARF family genes in lily scale-derived bulblet regeneration remain largely unclear. In this study, 24 LdARF genes were identified from the genome of Lilium davidii var. unicolor. Phylogenetic analysis revealed that LdARF proteins showed evolutionary conservation with ARF homologs from other monocot species. Genome-wide identification, phylogenetic analysis, and expression profiling revealed functional divergence among LdARF genes during scale-derived bulblet regeneration. Among them, LdARF17 exhibited a distinct regeneration-associated expression pattern, characterized by rapid induction after scale excision and sustained high expression during subsequent bulblet initiation and formation. Subcellular localization analysis demonstrated that LdARF17 is localized in the nucleus. Transient overexpression of LdARF17 significantly promoted bulblet regeneration and was associated with increased expression of auxin-responsive and regeneration-related genes, including IAA14, LBD16, and LBD29. These findings suggest that LdARF17 acts as a positive regulator of lily scale regeneration and may influence auxin-responsive transcriptional processes associated with early cell proliferation, providing new insights into the molecular mechanisms underlying vegetative regeneration in lilies.

Auxin response factor↗
PubMed2026

Quantitative trait locus qLDC5 regulates primary root branching in an auxin-dependent manner.

L-type lateral root (LLR) density determines root system architecture, affecting nutrient acquisition in rice (Oryza sativa L.), particularly under low-phosphorus conditions. Previous studies identified genotypic differences in LLR density and a quantitative trait locus (QTL) enhancing LLR density on crown roots (qLDC5). We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in qLDC5 donor DJ123 compared with the African variety NERICA4 using X-ray micro-computed tomography. We confirmed the qLDC5 effect in a field experiment for LLR density on primary roots. LLR densities on primary and crown roots, therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188-a derivative line harboring qLDC5-initiate more lateral root primordia than NERICA4, with a higher proportion progressing to elongation, but that exogenous auxin application reversed this ranking. Within qLDC5, auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were up-regulated in DJ123. Transcriptome analysis revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes in DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways.

Oryza↗
PubMed2026

OsMYB8-OsARF12/25 module fine-tunes tiller angle via auxin signaling pathway in rice.

Tiller angle is a critical determinant of rice plant architecture and significantly impacts grain yield by influencing planting density and photosynthetic efficiency. Although auxin signaling is known to affect tiller angle in rice, the detailed regulatory networks remain largely unknown. In this study, we identify OsMYB8, an R2R3-MYB transcription factor, as a positive regulator of rice tiller angle. Functional analyses revealed that loss-of-function mutants of OsMYB8 exhibited reduced tiller angles and a more compact architecture, while overexpression of OsMYB8 resulted in more expanded tiller angles. Further investigations found that OsMYB8 might negatively regulate the shoot gravitropic response by disrupting asymmetric auxin distribution. At the molecular level, OsMYB8 directly binds to the promoters of 2 auxin response factors, OsARF12 and OsARF25, and represses their transcription. Genetic analyses confirmed that OsMYB8 acts upstream of OsARF12 and OsARF25 in regulating rice tiller angle. Our finding elucidates a previously uncharacterized OsMYB8-OsARF12/25 transcriptional module that fine-tunes auxin signaling to regulate tiller angle in rice, and offers valuable genetic targets for the optimization of rice architecture and yield potential.

Oryza↗
PubMed2025

Water shortage reduces PHYTOCHROME INTERACTING FACTOR 4, 5 and 3 expression and shade avoidance in Arabidopsis.

In agricultural crops, forests and grasslands, water deficit often occurs in the presence of cues from neighbouring vegetation. However, most studies have addressed separately the mechanisms of plant growth responses to these two aspects of the environment. Here we show that transferring Arabidopsis thaliana seedlings to agar containing polyethylene glycol (PEG) to restrict water availability reduces hypocotyl growth responses to shade without simultaneously affecting cotyledon expansion or its response to shade. Hypocotyl growth showed significant triple interaction among water availability, shade and the presence of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), PIF5 and PIF3. Water restriction diminished auxin signalling and the activity of the PIF4, PIF5, PIF3 gene promoters and their transcript levels. The responses of PIF4 expression and hypocotyl growth to PEG were reduced in mutants of its positive morning regulators CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The CCA1 and LHY gene promoters also reduced their activity in response to PEG. In addition to the changes in PIF4 levels, post-transcriptional processes also contributed to the PIF4 protein response to PEG. Collectively, these results unveil PIFs as a hub that interlinks shade and drought information to control growth.

Arabidopsis↗
PubMed2026

A FERONIA-MPK3/6-WRKY3/4 module links auxin signaling to lateral root development in Arabidopsis.

