Polar Auxin Transport Research Articles

Melon short internode (CmSi) encodes an ERECTA-like receptor kinase regulating stem elongation through auxin signaling

SummaryPlant height is one of the most important agronomic traits that directly determines plant architecture, and compact or dwarf plants can allow for increased planting density and land utilization as well as increased lodging resistance and economic yield. At least four dwarf/semidwarf genes have been identified in different melon varieties, but none of them have been cloned, and little is known about the molecular mechanisms underlying internode elongation in melon. Here, we report map-based cloning and functional characterization of the first semidwarf gene short internode (Cmsi) in melon, which encodes an ERECTA-like receptor kinase regulating internode elongation. Spatial-temporal expression analyses revealed that CmSI exhibited high expression in the vascular bundle of the main stem during internode elongation. The expression level of CmSI was positively correlated with stem length in the different melon varieties examined. Ectopic expression of CmSI in Arabidopsis and cucumber suggested CmSI as a positive regulator of internode elongation in both species. Phytohormone quantitation and transcriptome analysis showed that the auxin content and the expression levels of a number of genes involved in the auxin signaling pathway were altered in the semidwarf mutant, including several well-known auxin transporters, such as members of the ABCB family and PIN-FORMED genes. A melon polar auxin transport protein CmPIN2 was identified by protein–protein interaction assay as physically interacting with CmSI to modulate auxin signaling. Thus, CmSI functions in an auxin-dependent regulatory pathway to control internode elongation in melon. Our findings revealed that the ERECTA family gene CmSI regulates stem elongation in melon through auxin signaling, which can directly affect polar auxin transport.

Modelling the spatial crosstalk between two biochemical signals explains wood formation dynamics and tree-ring structure.

In conifers, xylogenesis during a growing season produces a very characteristic tree-ring structure: large, thin-walled earlywood cells followed by narrow, thick-walled latewood cells. Although many factors influence the dynamics of differentiation and the final dimensions of xylem cells, the associated patterns of variation remain very stable from one year to the next. While radial growth is characterized by an S-shaped curve, the widths of xylem differentiation zones exhibit characteristic skewed bell-shaped curves. These elements suggest a strong internal control of xylogenesis. It has long been hypothesized that much of this regulation relies on a morphogenetic gradient of auxin. However, recent modelling studies have shown that while this hypothesis could account for the dynamics of stem radial growth and the zonation of the developing xylem, it failed to reproduce the characteristic tree-ring structure. Here, we investigated the hypothesis of regulation by a crosstalk between auxin and a second biochemical signal, by using computational morphodynamics. We found that, in conifers, such a crosstalk is sufficient to simulate the characteristic features of wood formation dynamics, as well as the resulting tree-ring structure. In this model, auxin controls cell enlargement rates while another signal (e.g. cytokinin, tracheary element differentiation inhibitory factor) drives cell division and auxin polar transport.

Protein assemblages and tight curves in the plasma membranes of photosynthetic eukaryotes

Protein assemblages in the plasma membrane of photosynthetic organisms include the polar occurrence of PIN proteins permitting polar auxin transport in embryophytes and Charales, and the H+ ATPase in acid zones of Charales cells. Production of small radius of curvature membrane areas in transfer cells and charasomes is incompletely understood.

MtPIN1 and MtPIN3 Play Dual Roles in Regulation of Shade Avoidance Response under Different Environments in Medicago truncatula.

Polar auxin transport mediated by PIN-FORMED (PIN) proteins is critical for plant growth and development. As an environmental cue, shade stimulates hypocotyls, petiole, and stem elongation by inducing auxin synthesis and asymmetric distributions, which is modulated by PIN3,4,7 in Arabidopsis. Here, we characterize the MtPIN1 and MtPIN3, which are the orthologs of PIN3,4,7, in model legume species Medicago truncatula. Under the low Red:Far-Red (R:FR) ratio light, the expression of MtPIN1 and MtPIN3 is induced, and shadeavoidance response is disrupted in mtpin1 mtpin3 double mutant, indicating that MtPIN1 and MtPIN3 have a conserved function in shade response. Surprisingly, under the normal growth condition, mtpin1 mtpin3 displayed the constitutive shade avoidance responses, such as the elongated petiole, smaller leaf, and increased auxin and chlorophyll content. Therefore, MtPIN1 and MtPIN3 play dual roles in regulation of shadeavoidance response under different environments. Furthermore, these data suggest that PIN3,4,7 and its orthologs have evolved conserved and specific functions among species.

