Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19

BSISTER transcription factors directly binds to the promoter of IAA19 and IAA29 genes to up-regulate gene expression and promote the root development

Roots play an important role in the growth and development of plants and auxin participates in regulating plant root development. Some studies have shown that BS (BSISTER) gene (the closest gene of class B gene) is involved in plant root development, but whether BS regulates root development via auxin signaling still not clear. To explore VviBS1 and VviBS2 roles in root development, VviBS1 and VviBS2 were overexpressedin Arabidopsis tt16 mutant and we found that they could restore the phenotype of shorter PR (primary roots) and high density of LR (lateral root) of tt16 compared with the wild type Ws Arabidopsis seedlings. However, the addition of exogenous NAA (naphthalene acetic acid) could not significantly promote the PR length of tt16 Arabidopsis, and the auxin signal transduction of tt16 may be blocked. The expression levels of auxin signal transduction pathway genes in Ws, tt16, p35s:VviBS1 in tt16 and p35s:VviBS2 in tt16 seedlings were detected. It was found that the expression of AtARF2, AtARF12, AtARF14, AtARF15, AtARF20, AtGH3, AtGH3-2 and AtSAUR51 genes in tt16 seedlings was higher than that in Ws, while the expression of AtIAA19 and AtIAA29 in Ws seedlings was higher than that of tt16. More importantly, BS may up regulate AtIAA19 and AtIAA29 expression directly by binding to their promoter. In addition, VviBS1 and VviBS2 also affect seed germination and may regulate leaf yellowing by regulating ethylene synthase. Therefore, our findings reveal a molecular mechanism that BS may modulate root system development via Aux/IAA-based auxin signaling, and provide insight into the BS function in regulation of leaf yellowing.

Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

Temperature-sensitive genic male sterile (TGMS) line Beijing Sterility 366 (BS366) has been utilized in hybrid breeding for a long time, but the molecular mechanism underlying male sterility remains unclear. Expression arrays, small RNA, and degradome sequencing were used in this study to explore the potential role of miRNA in the cold-induced male sterility of BS366. Microspore observation showed defective cell plates in dyads and tetrads and shrunken microspores at the vacuolated stage. Differential regulation of Golgi vesicle transport, phragmoplast formation, sporopollenin biosynthesis, pollen exine formation, and lipid metabolism were observed between cold and control conditions. Pollen development was significantly represented in the 352 antagonistic miRNA-target pairs in the integrated analysis of miRNA and mRNA profiles. The specific cleavage of ARF17 and TIR1 by miR160 and miR393 were found in the cold-treated BS366 degradome, respectively. Thus, the cold-mediated miRNAs impaired cell plate formation through repression of Golgi vesicle transport and phragmoplast formation. The repressed expression of ARF17 and TIR1 impaired pollen exine formation. The results of this study will contribute to our understanding of the roles of miRNAs in male sterility in wheat.

Identification and characterization of auxin response factor (ARF) family members involved in fig (Ficus carica L.) fruit development

The auxin response factor (ARF) combines with AuxREs cis-acting elements in response to auxin to regulate plant development. To date, no comprehensive analysis of ARF genes expressed during fruit development has been conducted for common fig (Ficus carica L.). In this study, members of the FcARF gene family were screened, identified in the fig genome database and their features characterized using bioinformatics. Twenty FcARF genes were clustered into three classes, with almost similar highly conserved DBD (B3-like DNA binding domain), AUX/IAA (auxin/indole-3-acetic acid gene family) and MR domain structure among class members. Analysis of amino acid species in MR domain revealed 10 potential transcription activators and 10 transcription inhibitors, and 17 FcARF members were predicted to be located in the nucleus. DNA sequence analysis showed that the ARF gene family consisted of 4-25 exons, and the promoter region contained 16 cis-acting elements involved in stress response, hormone response and flavonoid biosynthesis. ARF genes were expressed in most tissues of fig, especially flower and peel. Transcriptomics analysis results showed that FcARF2, FcARF11 and FcARF12, belonging to class-Ia, were stably and highly expressed in the early development stage of flower and peel of 'Purple peel' fig. However, their expression levels decreased after maturity. Expression of class-Ic member FcARF3 conformed to the regularity of fig fruit development. These four potential transcription inhibitors may regulate fruit growth and development of 'Purple Peel' fig. This study provides comprehensive information on the fig ARF gene family, including gene structure, chromosome position, phylogenetic relationship and expression pattern. Our work provides a foundation for further research on auxin-mediated fig fruit development.

Overexpression of AcEXPA23 Promotes Lateral Root Development in Kiwifruit

Kiwifruit is loved by consumers for its unique taste and rich vitamin C content. Kiwifruit are very sensitive to adverse soil environments owing to fleshy and shallow roots, which limits the uptake of water and nutrients into the root system, resulting in low yield and poor fruit quality. Lateral roots are the key organs for plants to absorb water and nutrients. Improving water and fertilizer use efficiency by promoting lateral root development is a feasible method to improve yield and quality. Expansin proteins plays a major role in lateral root growth; hence, it is important to identify expansin protein family members, screen key genes, and explore gene function in root development. In this study, 41 expansin genes were identified based on the genome of kiwifruit (‘Hongyang’, Actinidia chinensis). By clustering with the Arabidopsis thaliana expansin protein family, the 41 AcExpansin proteins were divided into four subfamilies. The AcExpansin protein family was further analysed by bioinformatics methods and was shown to be evolutionarily diverse and conserved at the DNA and protein levels. Based on previous transcriptome data and quantitative real-time PCR assays, we screened the candidate gene AcEXPA23. Overexpression of AcEXPA23 in kiwifruit increased the number of kiwifruit lateral roots.

Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning

Auxin critically regulates plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARF protein condensation attenuates ARF activity, resulting in dramatic shifts in the auxin transcriptional landscape. Here, we perform a forward genetics screen for ARF hypercondensation, identifying an F-box protein, which we named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). Functional characterization of SCFAFF1 revealed that this E3 ubiquitin ligase directly interacts with ARF19 and ARF7 to regulate their accumulation, condensation, and nucleo-cytoplasmic partitioning. Mutants defective in AFF1 display attenuated auxin responsiveness, and developmental defects, suggesting that SCFAFF1 -mediated regulation of ARF protein drives aspects of auxin response and plant development.

Red and Blue Light Affect the Formation of Adventitious Roots of Tea Cuttings (Camellia sinensis) by Regulating Hormone Synthesis and Signal Transduction Pathways of Mature Leaves

Light is an important environmental factor which affects plant growth, through changes of intensity and quality. In this study, monochromatic white (control), red (660 nm), and blue (430 nm) light-emitting diodes (LEDs) were used to treat tea short cuttings. The results showed the most adventitious roots in blue light treated tea cuttings, but the lowest roots in that treated by red light. In order to explore the molecular mechanism of light quality affecting adventitious root formation, we performed full-length transcriptome and metabolome analyses of mature leaves under three light qualities, and then conducted weighted gene co-expression network analysis (WGCNA). Phytohormone analysis showed that Indole-3-carboxylic acid (ICA), Abscisic acid (ABA), ABA-glucosyl ester (ABA-GE), trans-Zeatin (tZ), and Jasmonic acid (JA) contents in mature leaves under blue light were significantly higher than those under white and red light. A crosstalk regulatory network comprising 23 co-expression modules was successfully constructed. Among them, the "MEblue" module which had a highly positive correlation with ICA (R = 0.92, P = 4e-04). KEGG analysis showed that related genes were significantly enriched in the "Plant hormone signal transduction (ko04075)" pathway. YUC (a flavin-containing monooxygenase), AUX1, AUX/IAA, and ARF were identified as hub genes, and gene expression analysis showed that the expression levels of these hub genes under blue light were higher than those under white and red light. In addition, we also identified 6 auxin transport-related genes, including PIN1, PIN3, PIN4, PILS5, PILS6, and PILS7. Except PILS5, all of these genes showed the highest expression level under blue light. In conclusion, this study elucidated the molecular mechanism of light quality regulating adventitious root formation of tea short cutting through WGCNA analysis, which provided an innovation for "rapid seedling" of tea plants.

MicroRNA172 controls inflorescence meristem size through regulation of APETALA2 in Arabidopsis

The APETALA2 (AP2) transcription factor regulates flower development, floral transition and shoot apical meristem (SAM) maintenance in Arabidopsis. AP2 is also regulated at the post-transcriptional level by microRNA172 (miR172), but the contribution of this to SAM maintenance is poorly understood. We generated transgenic plants carrying a form of AP2 that is resistant to miR172 (rAP2) or carrying a wild-type AP2 susceptible to miR172. Phenotypic and genetic analyses were performed on these lines and mir172 mutants to study the role of AP2 regulation by miR172 on meristem size and the rate of flower production. We found that rAP2 enlarges the inflorescence meristem by increasing cell size and cell number. Misexpression of rAP2 from heterologous promoters showed that AP2 acts in the central zone (CZ) and organizing center (OC) to increase SAM size. Furthermore, we found that AP2 is negatively regulated by AUXIN RESPONSE FACTOR 3 (ARF3). However, genetic analyses indicated that ARF3 also influences SAM size and flower production rate independently of AP2. The study identifies miR172/AP2 as a regulatory module controlling inflorescence meristem size and suggests that transcriptional regulation of AP2 by ARF3 fine-tunes SAM size determination.

Auxin response factors are keys to the many auxin doors

In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.

A feedback regulation between ARF7-mediated auxin signaling and auxin homeostasis involving MES17 affects plant gravitropism

Gravitropism is an essential adaptive response of land plants. Asymmetric auxin gradients across plant organs, interpreted by multiple auxin signaling components including AUXIN RESPONSE FACTOR7 (ARF7), trigger differential growth and bending response. However, how this fundamental process is strictly maintained in nature remains unclear. Here, we report that gravity stimulates the transcription of METHYL ESTERASE17 (MES17) along the lower side of the hypocotyl via ARF7-dependent auxin signaling. The asymmetric distribution of MES17, a methyltransferase that converts auxin from its inactive form methyl indole-3-acetic acid ester (MeIAA) to its biologically active form free-IAA, enhanced the gradient of active auxin across the hypocotyl, which in turn reversely amplified the asymmetric auxin responses and differential growth that shape gravitropic bending. Taken together, our findings reveal the novel role of MES17-mediated auxin homeostasis in gravitropic responses and identify an ARF7-triggered feedback mechanism that reinforces the asymmetric distribution of active auxin and strictly controls gravitropism in plants.

Dynamic Transcriptome Analysis Reveals Complex Regulatory Pathway Underlying Induction and Dose Effect by Different Exogenous Auxin IAA and 2,4-D During in vitro Embryogenic Redifferentiation in Cotton

Plant somatic cells can reprogram into differentiated embryos through somatic embryogenesis (SE) on the condition of plant growth regulators (PGRs). RNA sequencing analysis was performed to investigate transcriptional profiling on cotton redifferentiated callus that was induced by different auxin types (IAA and 2,4-D), different concentrations (0, 0.025, and 0.05 mg L^-1), and different incubation times (0, 5, and 20 days). Under the 2,4-D induction effect, signal transduction pathways of plant hormones were significantly enriched in the embryogenic response stage (5 days). These results indicated that auxin signal transduction genes were necessary for the initial response of embryogenic differentiation. In the pre-embryonic initial period (20 days), the photosynthetic pathway was significantly enriched. Most differentially expressed genes (DEGs) were downregulated under the induction of 2,4-D. Upon the dose effect of IAA and 2,4-D, respectively, pathways were significantly enriched in phenylpropanoid biosynthesis, fatty acid metabolism, and carbon metabolic pathways. Therefore, primary and secondary metabolism pathways were critical in cotton SE. These results showed that complex synergistic mechanisms involving multiple cellular pathways were the causes of the induction and dose effect of auxin-induced SE. This study reveals a systematic molecular response to auxin signals and reveals the way that regulates embryogenic redifferentiation during cotton SE.

PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins

We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.

Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L

Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes' promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation; the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members' roles in floral organ development and hormone response.

Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis

Plant growth promoting rhizobacteria (PGPR) refer to bacteria that colonize the rhizosphere and contribute to plant growth or stress tolerance. To further understand the molecular mechanism by which PGPR exhibit symbiosis with plants, we performed a high-throughput single colony screening from the rhizosphere, and uncovered a bacterium (named promoting lateral root, PLR) that significantly promotes Arabidopsis lateral root formation. By 16S rDNA sequencing, PLR was identified as a novel sub-species of Serratia marcescens. RNA-seq analysis of Arabidopsis integrated with phenotypic verification of auxin signalling mutants demonstrated that the promoting effect of PLR on lateral root formation is dependent on auxin signalling. Furthermore, PLR enhanced tryptophan-dependent indole-3-acetic acid (IAA) synthesis by inducing multiple auxin biosynthesis genes in Arabidopsis. Genome-wide sequencing of PLR integrated with the identification of IAA and its precursors in PLR exudates showed that tryptophan treatment significantly enhanced the ability of PLR to produce IAA and its precursors. Interestingly, PLR induced the expression of multiple nutrient (N, P, K, S) transporter genes in Arabidopsis in an auxin-independent manner. This study provides evidence of how PLR enhances plant growth through fine-tuning auxin biosynthesis and signalling in Arabidopsis, implying a potential application of PLR in crop yield improvement through accelerating root development.

The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple

Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.

Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance

Auxin response factors (ARFs) play important roles in plant development and environmental adaption. However, the function of ARFs in cadmium (Cd) accumulation are still unknown. Here, 23 SaARFs were detected in the genome of hyperaccumulating ecotype of Sedum alfredii Hance (HE), and they were not evenly distributed on the chromosomes. Their protein domains remained highly conservative. SaARFs in the phylogenetic tree can be divided into three groups. Genes in the group Ⅰ contained three introns at most. However, over ten introns were found in other two groups. Collinearity relationships were exhibited among ten SaARFs. The reasons for generating SaARFs may be segmental duplication and rearrangements. Collinearity analysis among different species revealed that more collinear genes of SaARFs can be found in the species with close relationships of HE. A total of eight elements in SaARFs promoters were related with abiotic stress. The qRT-PCR results indicated that four SaARFs can respond to Cd stress. Moreover, that there may be functional redundancy among six SaARFs. The adaptive selection and functional divergence analysis indicated that SaARF4 may undergo positive selection pressure and an adaptive-evolution process. Overexpressing SaARF4 effectively declined Cd accumulation. Eleven single nucleotide polymorphism (SNP) sites relevant to Cd accumulation can be detected in SaARF4. Among them, only one SNP site can alter the sequence of the SaARF4 protein, but the SaARF4 mutant of this site did not cause a significant difference in cadmium content, compared with wild-type plants. SaARFs may be involved in Cd-stress responses, and SaARF4 may be applied for decreasing Cd accumulation of plants.

Genome-wide analysis of pathogenesis-related protein 1 (PR-1) gene family from Musa spp. and its role in defense response during stresses

Pathogenesis related protein-1 (PR-1) is the most abundantly produced protein during defense response against many biotic and abiotic stresses. However, knowledge on PR-1 gene family and its evolutionary relationship in banana is very limited. In order to study the potential role of PR-1 genes in banana, genome wide identification, structure analysis and expressions were performed. A total of 15 and 11 PR-1 genes were identified from A and B genomes of banana and the proteins encoded by this gene family are of varying lengths and harbor conserved domains and motifs. PR-1 genes are unevenly dispersed on 11 chromosomes with segmental duplication in both A and B genome, suggesting an important contribution of duplication in expansion of PR-1 gene family in banana. qRT-PCR analysis of PR-1 gene showed positive correlation with the RNAseq data under various stresses and examination of expression pattern of selected MaPR-1 genes in banana revealed its role in biotic and abiotic stresses in general and fusarium wilt in particular. This study provides significant insight into the functions of PR-1 genes which can be further exploited as a promising candidate for developing multiple stress tolerant banana varieties.

Identification of ARF family in blueberry and its potential involvement of fruit development and pH stress response

Background

Auxin responsive factor (ARF) family is one of core components in auxin signalling pathway, which governs diverse developmental processes and stress responses. Blueberry is an economically important berry-bearing crop and prefers to acidic soil. However, the understandings of ARF family has not yet been reported in blueberry.

Results

In the present study, 60 ARF genes (VcARF) were identified in blueberry, and they showed diverse gene structures and motif compositions among the groups and similar within each group in the phylogenetic tree. Noticeably, 9 digenic, 5 trigenic and 6 tetragenic VcARF pairs exhibited more than 95% identity to each other. Computational analysis indicated that 23 VcARFs harbored the miRNA responsive element (MRE) of miR160 or miR167 like other plant ARF genes. Interestingly, the MRE of miR156d/h-3p was observed in the 5’UTR of 3 VcARFs, suggesting a potentially novel post-transcriptional control. Furthermore, the transcript accumulations of VcARFs were investigated during fruit development, and three categories of transcript profiles were observed, implying different functional roles. Meanwhile, the expressions of VcARFs to different pH conditions (pH4.5 and pH6.5) were surveyed in pH-sensitive and tolerant blueberry species, and a number of VcARFs showed different transcript accumulations. More importantly, distinct transcriptional response to pH stress (pH6.5) were observed for several VcARFs (such as VcARF6s and VcARF19-3/19–4) between pH-sensitive and tolerant species, suggesting their potential roles in adaption to pH stress.

