Search Results (51)

Auxin/induced-3-acetic acid (Aux/IAA) serves as a key regulator in the auxin signaling pathway of plants, which exhibits crucial functions in the development of plants. However, the Aux/IAA gene family has not yet been characterized in the genome of Castanea mollissima, an important food source in the Northern Hemisphere. During this research, 23 Aux/IAA genes were identified in the C. mollissima genome, which were unevenly distributed across seven chromosomes. CmAux/IAA genes were assigned to four subfamilies by phylogenetic analysis, and members of the same subfamily exhibited similar molecular characteristics. Collinear analysis revealed that the expansion of CmAux/IAA genes was primarily driven by whole-genome duplication (WGD) and purifying selection. The promoter regions of CmAux/IAA genes were enriched with development-related and hormone-related cis-acting elements, suggesting their crucial functions in the growth and hormonal regulation of C. mollissima. Upon the maturation of the seed kernels, the size and starch content exhibited a significant increasing trend, alongside notable changes in hormone levels. Given the connections between expression levels and physiological indicators, as well as weighted gene co-expression network analysis (WGCNA) analysis, CmIAA27a, CmIAA27b, and CmIAA27c were identified as potential regulators involved in the development of C. mollissima seed kernels. Furthermore, the reliability of the transcriptomic data was further confirmed by RT-qPCR experiments. Overall, this study provides a theoretical basis for the evolutionary expansion of the Aux/IAA gene family in C. mollissima, alongside its potential functions in seed kernel development. Full article

Auxin plays a crucial role throughout the entire life cycle of plants. The auxin/indole-3-acetic acid (Aux/IAA) gene family serves as a negative regulator of auxin response and is one of the earliest auxin-responsive gene families. It regulates the expression of auxin-responsive genes by specifically binding to auxin response factors. This review summarizes the protein structural characteristics of the Aux/IAA gene family and its typical and atypical transduction mechanisms in auxin signaling. Additionally, it examines the role of Aux/IAA in regulating plant growth and development, as well as its function in modulating plant resistance to abiotic stress through hormonal signaling pathways. Our findings indicate that the Aux/IAA gene family plays a significant role in plant growth and development, as well as in abiotic stress resistance. However, research on the functional roles of the Aux/IAA gene family in crops such as rice, wheat, and maize remains relatively scarce. Furthermore, we identified key questions and proposed new research directions regarding the Aux/IAA gene family, aiming to provide insights for future research on plant hormone signaling and molecular breeding in crop design. 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

The Aux/IAA proteins are key regulators of auxin signaling transduction, mediating various physiological and developmental processes in higher plants; however, little information on Aux/IAAs is known in lettuce, an economically important vegetable. In this study, a total of 29 LsAux/IAA genes were identified from the lettuce genome. Sequence alignment and domain analyses suggested the presence of conserved Aux/IAA subdomains (Domain I-IV) in those LsIAAs, and Phylogenetic analysis indicated that members of LsAux/IAA could be classified into 10 subgroups by their homology to Arabidopsis Aux/IAAs, which is also supported by exon-intron structure, consensus motifs, and domain compositions. Transcriptome data suggested that most of the LsIAA genes were expressed in all tissues, whereas some of them were preferentially expressed in specific tissues. Analysis of cis-acting elements indicated the LsIAA genes might be regulated by hormonal treatments and abiotic stresses, which was confirmed by qRT-PCR experiments. Taken together, our study provides valuable information for further investigation of the biological roles of LsIAA genes in high-temperature conditions. Full article

Zanthoxylum armatum (Z. armatum) is a significant economic tree species known for its medicinal and edible properties. However, the presence of prickles on Z. armatum poses a considerable challenge to the advancement of its industry. Numerous studies have indicated that the C2H2 zinc finger protein (C2H2-ZFPs) families are crucial in the development of plant trichomes or prickles. This study identified 78 ZaC2H2 genes from the Z. armatum genome, categorizing them into three groups and analyzing their protein physicochemical properties, chromosomal locations, conserved domains, and gene structures. The evolutionary analysis indicates that the amplification of ZaC2H2 genes primarily results from whole-genome duplication or segmental duplication, and these genes have undergone strong purifying selection pressure throughout their evolutionary history. The analysis of cis-acting elements revealed that they contain various hormone response elements, such as ABRE, AuxRR, the CGTCA motif, GARE motifs, and TCA elements, which are responsive to ABA, IAA, MeJA, GA, and SA signals. RT-qPCR was employed to assess the expression levels of the candidate genes ZaC2H2-45, ZaC2H2-46, ZaC2H2-49, and ZaC2H2-55 under the treatment of five hormones. The results indicated that the expression levels of the ZaC2H2-46 and ZaC2H2-55 genes were significantly up-regulated under NAA, SA, and MeJA treatments. These results will help to further understand the characteristics of the ZaC2H2 gene family and provide a theoretical basis for studying the development of prickles. Full article