Flavonol‐mediated stabilization of PIN efflux complexes regulates polar auxin transport

The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. However, little is known about the composition and regulation of the PIN protein complex. Here, using blue‐native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo‐ and heteromers assembled from PIN1, PIN2, PIN3, PIN4 and PIN7 subunits only. Furthermore, we show that endogenous flavonols stabilize PIN dimers to regulate auxin efflux in the same way as does the auxin transport inhibitor 1‐naphthylphthalamic acid (NPA). This inhibitory mechanism is counteracted both by the natural auxin indole‐3‐acetic acid and by phosphomimetic amino acids introduced into the PIN1 cytoplasmic domain. Our results lend mechanistic insights into an endogenous control mechanism which regulates PIN function and opens the way for a deeper understanding of the protein environment and regulation of the polar auxin transport complex.

WUSCHEL-related homeobox1 (WOX1) regulates vein patterning and leaf size in Cucumis sativus

In plants, WUSCHEL-related homeobox1 (WOX1) homologs promote lamina mediolateral outgrowth. However, the downstream components linking WOX1 and lamina development remain unclear. In this study, we revealed the roles of WOX1 in palmate leaf expansion in cucumber (Cucumis sativus). A cucumber mango fruit (mf) mutant, resulting from truncation of a WOX1-type protein (CsWOX1), displayed abnormal lamina growth and defects in the development of secondary and smaller veins. CsWOX1 was expressed in the middle mesophyll and leaf margins and rescued defects of the Arabidopsis wox1 prs double mutant. Transcriptomic analysis revealed that genes involved in auxin polar transport and auxin response were highly associated with leaf development. Analysis of the cucumber mf rl (round leaf) double mutant revealed that CsWOX1 functioned in vein development via PINOID (CsPID1)-controlled auxin transport. Overexpression of CsWOX1 in cucumber (CsWOX1-OE) affected vein patterning and produced ‘butterfly-shaped’ leaves. CsWOX1 physically interacted with CsTCP4a, which may account for the abnormal lamina development in the mf mutant line and the smaller leaves in the CsWOX1-OE plants. Our findings demonstrated that CsWOX1 regulates cucumber leaf vein development by modulating auxin polar transport; moreover, CsWOX1 regulates leaf size by controlling CIN-TCP genes.

Современные представления о действии ауксина. 1. История открытия, метаболизм, транспорт

Auxin (indolyl-3-acetic acid, IAA) is one of the key classical phytohormones with a very wide range of physiological effects. The first part of the scientific lecture describes the main stages of discovery of the hormone. The main pathways of auxin synthesis in plant tissues, which is carried out in two different ways: tryptophan-dependent and tryptophan-independent, are considered in detail. At the same time, multiple pathways of the auxin formation from tryptophan have been found in plant tissues. Among them, the mechanisms that occur with the formation of such intermediate metabolites as indole-3-acetaldoxime, indole-3-pyruvate and indole-3-acetamide are considered. The indole-3-pyruvate pathway is currently considered the main mechanism of hormone synthesis. Experimental evidence has also been obtained for the functioning of the tryptophan-independent pathway of auxin synthesis, the key enzyme of which is cytoplasmic indole synthase. It is assumed that the precursor of auxin in the tryptophan-independent pathway may be some intermediate metabolite between anthranilic acid and tryptophan. The article also describes the routes of auxin inactivation through the formation of conjugated forms and oxidation. A brief characterization of IAA dioxygenases, belonging to the 2-oxoglutarate-Fe (II)-oxygenases family, which are currently considered the main catalytic systems for auxin oxidation, is presented. The mechanisms and significance of polar and lateral transport of auxin are discussed. The characteristics of transmembrane auxin transporters belonging to the families PIN/PIL, ABCB/PGP and AUX/LAX are given.