Conclusions

Sixty VcARF genes were identified and characterized, and their transcript profiles were surveyed during fruit development and in response to pH stress. These findings will contribute to future research for eliciting the functional roles of VcARFs and regulatory mechanisms, especially fruit development and adaption to pH stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08556-y.

Pericycle cell division competence underlies various developmental programs

Pericycle cells possess proliferative activity long after leaving the root apical meristem. Depending on the developmental stage and external stimuli, pericycle cell division leads to the production of lateral roots, vascular cambium and periderm, and callus. Therefore, pericycle cell division competence underlies root branching and secondary growth, as well as plant regeneration capacity. In this review, we first briefly present an overview of the molecular pathways of the four developmental programs originated, exclusively or partly, from pericycle cells. Then, we provide a review of up-to-date knowledge in the mechanisms determining pericycle cells' competence to undergo cell division. Furthermore, we discuss directions of future research to further our understanding of the pericycle's characteristics and functions.

Insights into Factors Controlling Adventitious Root Formation in Apples

Adventitious root (AR) formation is required for the vegetative propagation of economically important horticultural crops, such as apples. Asexual propagation is commonly utilized for breeding programs because of its short life cycle, true-to-typeness, and high efficiency. The lack of AR formation from stem segments is a barrier to segment survival. Therefore, understanding the AR regulatory mechanisms is vital for the prolonged and effective use of biological resources. Several studies have been undertaken to comprehend the molecular and physiological control of AR, which has greatly extended our knowledge regarding AR formation in apples and other crops. Auxin, a master controller of AR formation, is widely used for inducing AR formation in stem cutting. At the same time, cytokinins (CKs) are important for cell division and molecular reprograming, and other hormones, sugars, and nutrients interact with auxin to control excision-induced AR formation. In this review, we discuss the present understandings of ARs’ formation from physiological and molecular aspects and highlight the immediate advancements made in identifying underlying mechanisms involved in the regulation of ARs. Despite the progress made in the previous decades, many concerns about excision-induced AR formation remain unanswered. These focus on the specific functions and interactions of numerous hormonal, molecular, and metabolic components and the overall framework of the entire shoot cutting in a demanding environment.

Interplay between Arabidopsis thaliana Genotype, Plant Growth and Rhizosphere Colonization by Phytobeneficial Phenazine-Producing Pseudomonas chlororaphis

Rhizosphere colonization by phytobeneficial Pseudomonas spp. is pivotal in triggering their positive effects on plant health. Many Pseudomonas spp. Determinants, involved in rhizosphere colonization, have already been deciphered. However, few studies have explored the role played by specific plant genes in rhizosphere colonization by these bacteria. Using isogenic Arabidopsis thaliana mutants, we studied the effect of 20 distinct plant genes on rhizosphere colonization by two phenazine-producing P. chlororaphis strains of biocontrol interest, differing in their colonization abilities: DTR133, a strong rhizosphere colonizer and ToZa7, which displays lower rhizocompetence. The investigated plant mutations were related to root exudation, immunity, and root system architecture. Mutations in smb and shv3, both involved in root architecture, were shown to positively affect rhizosphere colonization by ToZa7, but not DTR133. While these strains were not promoting plant growth in wild-type plants, increased plant biomass was measured in inoculated plants lacking fez, wrky70, cbp60g, pft1 and rlp30, genes mostly involved in plant immunity. These results point to an interplay between plant genotype, plant growth and rhizosphere colonization by phytobeneficial Pseudomonas spp. Some of the studied genes could become targets for plant breeding programs to improve plant-beneficial Pseudomonas rhizocompetence and biocontrol efficiency in the field.

miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development

MicroRNAs (miRNAs) are key regulators of several plant developmental processes including embryogenesis. Most miRNA families are conserved across major groups of plant species, but their regulatory roles have been studied mainly in model species like Arabidopsis and other angiosperms. In gymnosperms, miRNA-dependent regulation has been less studied since functional approaches in these species are often difficult to establish. Given the fundamental roles of auxin signaling in somatic embryogenesis (SE) induction and embryo development, we investigated a previously predicted interaction between miR160 and a putative target encoding AUXIN RESPONSE FACTOR 18 in Pinus pinaster (PpARF18) embryonic tissues. Phylogenetic analysis of AUXIN RESPONSE FACTOR 18 (ARF18) from Pinus pinaster and Picea abies, used here as a model system of conifer embryogenesis, showed their close relatedness to AUXIN RESPONSE FACTOR (ARF) genes known to be targeted by miR160 in other species, including Arabidopsis ARF10 and ARF16. By using a luciferase (LUC) reporter system for miRNA activity in Arabidopsis protoplasts, we have confirmed that P. pinaster miR160 (ppi-miR160) interacts in vivo with PpARF18 target site. When the primary miR160 from P. pinaster was overexpressed in protoplasts under non-limiting levels of ARGONAUTE1, a significant increase of miR160 target cleavage activity was observed. In contrast, co-expression of the primary miRNA and the target mimic MIM160 led to a decrease of miR160 activity. Our results further support that this interaction is functional during consecutive stages of SE in the conifer model P. abies. Expression analyses conducted in five stages of development, from proembryogenic masses (PEMs) to the mature embryo, show that conifer ARF18 is negatively regulated by miR160 toward the fully developed mature embryo when miR160 reached its highest expression level. This study reports the first in vivo validation of a predicted target site of a conifer miRNA supporting the conservation of miR160 interaction with ARF targets in gymnosperms. The approach used here should be useful for future characterization of miRNA functions in conifer embryogenesis.

Plant phosphate nutrition: sensing the stress

Phosphorus (P) is obtained by plants as phosphate (Pi) from the soil and low Pi levels affects plant growth and development. Adaptation to low Pi condition entails sensing internal and external Pi levels and translating those signals to molecular and morphophysiological changes in the plant. In this review, we present findings related to local and systemin Pi sensing with focus the molecular mechanisms behind root system architectural changes and the impact of hormones and epigenetic mechanisms affecting those changes. We also present some of the recent advances in the Pi sensing and signaling mechanisms focusing on inositol pyrophosphate InsP8 and its interaction with SPX domain proteins to regulate the activity of the central regulator of the Pi starvation response, PHR.

