Search Results (123)

Grain size and grain weight are critical factors influencing crop yield. In rice (Oryza sativa L.), the auxin response factor (OsARF) family proteins, key components of the auxin signaling pathway, function as transcription factors and play essential roles in regulating various plant growth and development processes, including seed development. Here, we identified that Oryza sativa AUXIN RESPONSE FACTOR 25 (OsARF25) plays an essential role in regulating grain size and grain weight by activating the expression of SHORT GRAIN 1 (SG1) and Oryza sativa OVATE FAMILY PROTEIN 04 (OsOFP04). The osarf25 mutants showed larger grains with increased grain length, grain width, and 1000-grain weight. Furthermore, molecular evidence demonstrated that OsARF25 functions as a transcriptional activator. RNA-seq analysis further identified its target genes SG1 and OsOFP04. In addition, OsARF25 directly binds to the promoters of SG1 and OsOFP04 and activates their expression. Further, the osarf25 mutant exhibited enhanced sensitivity to brassinolide treatment, confirming that the targeting of SG1 and OsOFP04 by OsARF25 mediates BR signaling. Taken together, our study revealed that OsARF25 functions as a regulator of grain length, grain width, and grain weight by participating in the BR signaling pathway, and it has potential value for molecular breeding in rice. Full article

Longer inflorescence stalks in oil palm enhance harvesting efficiency and reduce labor costs. However, the research on this topic is limited. This study aimed to investigate the differences in stalk lengths between male and female inflorescences in Tenera oil palm and to elucidate the underlying hormonal and transcriptomic mechanisms. The stalk lengths from inflorescences associated with the fourth to eighteenth leaf positions of Tenera oil palm trees were measured, and hormone profiling and RNA sequencing (RNA-seq) were conducted in immature (F4 and M5) and mature (F14 and M13) stalks from an individual tree. The male stalks were significantly longer than the female stalks since the thirteenth inflorescences and the differences increased with maturation. The elevated levels of indole-3-acetic acid (IAA) in both immature and mature male stalks suggested auxin’s critical role in promoting stalk elongation. In M13, we identified the upregulated auxin influx carrier LAX2, Gibberellic Acid-Stimulated Arabidopsis 6 (GASA6), and SMALL AUXIN UP RNA (SAUR) genes, indicating enhanced auxin accumulation, signaling, and response. Moreover, the auxin response factor (ARF11) was upregulated, linking auxin transport to gene activation for cell elongation. Conversely, in F14, higher levels of abscisic acid (ABA) and the expression of ABA receptor PYL3 and gibberellin 2-beta-dioxygenase 8 GA2ox8, which may inhibit stalk elongation, were identified. The results suggested that LAX2-mediated IAA accumulation activates ARF11 and SAURs, promoting stalk elongation, with GASA6 possibly acting as a downstream modulator. This study provides insights into the hormonal and genetic regulators of stalk elongation in oil palm and may guide breeding strategies for oil palm varieties with longer stalks of female inflorescences, thereby enhancing harvesting efficiency. Full article