The phytohormone auxin orchestrates root development through intricate signaling networks. In the non-canonical auxin pathway, both the transmembrane kinase (TMK)-mediated signaling and the mitogen-activated protein kinase (MAPK) cascade are shown to be involved in the auxin-regulated lateral root (LR) formation. However, the role and mechanism of the receptor-like kinase FERONIA (FER) in this process remain unclear. Here, quantitative proteomic and phosphoproteomic analyses of Arabidopsis roots identify FER, MPK3/6, and WRKY3/4 as auxin-responsive components. Further analyses reveal that FER functions as a negative regulator of LR development by modulating cell division patterns within LR primordia. FER interacts with and phosphorylates MPK3/6, which then phosphorylate the transcription factors WRKY3 and WRKY4 to form a repressive module that ultimately suppresses LR organogenesis. Collectively, our findings define a FER-MPK3/6-WRKY3/4 signaling module that negatively regulates LR formation, demonstrating a previously unknown integration of FER-mediated signaling into the MAPK cascade in auxin-triggered organogenesis.

Arabidopsis↗
PubMed2026

MdWRKY75 interacts with MdWOX11 to modulate root growth under salt stress in apple.

The root system is pivotal for plant development, enabling both vegetative growth and tolerance to abiotic stresses like salinity. However, the molecular mechanisms governing root adaptive development in response to salt stress remain poorly understood in apple (Malus domestica Borkh.). In this study, we identified the salt stress-responsive WRKY transcription factor MdWRKY75. Overexpression of MdWRKY75 in transgenic apple negatively regulates adventitious root (AR) formation and salt stress tolerance, whereas reducing MdWRKY75 expression yields the opposite phenotype. Moreover, MdWRKY75 directly binds to the promoter of MdSAUR15 (SMALL AUXIN UP RNA15) and transcriptionally represses the expression of MdSAUR15, which, when overexpressed, promotes AR formation and enhances salt stress tolerance. We further demonstrated that MdWRKY75 interacts with MdWOX11, a WUSCHEL-related homeobox (WOX) transcription factor, both in vitro and in vivo. MdWOX11 expression is upregulated and enhances AR formation under salt stress. Additionally, MdWOX11 reduces the binding of MdWRKY75 to the MdSAUR15 promoter, and alleviates the MdWRKY75-mediated inhibitory effect on MdSAUR15 expression. Collectively, our study provides a MdWOX11-MdWRKY75-MdSAUR15 module regulating root adaptation in response to salt stress in apple.

Malus↗
PubMed2026

Long-day photoperiod promotes growth of pea (Pisum sativum L.) via auxin biosynthesis and polar transport.

Photoperiodic sensitivity is an essential factor that may affect agricultural practices under current climate scenarios. This study used pea (Pisum sativum) to examine effects of varying photoperiods on growth and photosynthetic parameters and then reveal the mechanistic basis of this process by linking them with tissue-specific distribution of auxin and regulation of related genes. This was achieved by transcriptome sequencing, genome-wide gene family identification, and expression pattern analysis. Best results in terms of growth and yield were obtained with a 20 h/4 h light/dark photoperiod and these plants had the highest content of endogenous indole-3-acetic acid (IAA) in both the shoot apex and the root. Genes consistently upregulated with prolonged light exposure were significantly enriched in pathways related to light signal transduction, photosynthetic carbon metabolism, and phytohormone signal transduction. Through genome-wide identification, we characterized the TAA/TAR and YUCCA families (key gene families involved in auxin biosynthesis) as well as the PIN family (responsible for auxin polar transport) in pea. Extending the light duration positively affected expression of several genes related to auxin biosynthesis and transport, among them members of the Elongated Hypocotyl (HY) and Phytochrome-Interacting Factor (PIF) families being key light-induced transcription factors, PsTAR2, the principal gene regulating auxin biosynthesis, as well as PsPIN4, PsPIN5, PsPIN11, and PsPIN13 which mediate polar auxin transport. By elucidating mechanisms underlying the coordinated regulation of pea growth by light and auxin, this work provides a significant reference for photoperiod research on long-day crops for both protected- and field-based horticulture.

Auxin↗
PubMed2025

Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures.

We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant, named Twisted Sister1 (TS1), had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of TS1 were insensitive to externally applied auxin, with the genetics and physiology suggestive of a mutated AUX/IAA transcription factor gene. Hexaploid wheat possesses over 80 AUX/IAA genes, and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2 population mapped the mutation to chromosome 5A, and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the TraesCS5A03G0149800 gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed TraesCS5A03G0149800 as underlying the mutant phenotype by generating transgenic Arabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of AUX/IAA genes in gravity responses, although there were marked differences. Here we show that the sequenced wheat genome, along with previous knowledge of the physiology of gravity responses from other plant species, gene mapping, RNA-seq, and expression in Arabidopsis have enabled the cloning of a key wheat gene that defines plant architecture.