The volatile cedrene from Trichoderma guizhouense modulates Arabidopsis root development through auxin transport and signalling

Rhizosphere microorganisms interact with plant roots by producing chemical signals that regulate root development. However, the distinct bioactive compounds and signal transduction pathways remain to be identified. Here, we showed that sesquiterpenes are the main volatile compounds produced by plant-beneficial Trichoderma guizhouense NJAU4742. Inhibition of sesquiterpene biosynthesis eliminated the promoting effect of this strain on root growth, indicating its involvement in plant-fungus cross-kingdom signalling. Sesquiterpene component analysis identified cedrene, a highly abundant sesquiterpene in strain NJAU4742, to stimulate plant growth and root development. Genetic analysis and auxin transport inhibition showed that the TIR1 and AFB2 auxin receptors, IAA14 auxin-responsive protein, and ARF7 and ARF19 transcription factors affected the response of lateral roots to cedrene. Moreover, the AUX1 auxin influx carrier and PIN2 efflux carrier were also found to be indispensable for cedrene-induced lateral root formation. Confocal imaging showed that cedrene affected the expression of pPIN2:PIN2:GFP and pPIN3:PIN3:GFP, which might be related to the effect of cedrene on root morphology. These results suggested that a novel sesquiterpene molecule from plant-beneficial T. guizhouense regulates plant root development through the transport and signalling of auxin.

Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean (Ricinus communis)

The B3 transcription factors (TFs) in plants play vital roles in numerous biological processes. Although B3 genes have been broadly identified in many plants, little is known about their potential functions in mediating seed development and material accumulation. Castor bean (Ricinus communis) is a non-edible oilseed crop considered an ideal model system for seed biology research. Here, we identified a total of 61 B3 genes in the castor bean genome, which can be classified into five subfamilies, including ABI3/VP1, HSI, ARF, RAV and REM. The expression profiles revealed that RcABI3/VP1 subfamily genes are significantly up-regulated in the middle and later stages of seed development, indicating that these genes may be associated with the accumulation of storage oils. Furthermore, through yeast one-hybrid and tobacco transient expression assays, we detected that ABI3/VP1 subfamily member RcLEC2 directly regulates the transcription of RcOleosin2, which encodes an oil-body structural protein. This finding suggests that RcLEC2, as a seed-specific TF, may be involved in the regulation of storage materials accumulation. This study provides novel insights into the potential roles and molecular basis of B3 family proteins in seed development and material accumulation.

Maize Transcription Factor ZmARF4 Confers Phosphorus Tolerance by Promoting Root Morphological Development

Plant growth and development are closely related to phosphate (Pi) and auxin. However, data regarding auxin response factors (ARFs) and their response to phosphate in maize are limited. Here, we isolated ZmARF4 in maize and dissected its biological function response to Pi stress. Overexpression of ZmARF4 in Arabidopsis confers tolerance of Pi deficiency with better root morphology than wild-type. Overexpressed ZmARF4 can partially restore the absence of lateral roots in mutant arf7 arf19. The ZmARF4 overexpression promoted Pi remobilization and up-regulated AtRNS1, under Pi limitation while it down-regulated the expression of the anthocyanin biosynthesis genes AtDFR and AtANS. A continuous detection revealed higher activity of promoter in the Pi-tolerant maize P178 line than in the sensitive 9782 line under low-Pi conditions. Meanwhile, GUS activity was specifically detected in new leaves and the stele of roots in transgenic offspring. ZmARF4 was localized to the nucleus and cytoplasm of the mesophyll protoplast and interacted with ZmILL4 and ZmChc5, which mediate lateral root initiation and defense response, respectively. ZmARF4 overexpression also conferred salinity and osmotic stress tolerance in Arabidopsis. Overall, our findings suggest that ZmARF4, a pleiotropic gene, modulates multiple stress signaling pathways, and thus, could be a candidate gene for engineering plants with multiple stress adaptation.

Chinese Cherry (Cerasus pseudocerasus Lindl.) ARF7 Participates in Root Development and Responds to Drought and Low Phosphorus

In this paper, an auxin-responsive transcription factor, CpARF7, was isolated from the roots of Chinese cherry (Cerasus pseudocerasus Lindl. Cv. “Manao Hong”). CpARF7 is highly homologous to AtARF7 or AtARF19 in Arabidopsis, and PavARF1 or PavARF14 in sweet cherry. However, in the phenotype of transgenic tomatoes, the root morphology changed, the main root elongated, and the lateral root increased. Both drought treatment and low-phosphorus conditions can elongate the roots of transgenic tomatoes. In addition, the drought resistance and low-phosphorus tolerance of the transgenic lines are improved, and the POD, SOD, and CAT activities under drought and low-phosphorus environments are increased. There is an effect on the tomato somatotropin suppressor gene, SlIAAs, in which SlIAA1/14/19/29 are up-regulated and SlIAA2/11/12/16 are down-regulated. These results indicate that CpARF7 plays an essential regulatory role in root formation and abiotic stress response, and deepens the understanding of auxin-responsive genes in root growth and abiotic stress.