\u03b3-Aminobutyric Acid Participates in the Adult-Phase Adventitious Rooting Recalcitrance

In many tree species especially the rooting-recalcitrant woody perennials, the adventitious root (AR) in the juvenile phase can be easily induced by exogenous auxin, but AR formation becomes recalcitrant in the adult phase. Also, it is reported that the γ-aminobutyric acid (GABA) inhibits primary root growth in Arabidopsis and the AR formation in poplar (Populus ssp). So far, how GABA affects or is affected by the ontogenetic phase or auxin remains unclear. Here, we used an apple rootstock, Malus xiaojinensis, and tobacco (Nicotiana benthamiana) to investigate this question. We first analyzed the content of GABA, the activity of GABA synthetic enzyme GAD, and the expression of the coding gene MxGADs, respectively, in leafy cuttings of juvenile and adult phase. Next, the effect of exogenous GABA on AR formation was examined in in vitro shoots of M. xiaojinensis and tobacco. Interestingly, significant and consistent increases in GABA concentration, GAD activity, and expression of MxGAD genes in response to exogenous indole butyric acid (IBA) were detected in adult-phase cuttings, but not in juvenile-phase cuttings. Exogenous GABA application inhibited the AR formation by delaying rooting time and reducing root number and the total root length in in vitro shoots of both M. xiaojinensis and tobacco. The expression of MxPIN members increased in response to IBA application, but these changes were restrained by the addition of GABA. These results indicate that both the loss of juvenility and IBA are required to trigger GABA accumulation. GABA may affect the AR formation as a co-actor by inhibiting polar auxin transport. Together, these findings facilitate the understanding of the regulatory network among GABA, juvenility, and auxin signaling on the AR formation.

OsPIN9, an auxin efflux carrier, is required for the regulation of rice tiller bud outgrowth by ammonium.

The degree of rice tillering is an important agronomic trait that can be markedly affected by nitrogen supply. However, less is known about how nitrogen-regulated rice tillering is related to polar auxin transport. Compared with nitrate, ammonium induced tiller development and was paralleled with increased 3 H-indole-acetic acid (IAA) transport and greater auxin into the junctions. OsPIN9, an auxin efflux carrier, was selected as the candidate gene involved in ammonium-regulated tillering based on GeneChip data. Compared with wild-type plants, ospin9 mutants had fewer tillers, and OsPIN9 overexpression increased the tiller number. Additionally, OsPIN9 was mainly expressed in vascular tissue of the junction and tiller buds, and encoded a membrane-localised protein. Heterologous expression in Xenopus oocytes and yeast demonstrated that OsPIN9 is a functional auxin efflux transporter. More importantly, its RNA and protein levels were induced by ammonium but not by nitrate, and tiller numbers in mutants did not respond to nitrogen forms. Further advantages, including increased tiller number and grain yield, were observed in overexpression lines grown in the paddy field at a low-nitrogen rate compared with at a high-nitrogen rate. Our data revealed that ammonium supply and an auxin efflux transporter co-ordinately control tiller bud elongation in rice.

Expression Analysis of Key Auxin Biosynthesis, Transport, and Metabolism Genes of Betula pendula with Special Emphasis on Figured Wood Formation in Karelian Birch.

Auxin status in woody plants is believed to be a critical factor for the quantity and quality of the wood formed. It has been previously demonstrated that figured wood formation in Karelian birch (Betula pendula Roth var. carelica (Merckl.) Hämet-Ahti) is associated with a reduced auxin level and elevated sugar content in the differentiating xylem, but the molecular mechanisms of the abnormal xylogenesis remained largely unclear. We have identified genes involved in auxin biosynthesis (Yucca), polar auxin transport (PIN) and the conjugation of auxin with amino acids (GH3) and UDP-glucose (UGT84B1) in the B. pendula genome, and analysed their expression in trunk tissues of trees differing in wood structure. Almost all the investigated genes were overexpressed in Karelian birch trunks. Although Yucca genes were overexpressed, trunk tissues in areas developing figured grain had traits of an auxin-deficient phenotype. Overexpression of GH3s and UGT84B1 appears to have a greater effect on figured wood formation. Analysis of promoters of the differentially expressed genes revealed a large number of binding sites with various transcription factors associated with auxin and sugar signalling. These data agree with the hypothesis that anomalous figured wood formation in Karelian birch may be associated with the sugar induction of auxin conjugation.