Triticum↗
PubMed2025

Bimodal retrograde signaling disrupts a suppressor network and activates a key transcriptional activator to direct stress responses.

Plastid-to-nucleus communication, crucial for regulating stress-responsive gene expression, has long intrigued researchers. This study reveals how the plastidial metabolite 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEcPP) orchestrates transcriptional reprogramming by modulating the rapid stress response element (RSRE), a conserved regulatory hub in the plant general stress response network. Yeast one-hybrid assays identified HAT1, a class II HD-Zip protein, as a negative regulator of RSRE. Genetic analyses, including HAT1 overexpression and knockdowns, confirmed its role in suppressing RSRE activity. Interaction assays uncovered a suppression network involving HAT1, the co-repressor TOPLESS (TPL), and the nuclear importin IMPα-9. Furthermore, HAT1 interacts with calmodulin-binding transcription activator 3 (CAMTA3), a calcium/calmodulin-binding transcription factor known to activate RSRE. AlphaFold modeling provided insights into the architecture of the HAT1-RSRE complex and HAT-CAMTA3 interaction, supported by conserved domains across plant species. Under stress condition, MEcPP accumulation promotes the 26S proteasomal degradation of TPL and IMPα-9 while reduces auxin-dependent HAT1 expression. Additionally, MEcPP enhances Ca2+ influx, activating CAMTA3 and enabling it to bind RSRE, thereby initiating the transcription of stress response genes. This dual mechanism-dismantling suppressors (HAT1, TPL, and IMPα-9) and activating CAMTA3-underscores MEcPP's central role in plastid-to-nucleus signaling. These findings emphasize MEcPP's pivotal function in dynamically regulating gene expression to maintain cellular homeostasis under environmental stress.

Arabidopsis Proteins↗
PubMed2026

Integrated methylome and transcriptome analysis provides insight into DNA methylation-mediated networks in sexual dimorphism of Vernicia montana.

BACKGROUND: Sexual dimorphism is fundamental to reproduction in dioecious plants and is regulated by both genetic and epigenetic mechanisms. DNA methylation is a central epigenetic mark known to influence phenotypic variation in plants. However, its specific role in shaping sexual dimorphism in dioecious trees remains poorly understood. To address this question, we performed integrated genome-wide DNA methylome and transcriptome analyses of four tissue types in the dioecious tung tree (Vernicia montana), including male and female flower buds and their corresponding leaves. RESULTS: Our analysis revealed distinct DNA methylation patterns between male and female tissues. Notably, the coordination between DNA methylation reprogramming and transcriptional regulation appeared to be more strongly associated with reproductive development than with vegetative growth in V. montana. We identified a set of sex-biased genes that may reflect different reproductive strategies between the sexes. Further analysis identified several key transcription factors (TFs) potentially associated with promoter differentially methylated regions (DMRs), including flowering-time regulators (e.g., FRS5, REM16, and VRN1) and TFs involved in hormone signaling pathways such as jasmonic acid, auxin, and salicylic acid signaling. Cis-regulatory element analysis showed that some promoter DMRs overlapped with hormone response elements related to abscisic acid, auxin, and gibberellin. Co-expression network analysis further revealed potential regulatory correlations among promoter DMR-mediated TFs, hormone-responsive pathways, and key floral development regulators. CONCLUSIONS: Collectively, our results suggest that interactions among DNA methylation, transcriptional regulation, and hormone-responsive pathways may contribute to the establishment of sexual dimorphism in V. montana. This study provides the first integrated view of these regulatory layers in V. montana and supports a species-specific regulatory framework for understanding the epigenetic basis of sexual dimorphism in this economically important dioecious tree. The proposed framework is based on multi-omics analyses and warrants further validation through targeted functional studies.

DNA Methylation↗
PubMed2026

Natural leaf shape variation reveals diverse transcriptional targets of GmJAG1 during soybean leaf development.