Physio-Morphological, Biochemical and Transcriptomic Analyses Provide Insights Into Drought Stress Responses in Mesona chinensis Benth

Drought stress affects the normal growth and development of Mesona chinensis Benth (MCB), which is an important medicinal and edible plant in China. To investigate the physiological and molecular mechanisms of drought resistance in MCB, different concentrations of polyethylene glycol 6000 (PEG6000) (0, 5, 10, and 15%) were used to simulate drought conditions in this study. Results showed that the growth of MCB was significantly limited under drought stress conditions. Drought stress induced the increases in the contents of Chla, Chlb, Chla + b, soluble protein, soluble sugar, and soluble pectin and the activities of superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (TAC), hydrogen peroxide (H2O2), and malondialdehyde (MDA). Transcriptome analysis revealed 3,494 differentially expressed genes (DEGs) (1,961 up-regulated and 1,533 down-regulated) between the control and 15% PEG6000 treatments. These DEGs were identified to be involved in the 10 metabolic pathways, including "plant hormone signal transduction," "brassinosteroid biosynthesis," "plant-pathogen interaction," "MAPK signaling pathway-plant," "starch and sucrose metabolism," "pentose and glucuronate interconversions," "phenylpropanoid biosynthesis," "galactose metabolism," "monoterpenoid biosynthesis," and "ribosome." In addition, transcription factors (TFs) analysis showed 8 out of 204 TFs, TRINITY_DN3232_c0_g1 [ABA-responsive element (ABRE)-binding transcription factor1, AREB1], TRINITY_DN4161_c0_g1 (auxin response factor, ARF), TRINITY_DN3183_c0_g2 (abscisic acid-insensitive 5-like protein, ABI5), TRINITY_DN28414_c0_g2 (ethylene-responsive transcription factor ERF1b, ERF1b), TRINITY_DN9557_c0_g1 (phytochrome-interacting factor, PIF3), TRINITY_DN11435_c1_g1, TRINITY_DN2608_c0_g1, and TRINITY_DN6742_c0_g1, were closely related to the "plant hormone signal transduction" pathway. Taken together, it was inferred that these pathways and TFs might play important roles in response to drought stress in MCB. The current study provided important information for MCB drought resistance breeding in the future.

Transcriptional Regulation of Different Rhizome Parts Reveal the Candidate Genes That Regulate Rhizome Development in Poa pratensis

A strong rhizome can enhance the ability of a plant to resist drought, low temperature, and other stresses, as it can help plants rapidly obtain water and nutrients. Poa pratensis var. anceps Gaud. cv. Qinghai (QH) is a variant of P. pratensis that is widely distributed in natural grasslands above 3000 m above sea level on the Qinghai-Tibet Plateau. It forms turf easily and has strong soil-fixing ability due to its well-developed rhizomes. Understanding the molecular mechanism of rhizome development in this species is essential for cultivating new varieties of rhizome-type pasture for ecological protection. To clarify the transcriptional regulatory changes in different parts of the rhizome, we analyzed three different rhizome parts (rhizome buds, rhizome nodes, and rhizome internodes) of QH and weak-rhizome wild P. pratensis material (SN) using RNA sequencing. A total of 3806 genes were specifically expressed in Q_B, 1104 genes were specifically expressed in Q_N, and 1181 genes were specifically expressed in Q_I. Analysis showed that MYB, B3, NAC, BBR-BPC, AP2 MIKC_MADS, BSE1, and C2H2 may be key transcription factors regulating rhizome development. These genes interacted with multiple functional genes related to carbohydrate, secondary metabolism, and signal transduction, thus ensuring the normal development of the rhizomes. In particular, SUS (sucrose synthase) [EC:2.4.1.13] is specifically expressed in Q_I, which may be an inducing factor for the production of new plants from Q_B and Q_N. Additionally, PYL, PP2C, and SNRK2, which are involved in the abscisic acid signaling pathway, were differentially expressed in Q_N. In addition, genes related to protein modification and degradation, such as CIPKs, MAPKs, E2, and E3 ubiquitin ligases, were also involved in rhizome development. This study laid a foundation for further functional genomics studies on rhizome development in P. pratensis.

Two phylogenetically unrelated peptide-receptor modules jointly regulate lateral root initiation via a partially shared signaling pathway in Arabidopsis thaliana

Peptide-receptor signaling is an important system for intercellular communication, regulating many developmental processes. A single process can be controlled by several distinct signaling peptides. However, since peptide-receptor modules are usually studied separately, their mechanistic interactions remain largely unexplored. Two phylogenetically unrelated peptide-receptor modules, GLV6/GLV10-RGI and TOLS2/PIP2-RLK7, independently described as inhibitors of lateral root initiation, show striking similarities between their expression patterns and gain- and loss-of-function phenotypes, suggesting a common function during lateral root spacing and initiation. The GLV6/GLV10-RGI and TOLS2/PIP2-RLK7 modules trigger similar transcriptional changes, likely in part via WRKY transcription factors. Their overlapping set of response genes includes PUCHI and PLT5, both required for the effect of GLV6/10, as well as TOLS2, on lateral root initiation. Furthermore, both modules require the activity of MPK6 and can independently trigger MPK3/MPK6 phosphorylation. The GLV6/10 and TOLS2/PIP2 signaling pathways seem to converge in the activation of MPK3/MPK6, leading to the induction of a similar transcriptional response in the same target cells, thereby regulating lateral root initiation through a (partially) common mechanism. Convergence of signaling pathways downstream of phylogenetically unrelated peptide-receptor modules adds an additional, and hitherto unrecognized, level of complexity to intercellular communication networks in plants.

Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

Biphasic control of cell expansion by auxin coordinates etiolated seedling development

Seedling emergence is critical for food security. It requires rapid hypocotyl elongation and apical hook formation, both of which are mediated by regulated cell expansion. How these events are coordinated in etiolated seedlings is unclear. Here, we show that biphasic control of cell expansion by the phytohormone auxin underlies this process. Shortly after germination, high auxin levels restrain elongation. This provides a temporal window for apical hook formation, involving a gravity-induced auxin maximum on the eventual concave side of the hook. This auxin maximum induces PP2C.D1 expression, leading to asymmetrical H⁺-ATPase activity across the hypocotyl that contributes to the differential cell elongation underlying hook development. Subsequently, auxin concentrations decline acropetally and switch from restraining to promoting elongation, thereby driving hypocotyl elongation. Our findings demonstrate how differential auxin concentrations throughout the hypocotyl coordinate etiolated development, leading to successful soil emergence.

Postembryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs

Postembryonic organogenesis is a critical component in plant root and shoot development and its adaptation to the environment. Decades of scientific analyses have yielded a wealth of experimental data about the cellular and molecular processes orchestrating the postembryonic formation of new shoot and root organs. Among these, distribution and signaling of the plant hormone auxin play a prominent role. Systems biology approaches are now particularly interesting to study the emerging properties of such complex and dynamic regulatory networks. To fully explore the precise kinetics of these organogenesis processes, efficient protocols for the synchronized induction of shoot and root organogenesis are extremely valuable. Two protocols for shoot and root organ induction are detailed.

Genome-wide identification of auxin response factor (ARF) gene family and the miR160-ARF18-mediated response to salt stress in peanut (Arachis hypogaea L.)

Auxin response factors (ARFs) are transcription factors that regulate the transcription of auxin-responsive genes during plant growth and development. In this study, 29 and 30 ARF members were identified from the two wild peanut species, A. duranensis and A. ipaensis, respectively. The ARFs, including their classifications, conserved domains and evolutionary relationships were characterized. RNA-seq analyses revealed that some of the ARF genes were responsive to abiotic stress, particularly high salinity. In addition to abiotic stress, the expression of 2 ARF members was also regulated by biotic stress, specifically Bradyrhizobium infection in A. duranensis. The ARF gene Arahy.7DXUOK was predicted to be a potential target of miR160. Overexpression of miR160 could cause degradation of the Arahy.7DXUOK target gene transcript and increased salt tolerance in miR160OX transgenic plants. Therefore, these molecular characterization and expression profile analyses provide comprehensive information on ARF family members and will help to elucidate their functions to facilitate further research on peanuts.

Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum

Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.

Hydrogen Sulfide Improves the Cold Stress Resistance through the CsARF5-CsDREB3 Module in Cucumber

As an important gas signaling molecule, hydrogen sulfide (H₂S) plays a crucial role in regulating cold tolerance. H₂S cooperates with phytohormones such as abscisic acid, ethylene, and salicylic acid to regulate the plant stress response. However, the synergistic regulation of H₂S and auxin in the plant response to cold stress has not been reported. This study showed that sodium hydrosulfide (NaHS, an H₂S donor) treatment enhanced the cold stress tolerance of cucumber seedlings and increased the level of auxin. CsARF5, a cucumber auxin response factor (ARF) gene, was isolated, and its role in regulating H₂S-mediated cold stress tolerance was described. Transgenic cucumber leaves overexpressing CsARF5 were obtained. Physiological analysis indicated that overexpression of CsARF5 enhanced the cold stress tolerance of cucumber and the regulation of the cold stress response by CsARF5 depends on H₂S. In addition, molecular assays showed that CsARF5 modulated cold stress response by directly activating the expression of the dehydration-responsive element-binding (DREB)/C-repeat binding factor (CBF) gene CsDREB3, which was identified as a positive regulator of cold stress. Taken together, the above results suggest that CsARF5 plays an important role in H₂S-mediated cold stress in cucumber. These results shed light on the molecular mechanism by which H₂S regulates cold stress response by mediating auxin signaling; this will provide insights for further studies on the molecular mechanism by which H₂S regulates cold stress. The aim of this study was to explore the molecular mechanism of H₂S regulating cold tolerance of cucumber seedlings and provide a theoretical basis for the further study of cucumber cultivation and environmental adaptability technology in winter.

Bismuth Vanadium Oxide Can Promote Growth and Activity in Arabidopsis thaliana

The excellent properties of nanomaterials have been confirmed in many fields, but their effects on plants are still unclear. In this study, different concentrations of bismuth vanadate (BV) were added to the growth medium to analyze the growth of seedlings, including taproots, lateral roots, leaf stomata, root activity, and superoxide anion O₂^.- generation. Gene expression levels related to root growth were determined by quantitative PCR in Arabidopsis thaliana. The results showed that BV promoted the growth of taproots and the development of lateral roots, enhanced the length of the extension zone in roots, increased the number and size of leaf stomata and root activity, reduced the accumulation of ROS in seedlings, and changed the expression levels of genes related to polyamines or hormones. At the same time, we investigated the antibacterial activity of BV against a variety of common pathogens causing crop diseases. The results showed that BV could effectively inhibit the growth of Fusarium wilt of cotton and rice sheath blight. These results provide a new prospect for the development of nanomaterial-assisted plants, which is expected to become one of the ways to solve the problem of controlling and promoting the development of plants. At the same time, it also provides a reference for the study of the effect of BV on plants.

Vacuolar fructose transporter SWEET17 is critical for root development and drought tolerance

Root growth and architecture are markedly influenced by both developmental and environmental cues. Sugars integrate different stimuli and are essential building blocks and signaling molecules for modulating the root system. Members from the SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET) family facilitate the transport of different sugars over cellular membranes and steer both inter and intracellular distribution of sugars. SWEET17 represents a fructose-specific sugar porter localized to the vacuolar membrane, the tonoplast. Here, we analyzed how SWEET17-dependent fructose released from vacuoles affects root growth during drought stress in Arabidopsis (Arabidopsis thaliana). We found that the SWEET17 gene was predominantly expressed in the root vasculature and in meristematic cells of the root tip. SWEET17 expression appeared markedly induced during lateral root (LR) outgrowth and under drought. Moreover, fructose repressed primary root growth but induced density and length of first order LRs. Consistently, sweet17 knock-out mutants exhibited reduced LR growth and a diminished expression of LR-development-related transcription factors during drought stress, resulting in impaired drought tolerance of sweet17 mutants. We discuss how SWEET17 activity integrates drought-induced cellular responses into fructose signaling necessary for modulation of the root system and maximal drought tolerance.