The Aux/IAA family proteins, key components of the auxin signaling pathway, are plant-specific transcription factors with important roles in regulating a wide range of plant growth and developmental events. The Aux/IAA family genes have been extensively studied in Arabidopsis. However, most of the Aux/IAA family genes in rice have not been functionally studied. Only two IAA genes have been reported to be involved in the regulation of rice grain size. Grain size is a key factor affecting both rice yield and quality. Therefore, we selected an unreported IAA member, OsIAA19, based on bioinformatics analysis to investigate its potential role in grain size control. Our study showed that OsIAA19 was constitutively expressed in all tissues tested and that the encoding protein was nuclear localized. The osiaa19 mutants were then generated using CRISPR/Cas9 gene editing. Agronomic trait analyses showed that the OsIAA19 mutation significantly increased rice grain length and weight, but had no significant effect on plant height, number of tillers, flag leaf length and width. In addition, the chalkiness of the osiaa19 mutant seeds also increased, but their eating and cooking quality (ECQ) was not altered. Finally, seed germination analysis showed that knocking out OsIAA19 slightly suppressed rice seed germination. These results suggest that OsIAA19 may specifically regulate rice seed-related traits, such as grain shape, rice chalkiness and seed germination. This study not only enriched the functional study of the Aux/IAA genes and the auxin signaling pathway in rice, but also provided valuable genetic resources for breeding elite rice varieties. Full article

Auxin is the first plant hormone found to play a dominant role in fruit growth, from fruit set to fruit ripening. Strawberry plants represent a suitable model for studying auxin’s biosynthesis, sensing, and signaling machinery. Aux/IAA genes are a classical rapid auxin-responsive family. However, the Aux/IAA gene family in Fragaria genus is poorly understood. In this study, a total of 287 Aux/IAA genes were identified in the eight strawberry genomes. Their physicochemical properties, domain structure, and cis-regulatory elements revealed the functional multiplicity of the strawberry Aux/IAAs. We used a phylogenetic analysis to classify these genes into 12 classes. In addition, based on synteny analysis, gene duplications, and calculation of the Ka/Ks ratio, we found that segmental duplications promote the evolution of Aux/IAAs in Fragaria species, which is followed by purifying selection. Furthermore, the expression pattern and protein–protein interaction network of these genes in Fragaria vesca revealed various tissue-specific expressions and probable regulatory functions. Taken together, these results provide basic genomic information and a functional analysis of these genes, which will serve to expand our understanding of the direction in which the Aux/IAA gene family is evolving in Fragaria species. Full article

White clover (Trifolium repens L.) is an important forage and aesthetic plant species, but it is susceptible to drought and heat stress. The phytohormone auxin regulates several aspects of plant development and alleviates the effects of drought stress in plants, including white clover, by involving auxin/indole acetic acid (Aux/IAA) family genes. However, Aux/IAA genes and the underlying mechanism of auxin-mediated drought response remain elusive in white clover. To extend our understanding of the multiple functions of Aux/IAAs, the current study described the characterization of a member of the Aux/IAA family TrIAA27 of white clover. TrIAA27 protein had conserved the Aux/IAA family domain and shared high sequence similarity with the IAA27 gene of a closely related species and Arabidopsis. Expression of TrIAA27 was upregulated in response to heavy metal, drought, salt, NO, Ca²⁺, H₂O₂, Spm, ABA, and IAA treatments, while downregulated under cold stress in the roots and leaves of white clover. TrIAA27 protein was localized in the nucleus. Constitutive overexpression of TrIAA27 in Arabidopsis thaliana led to enhanced hypocotyl length, root length, plant height, leaf length and width, and fresh and dry weights under optimal and stress conditions. There was Improved photosynthesis activity, chlorophyll content, survival rate, relative water content, endogenous catalase (CAT), and peroxidase (POD) concentration with a significantly lower electrolyte leakage percentage, malondialdehyde (MDA) content, and hydrogen peroxide (H₂O₂) concentration in overexpression lines compared to wild-type Arabidopsis under drought and salt stress conditions. Exposure to stress conditions resulted in relatively weaker roots and above-ground plant growth inhibition, enhanced endogenous levels of major antioxidant enzymes, which correlated well with lower lipid peroxidation, lower levels of reactive oxygen species, and reduced cell death in overexpression lines. The data of the current study demonstrated that TrIAA27 is involved in positively regulating plant growth and development and could be considered a potential target gene for further use, including the breeding of white clover for higher biomass with improved root architecture and tolerance to abiotic stress. Full article