The JAGGED transcription factor family regulates lateral organ development across angiosperms. In soybean (Glycine max Merr.), a D9H mutation in the EAR repression motif of GmJAG1 causes a narrow-leaflet phenotype and explains over 70% of phenotypic variance in leaf shape. Because this mutation does not affect the zinc finger DNA-binding domain, both alleles bind identical targets but differ in repressor recruitment. Previous studies mapped GmJAG1 binding sites, but the functional targets controlling leaf morphology are uncharacterized. Here, we used comparative transcriptomics across four soybean genotypes with contrasting leaf shape, spanning a developmental time series from shoot apex to mature leaf, and identified 1567 putative candidate target genes. GmJAG1 expression was confined to the shoot apex, yet 99.1% of candidate targets maintained differential expression throughout development. We found that neither Kip-Related Protein (KRP) cell cycle inhibitors nor Cyclin-Dependent Kinases (CDKs) showed differential expression despite binding evidence in Arabidopsis. However, D-type cyclins were upregulated in narrow-leaf genotypes suggesting that soybean GmJAG1 acts through cyclin-mediated rather than KRP-mediated cell cycle regulation described in Arabidopsis- a divergence in regulatory logic between the two species. Pathway analysis revealed enrichment of auxin (1.8-fold, P = 0.02) and salicylic acid (fourfold, P = 0.016) genes among JAG1D9H targets. Filtering by differential expression, binding data, phenotype correlation, and co-expression network membership identified 79 high-confidence targets, including orthologs of NPH3 (phototropin-mediated leaf flattening), MIK2 (cell wall integrity sensing), RD22 (ABA-responsive stress signaling), and SCL23 (GRAS transcription factor in bundle sheath development). These candidates provide targets for functional validation and breeding in legumes.

Glycine max↗
PubMed2026

The CsTBH-CsROP2 Module Regulates Waterlogging Tolerance via Auxin-Mediated Adventitious Root Formation in Cucumber.

Cucumber (Cucumis sativus L.) requires frequent irrigation due to its shallow root system and high transpiration rate of the aboveground parts. However, it is also prone to waterlogging damage. Therefore, understanding its response to waterlogging is crucial for breeding waterlogging-tolerant varieties. Although Rho of Plants GTPases play well-established roles in regulating development and stress signalling, their functions in plant adaptation to waterlogging stress has yet to be fully elucidated. Here, we identified nine CsROP genes in the cucumber genome, which exhibit evolutionary diversification but retain conserved functional domains. Functional analysis revealed that CsROP2 acts as a negative regulator of adventitious root formation. It modulates auxin accumulation in hypocotyl vascular bundles, thereby suppressing adventitious root development and enhancing waterlogging sensitivity. The HD-Zip I transcription factor CsTBH directly binds the CsROP2 promoter and activates its expression. Our study uncovers a CsTBH-CsROP2 module that governs adventitious rooting and waterlogging tolerance by modulating auxin homeostasis. These findings provide new insights into the crosstalk between developmental programmes and stress signalling pathways and offer potential genetic targets for improving stress resilience in cucumber and other crops.

CsROP2↗
PubMed2026

Habitat-Adapted Fungal Symbionts Promote Salt Stress Tolerance Through Distinct Root Mechanisms and Shared Shoot Regulatory Networks in Arabidopsis thaliana.

Salinity is a major constraint to crop productivity. Beneficial plant-fungus interactions represent a promising strategy to enhance stress resilience. Here, we investigated fungal endophytes isolated from the roots of Oryza sativa cultivated in saline-prone marshlands of the Guadalquivir River, Spain. From a collection of 38 isolates, five salt-tolerant strains exhibiting plant growth-promoting activity were identified, including a previously uncharacterized Reticulascus sp. strain S5. Co-cultivation assays with the non-native host plant Arabidopsis thaliana demonstrated that S5 increased the root and shoot biomass under salt stress. To elucidate the underlying molecular mechanisms, a comprehensive RNA-Seq analysis of the roots and shoots under control and saline conditions was performed. Fungal colonization induced pronounced transcriptomic changes, particularly in the shoots, including rewiring of the auxin- and abscisic acid-related pathways and the induction of genes associated with cell wall remodeling. Concurrently, defense-related processes, including glucosinolate biosynthesis and ethylene signaling, were broadly repressed, suggesting attenuated stress perception in colonized plants. In the roots, S5 inoculation suppressed the expression of genes involved in root hair development and cell wall organization, indicating a fungus-driven reconfiguration of root development. Moreover, comparative analysis with Fusarium sp. K-23, a fungus that has previously been demonstrated to promote plant growth under salinity stress, revealed distinct root-associated mechanisms but convergence on a shared regulatory module in shoots involving ABA-responsive transcription factors and osmotic stress regulators. Collectively, our findings demonstrate that Reticulascus sp. S5 enhances plant salt stress tolerance through the coordinated transcriptional reprogramming of growth, hormone signaling, and stress responses, highlighting a possible potential of habitat-adapted endophytes for sustainable crop improvement.

Arabidopsis↗