Auxin Does the SAMba: Auxin Signaling in the Shoot Apical Meristem

Plants, in contrast to animals, are unique in their capacity to postembryonically develop new organs due to the activity of stem cell populations, located in specialized tissues called meristems. Above ground, the shoot apical meristem generates aerial organs and tissues throughout plant life. It is well established that auxin plays a central role in the functioning of the shoot apical meristem. Auxin distribution in the meristem is not uniform and depends on the interplay between biosynthesis, transport, and degradation. Auxin maxima and minima are created, and result in transcriptional outputs that drive the development of new organs and contribute to meristem maintenance. To uncover and understand complex signaling networks such as the one regulating auxin responses in the shoot apical meristem remains a challenge. Here, we will discuss our current understanding and point to important research directions for the future.

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.

Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L

Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.

Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I-VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

Uncovering How Auxin Optimizes Root Systems Architecture in Response to Environmental Stresses

Since colonizing land, plants have developed mechanisms to tolerate a broad range of abiotic stresses that include flooding, drought, high salinity, and nutrient limitation. Roots play a key role acclimating plants to these as their developmental plasticity enables them to grow toward more favorable conditions and away from limiting or harmful stresses. The phytohormone auxin plays a key role translating these environmental signals into developmental outputs. This is achieved by modulating auxin levels and/or signaling, often through cross talk with other hormone signals like abscisic acid (ABA) or ethylene. In our review, we discuss how auxin controls root responses to water, osmotic and nutrient-related stresses, and describe how the synthesis, degradation, transport, and response of this key signaling hormone helps optimize root architecture to maximize resource acquisition while limiting the impact of abiotic stresses.

Genome-Wide Analysis of the Glutathione S-Transferase (GST) Genes and Functional Identification of MdGSTU12 Reveals the Involvement in the Regulation of Anthocyanin Accumulation in Apple

Anthocyanins have essential biological functions, affecting the development of horticultural production. They are synthesized in the cytoplasm through flavonoid metabolic pathways and finally transported into vacuoles for storage. Plant glutathione S-transferases (GSTs) are multifunctional enzymes involved in anthocyanin transportation. In this study, we identified 38 GSTs from the apple (Malus domestica) genome (HFTH1 Whole Genome v1.0) based on the sequence similarity with the GST family proteins of Arabidopsis. These MdGST genes could be grouped into nine chief subclasses: U, F, L, Z, T, GHR, EF1Bγ, TCHQD, and DHAR. The structures, motifs, three-dimensional models, and chromosomal distribution of MdGST genes were further analyzed. Elements which are responsive for some hormones and stress, and others that involve genes related to flavonoid biosynthesis were forecast in the promoter of MdGST. In addition, we identified 32 orthologous gene pairs between apple and Arabidopsis. These genes indicated that numerous apple and Arabidopsis counterparts appeared to be derived from a common ancestor. Amongst the 38 MdGST genes, MdGSTU12 was considerably correlated with anthocyanin variation in terms of extracting expression profiles from reported. Finally, further functional identification in apple transgenic calli and subcellular localization confirmed that MdGSTU12 was of great significance in anthocyanin accumulation in apple.

Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc

Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling

Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.

Double Mutant Analysis with the Large Flower Mutant, ohbana1, to Explore the Regulatory Network Controlling the Flower and Seed Sizes in Arabidopsis thaliana

Two growth processes, cell proliferation and expansion, determine plant species-specific organ sizes. A large flower mutant in Arabidopsis thaliana, ohbana1 (ohb1), was isolated from a mutant library. In the ohb1 flowers, post-mitotic cell expansion and endoreduplication of nuclear DNA were promoted. The whole-genome resequencing and genetic analysis results showed that the loss of function in MEDIATOR16 (MED16), a mediator complex subunit, was responsible for the large flower phenotypes exhibited by ohb1. A phenotypic analysis of the mutant alleles in MED16 and the double mutants created by crossing ohb1 with representative large flower mutants revealed that MED16 and MED25 share part of the negative petal size regulatory pathways. Furthermore, the double mutant analyses suggested that there were genetically independent pathways leading to cell size restrictions in the floral organs which were not related to the MED complex. Several double mutants also formed larger and heavier seeds than the wild type and single mutant plants, which indicated that MED16 was involved in seed size regulation. This study has revealed part of the size-regulatory network in flowers and seeds through analysis of the ohb1 mutant, and that the size-regulation pathways are partially different between floral organs and seeds.

Genome-Wide Identification of ARF Transcription Factor Gene Family and Their Expression Analysis in Sweet Potato

Auxin response factors (ARFs) are a family of transcription factors that play an important role of auxin regulation through their binding with auxin response elements. ARF genes are represented by a large multigene family in plants; however, to our knowledge, the ARF gene family has not been well studied and characterized in sweet potatoes. In this study, a total of 25 ARF genes were identified in Ipomea trifida. The identified ItrARF genes’ conserved motifs, chromosomal locations, phylogenetic relationships, and their protein characteristics were systemically investigated using different bioinformatics tools. The expression patterns of ItfARF genes were analyzed within the storage roots and normal roots at an early stage of development. ItfARF16b and ItfARF16c were both highly expressed in the storage root, with minimal to no expression in the normal root. ItfARF6a and ItfARF10a exhibited higher expression in the normal root but not in the storage root. Subsequently, ItfARF1a, ItfARF2b, ItfARF3a, ItfARF6b, ItfARF8a, ItfARF8b, and ItfARF10b were expressed in both root types with moderate to high expression for each. All ten of these ARF genes and their prominent expression signify their importance within the development of each respective root type. This study provides comprehensive information regarding the ARF family in sweet potatoes, which will be useful for future research to discover further functional verification of these ItfARF genes.

Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor (ARF) Genes in Foxtail Millet (Setaria italica L.)

Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of ARF genes was seldom investigated in Setaria italica, an important crop and C₄ model plant. In the present study, genome-wide evolutionary analysis of ARFs was performed in S. italica. Twenty-four SiARF genes were identified and unevenly distributed on eight of the nine chromosomes in S. italica. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of SiARFs under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of SiARFs and benefit for further functional characterization.