Propagation of cuttings is the primary method of rose multiplication. Aux/IAA, early response genes to auxin, play an important role in regulating the process of adventitious root formation in plants. However, systematic research on the identification of RhAux/IAA genes and their role in adventitious root formation in roses is lacking. In this study, 34 RhAux/IAA genes were identified by screening the rose genome, distributed on seven chromosomes, and classified into three clades based on the evolutionary tree. An analysis of the cis-acting elements in the promoters of RhAux/IAA genes revealed the presence of numerous elements related to plant hormones, the light signal response, the growth and development of plants, and abiotic stress. RNA-seq analysis identified a key RhIAA25 gene that may play an important role in the generation of adventitious roots in roses. Subcellular localization, yeast self-activation, and tissue-specific expression experiments indicated that RhIAA25 encoded a nuclear protein, had no yeast self-activated activity, and was highly expressed in the stem. The overexpression of RhIAA25 promoted the elongation of the primary root in Arabidopsis but inhibited adventitious root formation. This study systematically identified and analyzed the RhAux/IAA gene family and identified a key gene, RhIAA25, that regulates adventitious root generation in roses. This study offers a valuable genetic resource for investigating the regulatory mechanism of adventitious root formation in roses. Full article

Sugarcane holds global promise as a biofuel feedstock, necessitating a deep understanding of factors that influence biomass yield. This study unravels the intricate dynamics of plant hormones that govern growth and development in sugarcane. Transcriptome analysis of F2 introgression hybrids, derived from the cross of Saccharum officinarum “LA Purple” and wild Saccharum robustum “MOL5829”, was conducted, utilizing the recently sequenced allele-specific genome of “LA Purple” as a reference. A total of 8059 differentially expressed genes were categorized into gene models (21.5%), alleles (68%), paralogs (10%), and tandemly duplicated genes (0.14%). KEGG analysis highlighted enrichment in auxin (IAA), jasmonic acid (JA), and abscisic acid (ABA) pathways, revealing regulatory roles of hormone repressor gene families (Aux/IAA, PP2C, and JAZ). Signaling pathways indicated that downregulation of AUX/IAA and PP2C and upregulation of JAZ repressor genes in high biomass segregants act as key players in influencing downstream growth regulatory genes. Endogenous hormone levels revealed higher concentrations of IAA and ABA in high biomass, which contrasted with lower levels of JA. Weighted co-expression network analysis demonstrated strong connectivity between hormone-related key genes and cell wall structural genes in high biomass genotypes. Expression analysis confirmed the upregulation of genes involved in the synthesis of structural carbohydrates and the downregulation of inflorescence and senescence-related genes in high biomass, which suggested an extended vegetative growth phase. The study underscores the importance of cumulative gene expression, including gene models, dominant alleles, paralogs, and tandemly duplicated genes and activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties. Full article

Background: Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date. Results: Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development. Conclusion: Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum. Full article

The auxin/indoleacetic acid (Aux/IAA) family plays a central role in regulating gene expression during auxin signal transduction. Nonetheless, there is limited knowledge regarding this gene family in sugarcane. In this study, 92 members of the IAA family were identified in Saccharum spontaneum, distributed on 32 chromosomes, and classified into three clusters based on phylogeny and motif compositions. Segmental duplication and recombination events contributed largely to the expansion of this superfamily. Additionally, cis-acting elements in the promoters of SsIAAs involved in plant hormone regulation and stress responsiveness were predicted. Transcriptomics data revealed that most SsIAA expressions were significantly higher in stems and basal parts of leaves, and at nighttime, suggesting that these genes might be involved in sugar transport. QRT-PCR assays confirmed that cold and salt stress significantly induced four and five SsIAAs, respectively. GFP-subcellular localization showed that SsIAA23 and SsIAA12a were localized in the nucleus, consistent with the results of bioinformatics analysis. In conclusion, to a certain extent, the functional redundancy of family members caused by the expansion of the sugarcane IAA gene family is related to stress resistance and regeneration of sugarcane as a perennial crop. This study reveals the gene evolution and function of the SsIAA gene family in sugarcane, laying the foundation for further research on its mode of action. Full article

