The improved auxin signalling via entire mutation enhances aluminium tolerance in tomato.

Tissue specific mechanisms of tuber dormancy after 1,4-dimethylnaphthalene treatment in potato.

Functional auxin signaling and phosphorus acquisition induced in planta by the extremophile bacterium Pseudomonas extremaustralis

SOC1 clade genes coordinate lateral root development and response to multiple phytohormonal and environmental stress signals in Arabidopsis.

This study demonstrates that CRISPR-mediated cis-regulatory element editing (CRE editing) of the SD1 promoter effectively reduces plant height in Kam sweet rice, without compromising yield or grain quality, offering a precise strategy for crop improvement. Kam sweet rice, a unique aromatic variety, faces challenges with excessive plant height and suboptimal yield. This study explores a precision breeding approach by strengthening an endogenous TCP19-SD1 repression module through CRISPR-Cas9-mediated CRE editing to modulate the expression of the SD1 gene, a key regulator of gibberellin biosynthesis and stem elongation. By introducing an adenine insertion in the GGCCCCCC cis-regulatory element in the SD1 promoter, we enhanced the binding affinity of the transcription factor TCP19, resulting in down-regulated SD1 expression. This led to a reduction in gibberellin levels, shortening internodes, and reducing plant height. Phenotypic evaluations revealed that the edited lines exhibited significantly shorter plant height while maintaining grain yield and nitrogen utilization efficiency compared to wild-type plants. Microscopic analysis of the internodes confirmed that the reduced plant height correlated with decreased cell length. Transcriptomic studies indicated that CRE editing modulated a network of genes involved in both gibberellin and auxin signaling pathways, critical for plant growth. Importantly, the genetic modification did not adversely affect grain quality. This study demonstrates the potential of strengthening endogenous transcriptional repression via CRE editing as a precise alternative to conventional gene knockout techniques, offering a powerful strategy for optimizing complex agronomic traits in rice, with applications in modern crop breeding strategies.

Tomato brown rugose fruit virus (ToBRFV) is a highly destructive and rapidly spreading tobamovirus that poses a serious threat to global tomato production. While low-dose gamma irradiation has emerged as a promising non-chemical strategy to enhance host resistance, the molecular mechanisms and transcriptomic reprogramming underlying this induced resistance remain largely unexplored. In this study, we employed a transcriptome-wide RNA sequencing approach to elucidate the specific gene expression networks and defense pathways activated in ToBRFV-infected tomato plants in response to low-dose gamma irradiation, addressing a critical gap in our understanding of host-virus interactions under irradiation priming. Naturally infected tomato seeds were exposed to an optimized gamma dose of 15Gy, and transcriptomic profiles of irradiated plants were compared with those of non-irradiated infected controls. RNA-Seq analysis identified 469 differentially expressed genes (DEGs), including 157 upregulated and 312 downregulated transcripts (FDR < 0.05), indicating that gamma irradiation induces extensive transcriptional reprogramming. Functional enrichment analyses revealed significant activation of pathways related to metabolic reorganization, antioxidant defense, plant hormone signal transduction, secondary metabolite biosynthesis, and MAPK signaling. Notably, key defense-associated genes encoding peroxidases, protein kinases, and tetratricopeptide repeat (TPR) domain-containing proteins were strongly upregulated, suggesting enhanced reactive oxygen species (ROS) detoxification, stress signal amplification, and potential restriction of viral replication. In contrast, several growth- and development-related transcription factors and heat shock proteins were markedly downregulated, reflecting a shift in resource allocation toward defense responses. Quantitative RT-PCR validation of selected hormone-related genes confirmed the reliability of the RNA-Seq data and highlighted the coordinated involvement of auxin, ethylene, and gibberellin signaling in stress adaptation. Collectively, our results provide novel molecular evidence defining how low-dose gamma irradiation primes endogenous defense networks to reduce viral accumulation. This study offers new insights into the host-mediated transcriptional regulation of resistance against ToBRFV, establishing a foundation for future functional studies on irradiation-induced immunity.