Salinity stress poses a major challenge to agricultural productivity worldwide, including for pumpkin, a globally cultivated vegetable crop with great economic value. To deal with salt stress, plants exhibit an array of responses such as changes in their root system architecture. However, the root phenotype and gene expression of pumpkin in response to different concentrations of NaCl remains unclear. To this end, this study evaluated the effects of salinity stress on root architecture in C. moschata (Cmo-1, Cmo-2 and Cmo-3) and C. maxima (Cma-1, Cma-2 and Cma-3), as well as their hybrids of C. moschata and C. maxima (Ch-1, Ch-2 and Ch-3) at the germination and seedling stages. The results showed that the total root length and the number of root tips decreased by more than 10% and 5%, respectively, under 180 mM NaCl conditions compared to those under the 0 mM NaCl conditions. In contrast, the total root length and the number of root tips were increased or decreased under 60 mM NaCl conditions. Meanwhile, salt stress was considered severe when treated with more than 120 mM NaCl, which could be used to evaluate the salt tolerance of the germplasm resources of pumpkin. In addition, the transcriptional changes in the roots of both Cmo-3 and Cma-2 under salt stress were analyzed via RNA-sequencing. We found 4299 and 2141 differential expression genes (DEGs) in Cmo-3 and Cma-2, respectively. Plant hormone signal transduction, Phenylpropanoid biosynthesis and the MAPK signaling pathway were found to be the significant KEGG pathways. The expression of ARF (auxin response factor), B-ARR (type-B response regulator) and PYR (pyrabactin resistance)/PYL (PYR-LIKE) genes was downregulated by NaCl treatment. In contrast, the expression of SnRK2 (sucrose non-fermenting-1-related protein kinase 2) and AHP (histidine-containing phosphotransmitter) genes was downregulated in Cmo-3 and upregulated in Cma-2. These findings will help us better understand the mechanisms of salt tolerance in pumpkins and potentially provide insight into enhancing salt tolerance in crop plants. Full article

Small auxin-up-regulated RNA (SAUR) genes are involved in the regulation of dynamic and adaptive growth in higher plants. However, their function and mode of action in citrus root growth are still unknown. Here, we demonstrate that in Poncirus trifoliata, PtrSAUR32 acted downstream of the auxin response factor PtrARF8 to regulate root growth by interacting with PtrPP2C.Ds, subfamily type 2C protein phosphatases which interacted with H-ATPase and PtrHA. In this study, several members of SAUR family in Poncirus trifoliata are identified to be associated with the growth and development of the roots. Among them, PtrSAUR32 was found to be highly expressed in the RT (root tip), and the level of its expression was significantly positively corelated to the length of primary roots (p < 0.01). The overexpression of PtrSAUR32 in citrus significantly promoted the growth of primary roots. In PtrSAUR32 transgenic citrus plants, the expressions of several auxin biosynthesis and transport genes were altered in accordance with the expression of PtrSAUR32. Y1H and dual-luciferase reporter assays proved that the expression of PtrSUAR32 is regulated by PtrARF8. Y2H and BiFC assay results indicated that PtrSAUR32 interacted with PtrPP2C.Ds subfamily members PtrPP2C.D1, PtrPP2C.D6, and PtrPP2C.D7, of which PtrPP2C.D7 could interact with PtrHA in vivo. Full article

Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). The anatomical and growth investigations demonstrated significant disparities between compatible (FZX as scion and ZNX as rootstock) and incompatible (ZNX as scion and FZX as rootstock) grafts, with the latter showing reduced levels of indole acetic acid (IAA). Exogenous 1-naphthalene acetic acid (NAA) application markedly improved the graft survival, shoot development, and hormonal synergy, whereas the auxin inhibitor tri-iodobenzoic acid (TIBA) diminished these parameters. The incompatible grafts showed downregulation of auxin transporter genes, including ATP-binding cassette (ABC) transporter, AUXIN1/LIKE AUX1 (AUX/LAX), and PIN-FORMED (PIN) genes, suggesting impaired vascular tissue growth. Metabolomic profiling revealed dynamic interactions between auxin, salicylic acid, and jasmonic acid, with NAA-treated grafts exhibiting enhanced levels of stress-responsive metabolites. Transcriptome sequencing identified differentially expressed genes (DEGs) linked to auxin signaling (ARF, GH3), seven additional phytohormones, secondary metabolism (terpenoids, anthocyanins, and phenylpropanoids), and ABC transporters. Gene ontology and KEGG analyses highlighted the significance of hormone interactions and the biosynthesis of secondary metabolites in successful grafting. qRT-PCR validation substantiated the veracity of the transcriptome data, emphasizing the significance of auxin transport and signaling in effective graft development. This study provides an in-depth review of the molecular and physiological factors influencing litchi grafting. These findings provide critical insights for enhancing graft success rates in agricultural operations via targeted hormonal and genetic approaches. Full article