Plant structure-related agronomic traits like plant height and leaf size are critical for growth, development, and crop yield. Defining the types of genes involved in regulating plant structure size is essential for the molecular-assisted breeding of peppers. This research conducted comparative transcriptome analyses using Capsicum baccatum germplasm HNUCB0112 and HNUCB0222 and their F₂ generation as materials. A total of 6574 differentially expressed genes (DEGs) were detected, which contain 379 differentially expressed transcription factors, mainly including transcription factor families such as TCP, WRKY, AUX/IAA, and MYB. Seven classes of DEGs were annotated in the plant hormone signal transduction pathway, including indole acetic acid (IAA), gibberellin (GA), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), ethylene (ET), and salicylic acid (SA). The 26 modules were obtained by WGCNA analysis, and the MEpink module was positively correlated with plant height and leaf size, and hub genes associated with plant height and leaf size were anticipated. Differential genes were verified by qRT-PCR, which was consistent with the RNA-Seq results, demonstrating the accuracy of the sequencing results. These results enhance our understanding of the developmental regulatory networks governing pepper key traits like plant height and leaf size and offer new information for future research on the pepper plant architecture system. Full article

Branching is an important agronomic trait that is conducive to plant architecture and yield in flowering Chinese cabbage. Plant branching is regulated by a complex network mediated by hormones; gibberellin (GA) is one of the important hormones which is involved in the formation of shoot branching. Research on the regulatory mechanism of GA influencing rosette branch numbers is limited for flowering Chinese cabbage. In this study, the exogenous application of 600 mg/L GA₃ effectively inhibited rosette branching and promoted internode elongation in flowering Chinese cabbage. RNA-Seq analysis further found that these DEGs were significantly enriched in ‘the plant hormone signal transduction’ pathways, and auxin-related genes were significantly differentially expressed between MB and MB_GA. The upregulation of auxin (AUX) and the upregulation of auxin/indole-3-acetic acid (AUX/IAA), as well as the downregulation of SMALL AUXIN-UPREGULATED RNA (SAUR), were found in the negative regulation of the rosette branching. The qRT-PCR results showed that the expression of AUX/IAA and SAUR from IAA gene family members were consistent with the results of transcriptome data. Phytohormone profiling by targeted metabolism revealed that endogenous auxin contents were significantly increased in MB_GA. Transcriptome and metabolome analysis clarified the main plant hormones and genes underlying the rosette branching in flowering Chinese cabbage, confirming that auxin could inhibit rosette branching. In this regard, the results present a novel angle for revealing the mechanism of gibberellin acting on the branching architecture in flowering Chinese cabbage. Full article

Panax ginseng C. A. Meyer (Ginseng) is one of the most used traditional Chinese herbal medicines, with its roots being used as the main common medicinal parts; its therapeutic potential has garnered significant attention. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) is a family of early auxin-responsive genes capable of regulating root development in plants through the auxin signaling pathway. In the present study, 84 Aux/IAA genes were identified from the ginseng genome and their complexity and diversity were determined through their protein domains, phylogenetic relationships, gene structures, and cis-acting element predictions. Phylogenetic analyses classified PgIAA into six subgroups, with members in the same group showing greater sequence similarity. Analyses of interspecific collinearity suggest that segmental duplications likely drove the evolution of PgIAA genes, followed by purifying selection. An analysis of cis-regulatory elements suggested that PgIAA family genes may be involved in the regulation of plant hormones. RNA-seq data show that the expression pattern of Aux/IAA genes in Ginseng is tissue-specific, and PgIAA02 and PgIAA36 are specifically highly expressed in lateral, fibrous, and arm roots, suggesting their potential function in root development. The PgIAA02 overexpression lines exhibited an inhibition of lateral root growth in Ginseng. In addition, yeast two-hybrid and subcellular localization experiments showed that PgIAA02 interacted with PgARF22/PgARF36 (ARF: auxin response factor) in the nucleus and participated in the biological process of root development. The above results lay the foundation for an in-depth study of Aux/IAA and provide preliminary information for further research on the role of the Aux/IAA gene family in the root development of Ginseng. Full article