Silicon promotes root development by modulating polar transport of auxin during cutting propagation of poinsettia

Silicon promotes root development by modulating polar transport of auxin during cutting propagation of poinsettia

FERONIA mediates root nutating growth.

Root nutation indicates the behavior that roots grow in a waving and skewing way due to unequal growth rates on different sides. Although a few developmental and environmental factors have been reported, genetic pathways mediating this process are obscure. We report here that the Arabidopsis CrRLK1L family member FERONIA (FER) is critical for root nutation. Functional loss of FER resulted in enhanced root waviness on tilted plates or roots forming anti-clockwise coils on horizontal plates. Suppressing polar auxin transport, either by pharmacological treatment or by introducing mutations at PIN-FORMED2 (PIN2) or AUXIN RESISTANT1 (AUX1), suppressed the asymmetric root growth (ARG) in fer-4, a null mutant of FER, indicating that FER suppression of ARG depends on polar auxin transport. We further showed by pharmacological treatments that dynamic microtubule organization and Ca2+ signaling are both critical for FER-mediated ARG. Results presented here demonstrate a key role of FER in mediating root nutating growth, through PIN2- and AUX1-mediated auxin transport, through dynamic microtubule organization, and through Ca2+ signaling.

Developmental Genetics of Corolla Tube Formation: Role of the tasiRNA-ARF Pathway and a Conceptual Model.

Over 80,000 angiosperm species produce flowers with petals fused into a corolla tube. The corolla tube contributes to the tremendous diversity of flower morphology and plays a critical role in plant reproduction, yet it remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower species Mimulus lewisii Loss-of-function mutations in the M. lewisii orthologs of ARGONAUTE7 and SUPPRESSOR OF GENE SILENCING3 cause a dramatic decrease in abundance of TAS3-derived small RNAs and a moderate upregulation of AUXIN RESPONSE FACTOR3 (ARF3) and ARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the interprimordial regions, resulting in unfused corollas. Using the DR5 auxin-responsive promoter, we discovered that auxin signaling is continuous along the petal primordium base and the interprimordial region during the critical stage of corolla tube formation in the wild type, similar to the spatial pattern of MlARF4 expression. Auxin response is much weaker and more restricted in the mutant. Furthermore, exogenous application of a polar auxin transport inhibitor to wild-type floral apices disrupted petal fusion. Together, these results suggest a new conceptual model highlighting the central role of auxin-directed synchronized growth of the petal primordium base and the interprimordial region in corolla tube formation.

Auxin regulation and MdPIN expression during adventitious root initiation in apple cuttings

Adventitious root (AR) formation is critical for the efficient propagation of elite horticultural and forestry crops. Despite decades of research, the cellular processes and molecular mechanisms underlying AR induction in woody plants remain obscure. We examined the details of AR formation in apple (Malus domestica) M.9 rootstock, the most widely used dwarf rootstock for intensive production, and investigated the role of polar auxin transport in postembryonic organogenesis. AR formation begins with a series of founder cell divisions and elongation of the interfascicular cambium adjacent to vascular tissues. This process is associated with a relatively high indole acetic acid (IAA) content and hydrolysis of starch grains. Exogenous auxin treatment promoted this cell division, as well as the proliferation and reorganization of the endoplasmic reticulum and Golgi membrane. In contrast, treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) inhibited cell division in the basal region of the cuttings and resulted in abnormal cell divisions during the early stage of AR formation. In addition, PIN-FORMED (PIN) transcripts were differentially expressed throughout the whole AR development process. We also detected upregulation of MdPIN8 and MdPIN10 during induction; upregulation of MdPIN4, MdPIN5, and MdPIN8 during extension; and upregulation of all MdPINs during AR initiation. This research provides an improved understanding of the cellular and molecular underpinnings of the AR process in woody plants.

