Auxin biosynthesis and its role in plant development

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Genome of the most noxious weed water hyacinth (Eichhornia crassipes) provides insights into plant invasiveness and its translational potential

The invasive character of Eichhornia crassipes (water hyacinth) is a major threat to global biodiversity and ecosystems. To investigate the genomic basis of invasiveness, we performed the genome and transcriptome sequencing of E. crassipes and reported the genome of 1.11 Gbp size with 63,299 coding genes and N50 of 1.98 Mb. We confirmed a recent whole genome duplication event in E. crassipes that resulted in high intraspecific collinearity and significant expansion in gene families. Further, the orthologs gene clustering analysis and comparative evolutionary analysis with 14 other aquatic invasive and non-invasive angiosperm species revealed adaptive evolution in genes associated with plant-pathogen interaction, hormone signaling, abiotic stress tolerance, heavy metals sequestration, photosynthesis, and cell wall biosynthesis with highly expanded gene families, which contributes toward invasive characteristics of the water hyacinth. However, these characteristics also make water hyacinth an excellent candidate for biofuel production, phytoremediation, and other translational applications.

Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50

Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, Marinomonas sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other Marinomonas genomes. Our findings revealed the presence of homologs of the Pseudomonas iac gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the Marinomonas iac gene cluster when compared to that of the model iac-containing Pseudomonas putida 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of iac genes across several Marinomonas species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in Marinomonas, laying the groundwork for future investigations into the role of iac genes in Marinomonas physiology and the regulation of marine plant/algae-bacteria interactions.

Anchorene, a carotenoid-derived growth regulator, modulates auxin homeostasis by suppressing GH3-mediated auxin conjugation

Anchorene, identified as an endogenous bioactive carotenoid-derived dialdehyde and diapocarotenoid, affects root development by modulating auxin homeostasis. However, the precise interaction between anchorene and auxin, as well as the mechanisms by which anchorene modulates auxin levels, remain largely elusive. In this study, we conducted a comparative analysis of anchorene's bioactivities alongside auxin and observed that anchorene induces multifaceted auxin-like effects. Through genetic and pharmacological examinations, we revealed that anchorene's auxin-like activities depend on the indole-3-pyruvate-dependent auxin biosynthesis pathway, as well as the auxin inactivation pathway mediated by Group II Gretchen Hagen 3 (GH3) proteins that mainly facilitate the conjugation of indole-3-acetic acid (IAA) to amino acids, leading to the formation of inactivated storage forms. Our measurements indicated that anchorene treatment elevates IAA levels while reducing the quantities of inactivated IAA-amino acid conjugates and oxIAA. RNA sequencing further revealed that anchorene triggers the expression of numerous auxin-responsive genes in a manner reliant on Group II GH3s. Additionally, our in vitro enzymatic assays and biolayer interferometry (BLI) assay demonstrated anchorene's robust suppression of GH3.17-mediated IAA conjugation with glutamate. Collectively, our findings highlight the significant role of carotenoid-derived metabolite anchorene in modulating auxin homeostasis, primarily through the repression of GH3-mediated IAA conjugation and inactivation pathways, offering novel insights into the regulatory mechanisms of plant bioactive apocarotenoids.

The Mechanism of the Development and Maintenance of Sexual Dimorphism in the Dioecious Mulberry Plant (Morus alba)

Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex evolution by revealing the differentially expressed genes (DEGs) between two sexes and the testing signals of selection for these DEGs. From the results, we found a total of 1543 DEGs. Interestingly, 333 and 66 genes expression were detected only in male and female inflorescences, respectively. Using comparative transcriptomics, the expression of 841 genes were found to be significantly higher in male than in female inflorescences and were mainly enriched in defense-related pathways including the biosynthesis of phenylpropanoids, cutin, suberine and waxes. Meanwhile, the expression of 702 genes was female-biased and largely enriched in pathways related to growth and development, such as carbohydrate metabolism, auxin signaling and cellular responses. In addition, 16.7% and 17.6% signals of selection were significantly detected in female- and male-biased genes, respectively, suggesting their non-negligible role in evolution. Our findings expanded the understanding of the molecular basis of intersexual differentiation and contribute to further research on sex evolution in dioecious plants.