Plant embryogenesis is a critical process characterized by extensive cellular differentiation and morphogenesis, regulated by complex epigenetic mechanisms. However, dynamic changes of DNA methylation during Arabidopsis early embryo development remain to be elucidated. In this study, Arabidopsis hybrid embryos from 2/4-cell to globular stage were subject to bisulfite sequencing and RNA-seq analysis. Our results revealed a local remodeling of DNA methylation during early embryogenesis, represented by a remarkable gain of CHH methylation and the progressive loss of CHG methylation. Genes with differential methylation were found to participate in cell division, morphogenesis, pattern specification and auxin signaling, indicating their potential role in embryo development. At globular stage, CHH hyper-methylation exhibited a notable association with TE repression. The divergences between allelic methylation primarily lied in CG context which increased with embryogenesis. CHH methylation variations between parental alleles underwent reprogramming. Our results implied a negative relevance between allele-specific expression and methylation at CHG sites in early embryos. This work provides new insights into DNA methylation remodeling and its association with transcriptional changes during Arabidopsis early embryogenesis, laying a foundation for future functional studies.

The SPL transcription factor OsSPL10 regulates rice tillering via the auxin signaling pathway to stabilize grain yield under drought stress.

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable strategy to enhance crop productivity, the multi-omics regulatory mechanisms underlying their growth-promoting effects in garlic remain poorly understood. In this study, we integrated physiological, phytohormone metabolomic, and transcriptomic analyses to systematically elucidate the growth-promoting mechanism of Pseudomonas sp. strain UW4 in garlic. Our results demonstrated that UW4 inoculation significantly improved aboveground morphological traits, including plant height, leaf length, leaf width, and pseudostem thickness, and optimized root system architecture by increasing total root length, root surface area, and root tip number. These morphological improvements were accompanied by enhanced photosynthetic pigment accumulation and increased biomass production. Phytohormone profiling revealed that UW4 inoculation elevated the levels of auxin (indole-3-acetic acid, IAA) and its precursors (L-tryptophan and tryptamine), while significantly reducing the content of 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene biosynthesis. Transcriptomic analysis identified 687 differentially expressed genes (DEGs), which were significantly enriched in auxin and ethylene signaling pathways. Mechanistically, UW4 upregulated the expression of SAUR (Small auxin-up RNA) to promote IAA synthesis, and suppressed the transcription of ethylene biosynthesis-related genes. Additionally, the downregulation of PYL (Pyrabactin resistance 1-like) genes indicated that UW4 also modulates the abscisic acid (ABA) signaling pathway. Quantitative real-time PCR (qRT-PCR) validation confirmed that the expression of ACO (ACC oxidase), a key rate-limiting enzyme in ethylene synthesis, was significantly downregulated in UW4 groups. Collectively, our findings demonstrate that UW4 optimizes garlic growth and yield potential by coordinately regulating auxin, ethylene, and ABA metabolism and gene expression, providing a theoretical foundation and elite microbial resource for the green and high-yield cultivation of garlic.

Peach (Prunus persica) and almond (P. dulcis) are closely related species within the Prunus genus that exhibit strikingly different fruit characteristics, particularly in mesocarp expansion and ripening behaviour. To investigate the biological processes driving these differences, we performed a comprehensive transcriptomic analysis of fruit development in the peach cultivar 'Earlygold', the almond cultivar 'Texas', and their interspecific F1 hybrid. Fruit samples were collected at three developmental stages that are key in the different ripening behaviour of peach and almond: initial phase of rapid growth (T1), cell expansion and lignification (T2), and ripening (T3). Global transcriptome profiling revealed almost identical expression patterns irrespective of the reference genome used for the RNA-seq analysis. We found 4,241, 3,862 and 2,922 DEGs between T1 and T2 in 'Earlygold', 'Texas' and F1 hybrid respectively, with most specific changes (55%, 76.6% and 51.3%) occurring during the first half of fruit development. Between T2 and T3, peach-type fruits continued active transcriptional regulation (2,665 DEGs in 'Earlygold', 2,199 in F1 hybrid), whereas almond showed limited late-stage changes (1,032 DEGs), reflecting its non-ripening phenotype. Enrichment analysis showed conserved cell division and photosynthesis-related genes enriched at T1 at both species. Peach displayed unique enrichment in pathways related to auxin signaling, DNA replication, and cyanogenic compound metabolism whereas almond for abscisic acid- and ethylene-related stress pathways. Allele-specific expression (ASE) analysis in the F1 hybrid revealed 79, 99 and 119 peach-biased ASE genes, and 27, 51 and 77 almond-biased ASE genes at T1, T2 and T3, respectively. These findings reveal that peach and almond share conserved early developmental programs but diverge markedly from mid-development. Our data highlight auxin signaling, DNA replication, and ethylene-mediated ripening as central processes driving these developmental differences. The limited number of ASE genes and their parental bias patterns further illuminate cis-regulatory divergence between both species. This study provides new insights into the genetic regulation of fruit development in Prunus species and demonstrates a robust pipeline for cross-species transcriptomic analysis.