Indeterminate domain 3 negatively regulates plant erectness and the resistance of rice to sheath blight by controlling PIN-FORMED gene expressions

ABSTRACT Plant architecture and disease resistance are the key factors that control the production of yield. However, the mechanism behind these factors is largely unknown. In this study, we identified that indeterminate domain 3 (IDD3) was obviously induced by inoculation of Rhizoctonia solani AG1-IA. Plants that overexpressed IDD3 (IDD3 OX) were more susceptible, while idd3 mutants showed a similar response to sheath blight disease compared with wild-type plants. Interestingly, IDD3 OX plants developed a wider tiller angle and exhibited altered shoot gravitropism, while idd3 knock-out mutants showed no visible morphological differences compared with the wild-type plants. IDD3 is ubiquitously expressed in different tissues and stages, and the IDD3 transcript was induced by exogenously applied auxin. Expression of the PIN-FORMED (PIN) and Aux/IAA genes was altered in IDD3 OX compared with wild-type plants. Furthermore, IDD3 OX plants are sensitive to auxin and the polar auxin transporter inhibitor N-1-naphthylphalamic acid (NPA). Further yeast-one hybrid, chromatin immunoprecipitation (ChIP) and transient assays revealed that IDD3 directly represses PIN1b via promoter binding. Inoculation with R. solani indicated that PIN1b RNAi plants are more susceptible to sheath blight disease (ShB) compared with the wild-type. Taken together, our analyses suggest that IDD3 controls plant architecture and the resistance of rice to ShB via the regulation of PIN auxin transporter genes.

Paclobutrazol elevates auxin and abscisic acid, reduces gibberellins and zeatin and modulates their transporter genes in Marubakaido apple (Malus prunifolia Borkh. var. ringo Asami) rootstocks

To examine the dwarfing mechanism in apples, one-year-old Marubakaido (Malus prunifolia Borkh.) (invigorating) apple rootstock stools were foliar-sprayed with 860 mg L−1 of paclobutrazol (PBZ) as a single application or without. M.9 apple rootstock (dwarf) was used as a positive control. The phytohormones were estimated in the shoot bark and sub-apical shoot and gene expression in the apices of terminal shoots. Evident responses to PBZ were observed a fortnight after treatment, as the shoot and internode lengths were suppressed significantly. Endogenous indole-3-acetic acid increased in the PBZ treatment, and the polar auxin transporter genes MdPIN1 and MdLAX1 and the biosynthesis gene MdYUCCA10a were upregulated along with the MdARF2 gene. Additionally, PBZ increased the abscisic acid (ABA) concentration and the biosynthesis-related gene MdNCED1 but repressed the degradation gene MdCYP707A1. The ABA transporter gene MdAITb-like was upregulated by PBZ. The concentrations of the gibberellins (GAs) GA1 and GA4 decreased in the PBZ-treated rootstocks. The GA transporter gene MdNFP3.1-like and the signaling gene MdGID1b-like were strongly downregulated by PBZ, whereas the catabolic gene MdGA2OX2 was upregulated. PBZ treatment significantly reduced trans-zeatin (tZ) levels and downregulated the cytokinin biosynthesis gene MdIPT6 but upregulated the MdCKX7 degradation gene. Additionally, PBZ upregulated the cytokinin-related transporter genes MdPUP7-like and MdPUP9-like. Collectively, our results show that the physiological and molecular effect of PBZ was observed within two weeks, and this was indicated by the modulation of phytohormonal levels as well as transporter and other gene expression in Marubakaido apple rootstocks.