HD-Zip (homeodomain-leucine zipper) transcription factors play a crucial role in plant growth, development, and stress response; however, the HD-Zip gene family of Coix lacryma-jobi L. has not been identified. In this study, a total of 40 HD-Zip gene family members were identified in the genome of Coix. According to phylogenetic analysis, the Coix HD-Zip gene was divided into four subfamilies (I–IV), of which the HD-Zip I subfamily can be further divided into five branches. Moreover, HD-Zip members of the same subfamily usually share similar gene structures and conserved motifs. The transcription factor binding site enrichment analysis showed that there are many motifs for binding with transcription factors such as ERF (Ethylene responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), and ARF (Auxin Response Factor) in the promoter region of the ClHDZ genes. The results of qPCR (Quantitative Polymerase Chain Reaction) and expression profile analysis showed that ClHD-Zip I genes showed different levels of expression under different stress treatments. Among them, ClHDZ4 was located in the nucleus, and its expression pattern was significantly upregulated under salt, drought, and high-temperature stress. In addition, ectopic expression of ClHDZ4 enhanced the growth of yeast strains under drought, salt, or high-temperature treatment. In summary, these results laid a foundation for further research on the resistance function of the Coix HD-Zip gene. Full article

Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family in Populus euphratica Oliv. using bioinformatics analysis, examining their conserved structural domains, gene structure, expression products, and evolutionary relationships. We found that the 34 PeARF genes were unevenly distributed on 19 chromosomes of P. euphratica. All 56 PeARF proteins were hydrophilic and unstable proteins localized in the nucleus, with secondary structures containing α-helices, extended strands, random coils, and β-turns but lacking transmembrane helices (TM-helices) and signal peptides. Evolutionary analysis divided the PeARF proteins into five subfamilies (A–E), with high conservation observed in the order and number of motifs, domains, gene structure, and other characteristics within each subfamily. Expression pattern analysis revealed that 17 PeARF genes were upregulated during cell growth and heterophylly development. This comprehensive analysis provides insights into the molecular mechanisms of ARF genes in P. euphratica growth, development, and stress response, serving as a basis for further studies on the auxin signaling pathway in P. euphratica. Full article

Auxin response factors (ARFs) are a class of transcription factors widely present in plants. As an important economic crop, research on the effects of safflower ARFs on endogenous auxin and effective components is relatively limited. In this study, a total of 23 ARF genes were identified from the safflower genome. Sequence alignment and domain analysis indicated the presence of conserved B3 and Auxin_resp domains in these ARFs. Phylogenetic analysis indicated that CtARF could be classified into five subfamilies, a conclusion also supported by gene structure, consensus motifs, and domain compositions. Transcriptome data showed that ARFs are expressed in all flower colors, but the expression levels of ARF family members vary among different flower colors. CtARF19 had relatively higher expression in deep red flowers, CtARF3 had higher expression in white flowers, CtARF2/12 had higher expression in yellow flowers, and CtARF21/22 had higher expression in light red flowers. Protein–protein interaction network analysis indicated that ARF family members (CtARF2/3/4/5/15/18/19/22) are located within the interaction network. Cis-acting element analysis suggested that CtARF genes may be regulated by hormone treatment (AuxRR-core) and abiotic stress, and the results of qRT-PCR also confirmed this. Additionally, the content of endogenous auxin and active components in safflower with different flower colors significantly changed upon treatment with hormones that affect IAA content. In summary, our study provides valuable insights into the biological functions of CtARF genes under exogenous hormone conditions and their effects on active components. Full article

Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses—particularly to abscisic acid and jasmonic acid and abiotic stresses—as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding. Full article