Cell-to-cell variation in gene expression can be highly detrimental and, in some contexts, is actively buffered out; however, in other contexts, it is crucial and actively amplified. For example, variation must be minimized to build organs with consistent size and shape, yet the initiation of organogenesis requires a subset of cells to take on a new fate, a process that often relies on small differences between cells. In plants, much of development is controlled by the hormone auxin, which has been hypothesized to coordinate cell responses by inducing degradation of transcriptional repressors. To quantify the level of variation in lateral root initiation and directly test its connection to auxin signaling, we assessed variation in expression of a lateral root founder cell marker GATA23 when auxin levels or responsiveness was modulated. We found that auxin promoted robustness in lateral root founder cell number in Arabidopsis thaliana, as interfering with auxin signaling resulted in more variable numbers of founder cells and, counterintuitively, an increased average number of founder cells per lateral root. These differences were eliminated when using an integrase recorder of GATA23 expression with an imposed expression threshold instead of a traditional transcriptional reporter. These results led us to posit that auxin acts as both an amplifier and a constrainer of variation during the initiation of a new root. To observe phenotypic effects in a naturally noisier context, we extended this work to analysis of root regeneration, where auxin was also found to affect the robustness of outcomes.

Plants rapidly adjust their root system architecture to enhance resource uptake and cope with fluctuating soil environments. One such adaptive response is the development of root hairs (RH), which increase the effective root surface area and thereby improve water and nutrient acquisition. Here, we show that Arabidopsis seedlings respond rapidly to boron (B) deficiency by increasing both RH density and length at the root tip. This response is strongly correlated with enhanced auxin signaling in the root apex, as revealed by the auxin-responsive reporters IAA2::GUS and DR5rev:GFP. Our findings support the idea that B deficiency leads to auxin accumulation in the root tip, likely mediated by enhanced shoot-to-root auxin transport. Furthermore, by using pharmacological and genetic approaches, we provide evidence that enhanced auxin signaling via TIR1/AFBs in the RH zone activates the RHD6-RSL4 cascade to promote RH elongation under B deficiency. In contrast, the increase in RH density under B-deficient conditions appears to involve additional auxin-independent regulatory mechanisms.

The symbiotic relationship between soybean and rhizobia facilitates nodulation and nitrogen fixation, providing a sustainable nutrient supply for increasing crop yields and reducing chemical fertilizer use. However, comparative studies on the conservation and strain-specificity of host gene expression regulated by different rhizobial strains remain limited. Here, we performed a comparative analysis between the previously isolated strain, Bradyrhizobium ottawaense Bott 59, and the model strain, Bradyrhizobium diazoefficiens USDA 110. Symbiotic phenotypes were evaluated after inoculation, and a root transcriptomic analysis was conducted at 3 dpi to assess early molecular responses. At 21 dpi, Bott 59-inoculated plants outperformed plants inoculated with USDA 110 in nodule number, nitrogenase activity, and biomass. Transcriptomic analysis revealed conserved host responses to both rhizobial strains, including NIN-mediated signaling, AON signaling, and the biosynthesis of phenylpropanoids and brassinosteroids. Further analysis revealed that Bott 59 specifically induced the expression of genes involved in isoflavonoid and flavonoid biosynthesis, including those encoding I2H, and HI4OMT. Moreover, Bott 59 triggered more pronounced transcriptional reprogramming in auxin, cytokinin, and jasmonic acid signaling pathways, along with differential expression of a broader set of transcription factor genes. Collectively, this study systematically unravels the conserved and strain-specific transcriptional regulatory events underlying host–rhizobium interactions. Our findings provide valuable theoretical insights and transcriptomic resources for further dissecting the molecular mechanisms of symbiotic nitrogen fixation (SNF), as well as for the targeted genetic improvement of crop nodulation and nitrogen fixation efficiency.