From one cell to many: Morphogenetic field of lateral root founder cells in Arabidopsis thaliana is built by gradual recruitment

The reiterative process of lateral root (LR) formation is widespread and underlies root system formation. However, early LR primordium (LRP) morphogenesis is not fully understood. In this study, we conducted both a clonal analysis and time-lapse experiments to decipher the pattern and sequence of pericycle founder cell (FC) participation in LR formation. Most commonly, LRP initiation starts with the specification of just one FC longitudinally. Clonal and anatomical analyses suggested that a single FC gradually recruits neighboring pericycle cells to become FCs. This conclusion was validated by long-term time-lapse live-imaging experiments. Once the first FC starts to divide, its immediate neighbors, both lengthwise and laterally, are recruited within the hour, after which they recruit their neighboring cells within a few hours. Therefore, LRP initiation is a gradual, multistep process. FC recruitment is auxin-dependent and is abolished by treatment with a polar auxin transport inhibitor. Furthermore, FC recruitment establishes a morphogenetic field where laterally peripheral cells have a lower auxin response, which is associated with a lower proliferation potential, compared to centrally located FCs. The lateral boundaries of the morphogenetic field are determined by phloem-adjacent pericycle cells, which are the last cells to be recruited as FCs. The proliferation potential of these cells is limited, but their recruitment is essential for root system formation, resulting in the formation of a new vascular connection between the nascent and parent root, which is crucial for establishing a continuous and efficient vascular system.

Physiological Responses to Fe Deficiency in Split-Root Tomato Plants: Possible Roles of Auxin and Ethylene?

Iron (Fe) bioavailability in soils is often limited and can be further exacerbated by a non- homogeneous distribution in the soil profile, which has been demonstrated to vary both in space and time. Consequently, plants respond with morphological and physiological modifications at the root level involving a complex local and systemic signaling machinery. The present work unravels the role of two phytohormones (i.e., ethylene and auxin) and their integrated signaling in plant response to Fe deficiency. Inhibitors of auxin polar transport and of ethylene biosynthesis (N-1-naphthylphthalamic acid - NPA and aminoethoxyvinylglycine - AVG, respectively) were applied on tomato (Solanum lycopersicum L.) plants grown by the split-root technique, which allows to simulate condition of Fe heterogeneous distribution. Results showed that plants, exposed to an uneven Fe supply, triggered a complex auxin-ethylene signaling. A systemic action of auxin on FERRIC REDUCTASE OXIDASE 1 (SlFRO1) expression was revealed, while ethylene signaling was effective both locally and systemically. In addition, the investigation of Fe concentration in tissues showed that when leaves overcame Fe deficiency a Fe “steady state” was maintained. Therefore, physiological adaptation to this heterogeneous Fe supply could be mediated by the integration of the complex signaling pathways prompted by both auxin and ethylene activities.

Early Endosomal Trafficking Component BEN2/VPS45 Plays a Crucial Role in Internal Tissues in Regulating Root Growth and Meristem Size in Arabidopsis.

Polar auxin transport is involved in multiple aspects of plant development, including root growth, lateral root branching, embryogenesis, and vasculature development. PIN-FORMED (PIN) auxin efflux proteins exhibit asymmetric distribution at the plasma membrane (PM) and collectively play pivotal roles in generating local auxin accumulation, which underlies various auxin-dependent developmental processes. In previous research, it has been revealed that endosomal trafficking components BEN1/BIG5 (ARF GEF) and BEN2/VPS45 (Sec1/Munc 18 protein) function in intracellular trafficking of PIN proteins in Arabidopsis. Mutations in both BEN1 and BEN2 resulted in defects in polar PIN localization, auxin response gradients, and in root architecture. In this study, we have attempted to gain insight into the developmental roles of these trafficking components. We showed that while genetic or pharmacological disturbances of auxin distribution reduced dividing cells in the root tips and resulted in reduced root growth, the same manipulations had only moderate impact on ben1; ben2 double mutants. In addition, we established transgenic lines in which BEN2/VPS45 is expressed under control of tissue-specific promoters and demonstrated that BEN2/VPS45 regulates the intracellular traffic of PIN proteins in cell-autonomous manner, at least in stele and epidermal cells. Furthermore, BEN2/VPS45 rescued the root architecture defects when expressed in internal tissues of ben1; ben2 double mutants. These results corroborate the roles of the endosomal trafficking component BEN2/VPS45 in regulation of auxin-dependent developmental processes, and suggest that BEN2/VPS45 is required for sustainable root growth, most likely through regulation of tip-ward auxin transport through the internal tissues of root.

Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice

As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.