The initiation and specification of germline cells are crucial for plant reproduction and the continuity of species. In Arabidopsis thaliana, auxin plays a vital role in guiding the transition of somatic cells into germline fate, orchestrating the specification of both male archesporial cells and female megaspore mother cells. This process is regulated through interaction with the transcription factor Sporocyteless/Nozzle, which forms a feedback mechanism that modulates germ cell specialization. Auxin biosynthesis, polar transport, and signal transduction pathways collectively ensure the accurate determination of germ cell fate. Furthermore, the coordination of auxin signaling with epigenetic regulation and miRNA-mediated control fine-tunes the differentiation between germline and somatic cells. This review discusses the mechanisms underlying auxin-guided germ cell specification. It proposes future research directions, including studies on PIN-FORMED-mediated polar transport, the role of the YUCCA family in auxin biosynthesis, and the involvement of the Transport Inhibitors Response 1/Auxn Signaling F-Box-Auxin Response Factor (TIR1/AFB-ARF) signaling pathway in germ cell fate determination. These insights will enhance our understanding of plant reproductive biology and provide new strategies for crop breeding. Full article

As a product and reproductive organ of ginger (Zingiber officinale Roscoe), the degree of rhizome bulking is a key factor in determining the yield and economic value of ginger. There are few studies on the regulatory mechanism of rhizome bulking in ginger. This study aims to identify the key hormone that regulates ginger rhizome bulking and to screen for critical hormone-associated genes. As research subjects, two ginger accessions—large (L) with a thickened rhizome and small (S) with a slender rhizome—were derived from the same parent plant. The ploidy differences between the two determine variations in gene dosage as well as differential expression patterns. The levels of eight hormones in the rhizome of L and S during different growth stages were analyzed. Differentially expressed genes (DEGs) were identified by combining third-generation transcriptome sequencing technology (PacBio SMART) with quantitative real time PCR (qRT-PCR). Through screening methods such as Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), auxin, cytokinin, and salicylic acid were identified as the key differential hormones across various growth periods. Among these, changes in IAA level showed a positive correlation with rhizome bulking. Among them, change in IAA levels was positively correlated with the degree of rhizome bulking. Transcriptome analysis combined with qRT-PCR revealed that the auxin response factor genes ZoARF7 and ZoARF23 are likely to act as positive regulators of rhizome bulking. This study provides a theoretical foundation for elucidating the molecular mechanisms underlying hormone-mediated rhizome bulking in ginger. Full article

The importance of fruit shape studies extends beyond fundamental plant biology, as it holds significant implications for breeding. Understanding the genetic and hormonal regulation of fruit morphology can facilitate targeted breeding strategies to enhance yield, quality, and stress resistance, ultimately contributing to sustainable farming and nutrition security. The diversity in fruit shapes is the result of complex hormone regulation and molecular pathways that affect key traits, including carpel number, fruit length, and weight. Fruit shape is a quality attribute that directly influences consumer preference, marketability and the ease of post-harvest processing. This article focuses on investigations carried out on molecular, genetic and hormonal regulation mechanisms of fruit shape, color, maturation in fruit plants and key genetic pathways such as CLV-WUS and OVATE, as well as their roles in shaping non-climacteric fruits such as strawberries, grapes and raspberries. Plant hormones, especially abscisic acid (ABA) and indole-3-acetic acid (IAA), play a crucial role in enhancing desirable traits such as color and taste, while regulating anthocyanin synthesis and growth time. In addition, the dynamic interactions between auxin, gibberellin, and ethylene are crucial for the ripening process. Jasmonate enhances stress response, brassinosteroids promote ripening and cytokinins promote early fruit development. In addition, this review also studied the fruit morphology of species such as tomatoes and cucumbers, emphasizing the importance of the CLV-WUS pathway, which regulates the number of carpels through genes such as WUSCHEL (WUS), FRUITFULL1 (FUL1), and auxin response factor 14 (ARF14). The weight of fresh fruit is affected by microRNAs such as miRNA156, which emphasizes the importance of post transcriptional regulation. The involvement of transcription factors such as SISHN1, CaOvate, and CISUN25-26-27a further emphasizes the complexity of hormone regulation. Understanding these regulatory mechanisms can enhance our understanding of fruit development and have a profound impact on agricultural practices and crop improvement strategies aimed at meeting the growing global demand for high-quality agricultural products. Full article