Tillering is a key trait that shapes rice (Oryza sativa L.) shoot architecture and directly influences yield. While tiller bud formation is largely genetically determined, bud outgrowth into functional tillers is highly responsive to environmental cues. However, integration of environmental signals with genetic regulators to determine tiller bud fate remains poorly understood. Here, we investigated the effects of nitrogen on early stages of tiller bud outgrowth. Comprehensive phenotyping and temporal transcriptomic analyses demonstrated that both nitrate and ammonium promote bud outgrowth and elicit overlapping transcriptional responses, with nitrate acting more slowly. Gene regulatory network analysis identified phytohormone signaling as a key interface for nitrogen- triggered tiller outgrowth. Pharmacological and molecular experiments demonstrated the involvement of cytokinin-auxin antagonism in nitrogen-mediated tillering. Cytokinin promoted bud activation by repressing the critical bud dormancy regulators rice TEOSINTE BRANCHED 1 (OsTB1) and a homolog of PIN-FORMED 1 (OsPIN1a) through the Cytokinin Response Factors OsERF53/54. In contrast, auxin maintained dormancy by inducing OsTB1 and OsPIN1a expression through Auxin Response Factors OsARF11/16. Consistently, OsTB1 overexpression lines showed reduced responsiveness to nitrogen and hormone treatments, placing OsTB1 downstream of these convergent inputs. Sequence and gene expression differences in OsERF53/54, along with phenotypic variations across contrasting rice accessions, further substantiated the crucial roles of OsERF53/54 in nitrogen-mediated tillering. Together, we identify a key regulatory role of the cytokinin-auxin antagonistic module for integrating nitrogen signals to determine tiller bud fate. Adequate nitrogen promotes cytokinin signaling while attenuating auxin signaling and transport in tiller buds, thereby releasing dormancy and initiating bud outgrowth.

Plant responses to salt stress include an altered root architecture mediated by ion imbalances, reactive oxygen species (ROS) accumulation, and altered hormonal responses. Auxin is implicated in these processes. To understand better the molecular network we investigated the role of VAMP714, an R-SNARE essential for correct trafficking of the auxin efflux carrier PIN-FORMED (PIN) proteins (implicated in the salt stress response), but also with a reported role in ROS vesicular transport in Arabidopsis. We show that under salt stress the VAMP714 gene shows a rapid transient increase in expression but subsequent perturbed localization of VAMP714 and PIN proteins and altered auxin-responsive gene expression. RNA-seq analysis revealed that pathways related to oxygen signaling, SALT OVERLY SENSITIVE (SOS) pathway activation and ROS response are influenced by salt stress in a VAMP714-dependent manner. Low levels of transgenic overexpression of VAMP714 enhanced root salt tolerance, an effect enhanced by exogenous auxin, showing that maintenance of VAMP714 expression under salt stress allows auxin-mediated maintenance of root growth. We conclude that VAMP714 contributes to the coordinated regulation of auxin signaling and the SOS pathway during salt stress via distinct roles in vesicle trafficking to the plasma membrane (for auxin) and vacuole (for SOS).

Bitter pit disorder development: Evidence from transcriptomic and cellular analysis in different tissues.

CsZAT6/12 response auxin signaling to differentially regulate theanine-dominated nitrogen flow in tea roots (Camellia sinensis).

Nitrogen fertilization remains a cornerstone of modern agriculture, yet its excessive use contributes to environmental degradation. Rapeseed (Brassica napus L.) is notably inefficient in N uptake, highlighting the importance of root traits that enhance soil exploration and nutrient acquisition. This study investigated root transcriptomic responses to nitrate availability across rapeseed genetic diversity. A panel of 40 lines was screened on vertical agar plates, revealing substantial variation in root morphology, strong heritability, and genetic control. Low nitrate supply increased the root-to-shoot biomass ratio and stimulated lateral root proliferation. Transcriptomic profiling was then conducted on three genotype pairs selected to represent distinct root system sizes. Hydroponically grown plants were exposed to two divergent nitrate levels for 24 h, and root tissues were harvested for RNA sequencing. Differential expression analysis identified over a 1000 genes significantly induced or repressed by nitrate treatment, with only 10% shared across genotypes. Gene ontology enrichment analysis revealed a central nitrate-responsive transcriptional program, accompanied by distinct molecular signatures associated with root size. Co-expression network analysis identified regulatory modules that integrate nitrate transporters with auxin signaling and energy metabolism. These modules also uncovered roles for glucosinolate biosynthesis and aquaporin-mediated water transport. This study provides a set of candidate genes and regulatory networks that represent promising targets for breeding rapeseed varieties with optimized root traits for sustainable agriculture.

Integrated transcriptomic and metabolomic analyses revealed paclobutrazol-mediated regulation of flower bud differentiation in Camellia japonica ‘High Fragrance’

The TCP transcription factor RmTCP5 shapes leaf development by modulating auxin and cytokinin homeostasis in Rosa multiflora.