Background/Objectives: Auxin response factors (ARFs) are important in plant growth and development, especially flower development. However, there is limited research on the comprehensive identification and characterization of ARF genes in roses. Methods: We employed bioinformatics tools to identify the ARF genes of roses. These genes were characterized for their phylogenetic relationships, chromosomal positions, conserved motifs, gene structures, and expression patterns. Results: In this study, a total of 17 ARF genes were identified in the genomes of Rosa chinensis ‘OB’, R. chinensis ‘CH’, R. rugosa, and R. wichurana. Based on RNA-seq analyses, we found that the ARF genes had diverse transcript patterns in various tissues and cultivars. In ‘CH’, the expression levels of RcCH_ARFs during different flower-development stages were classified into four clusters. In cluster 3 and cluster 4, RcCH_ARFs were specifically high and low in different stages of floral evocation. Gene expression and phylogenetic analyses showed that RcCH_ARF3, RcCH_ARF4, and RcCH_ARF18 were likely to be the key genes for rose flower development. Conclusions: The identification and characterization of ARF genes in Rosa were investigated. The results presented here provide a theoretical basis for the molecular mechanisms of ARF genes in plant development and flowering for roses, with a broader application for other species in the rose family and for the development of novel cultivars. Full article

DOUBLE-STRANDED RNA BINDING (DRB) proteins DRB1, DRB2, and DRB4 are essential for microRNA (miRNA) production in Arabidopsis thaliana (Arabidopsis) with miR160, and its target genes, AUXIN RESPONSE FACTOR10 (ARF10), ARF16, and ARF17, forming an auxin responsive miRNA expression module crucial for root development. Methods: Wild-type Arabidopsis plants (Columbia-0 (Col-0)) and the drb1, drb2, and drb12 mutants were treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D), and the miR160-mediated response of these four Arabidopsis lines was phenotypically and molecularly characterized. Results: In 2,4-D-treated Col-0, drb1 and drb2 plants, altered miR160 abundance and ARF10, ARF16, and ARF17 gene expression were associated with altered root system development. However, miR160-directed molecular responses to treatment with 2,4-D was largely defective in the drb12 double mutant. In addition, via profiling of molecular components of the miR160 expression module in the roots of the drb4, drb14, and drb24 mutants, we uncovered a previously unknown role for DRB4 in regulating miR160 production. Conclusions: The miR160 expression module forms a central component of the molecular and phenotypic response of Arabidopsis plants to exogenous auxin treatment. Furthermore, DRB1, DRB2, and DRB4 are all required in Arabidopsis roots to control miR160 production, and subsequently, to appropriately regulate ARF10, ARF16, and ARF17 target gene expression. Full article

Auxin response factors (ARFs) are involved in the mechanism of plant leaf color regulation, inhibiting chlorophyll synthesis while promoting anthocyanin production. However, it is not clear whether the ARF gene family is involved in autumn leaf color changes in maple. The differentially expressed genes for autumn leaf discoloration were obtained by transcriptome sequencing, and the AtARF family was constructed by homologous gene search. The results show that the AtARFs consist of 21 members distributed on 11 chromosomes and can be divided into three subfamilies, which are mainly distributed in the nucleus. The promoter regions of the AtARFs contain light-responsive elements, abiotic stress-responsive elements, and hormone-responsive elements. The analyses presented in this paper provide comprehensive information on ARFs and help to elucidate their functional roles in leaf color change in Acer truncatum. Full article