Auxin responsive factor MdARF17 promotes ethylene synthesis in apple fruits by activating MdERF003 expression

KEY MESSAGE

Auxin (AUX) promotion of apple fruit ripening is ethylene-dependent, and AUX-MdARF17-MdERF003 plays a role in AUX-promoted ethylene synthesis in apple. Phytohormones play important roles in plant growth and fleshy fruit ripening, and the phytohormone auxin (AUX) can either promote or inhibit the ripening of fleshy fruits. Although AUX can influence ethylene (ETH) synthesis in apple (Malus domestica) fruits by affecting ETH system II, this mechanism remains to be explored. Here, we identified an ETH response factor (ERF) family transcription factor, MdERF003, whose expression could be activated by naphthalene acetic acid. The transient silencing of MdERF003 inhibited ETH synthesis in fruits, and MdERF003 could bind to the MdACS1 promoter. To explore the upstream target genes of MdERF003, we screened the MdARF family members by yeast one-hybrid assays of the MdERF003 promoter, and found that the transcription factor MdARF17, which showed AUX-promoted expression, could bind to the MdERF003 promoter and promote its expression. Finally, we silenced MdERF003 in apple fruits overexpressing MdARF17 and found that MdERF003 plays a role in MdARF17-promoted ETH synthesis in apple. Thus, AUX-MdARF17-MdERF003 promotes ETH synthesis in apple fruits.

Genome-wide analysis of Citrus medica ABC transporters reveals the regulation of fruit development by CmABCB19 and CmABCC10

ATP-binding cassette (ABC) transporters are vital for plant growth and development as they facilitate the transport of essential molecules. Despite the family's significance, limited information exists about its functional distinctions in Citrus medica. Our study identified 119 genes encoding ABC transporter proteins in the C. medica genome. Through an evolutionary tree and qPCR analysis, two ABC genes, CmABCB19 and CmABCC10, were implicated in C. medica fruit development, showing upregulation in normal fruits compared to malformed fruits. CmABCB19 was found to localize to the plasma membrane of Nicotiana tabacum, exhibiting indole-3-acetic acid (IAA) efflux activity in the yeast mutant strain yap1. CmABCC10, a tonoplast-localized transporter, exhibited efflux of diosmin, nobiletin, and naringin, with rutin influx in strain ycf1. Transgenic expression of CmABCB19 and CmABCC10 in Arabidopsis thaliana induced alterations in auxin and flavonoid content, impacting silique and seed size. This effect was attributed to the modulation of structural genes in the auxin biosynthesis (YUC5/9, CYP79B2, CYP83B1, SUR1) and flavonoid biosynthesis (4CL2/3, CHS, CHI, FLS1/3) pathways. In summary, the functional characterization of CmABCB19 and CmABCC10 illuminates auxin and flavonoid transport, offering insights into their interplay with biosynthetic pathways and providing a foundation for understanding the transporter's role in fruit development.

Molecular Manipulation of the miR160/AUXIN RESPONSE FACTOR Expression Module Impacts Root Development in Arabidopsis thaliana

In Arabidopsis thaliana (Arabidopsis), microRNA160 (miR160) regulates the expression of AUXIN RESPONSE FACTOR10 (ARF10), ARF16 and ARF17 throughout development, including the development of the root system. We have previously shown that in addition to DOUBLE-STRANDED RNA BINDING1 (DRB1), DRB2 is also involved in controlling the rate of production of specific miRNA cohorts in the tissues where DRB2 is expressed in wild-type Arabidopsis plants. In this study, a miR160 overexpression transgene (MIR160B) and miR160-resistant transgene versions of ARF10 and ARF16 (mARF10 and mARF16) were introduced into wild-type Arabidopsis plants and the drb1 and drb2 single mutants to determine the degree of requirement of DRB2 to regulate the miR160 expression module as part of root development. Via this molecular modification approach, we show that in addition to DRB1, DRB2 is required to regulate the level of miR160 production from its precursor transcripts in Arabidopsis roots. Furthermore, we go on to correlate the altered abundance of miR160 or its ARF10, ARF16 and ARF17 target genes in the generated series of transformant lines with the enhanced development of the root system displayed by these plant lines. More specifically, promotion of primary root elongation likely stemmed from enhancement of miR160-directed ARF17 expression repression, while the promotion of lateral and adventitious root formation was the result of an elevated degree of miR160-directed regulation of ARF17 expression, and to a lesser degree, ARF10 and ARF16 expression. Taken together, the results presented in this study identify the requirement of the functional interplay between DRB1 and DRB2 to tightly control the rate of miR160 production, to in turn ensure the appropriate degree of miR160-directed ARF10, ARF16 and ARF17 gene expression regulation as part of normal root system development in Arabidopsis.

PagARGOS promotes low-lignin wood formation in poplar

Wood formation, which occurs mainly through secondary xylem development, is important not only for supplying raw material for the 'ligno-chemical' industry but also for driving the storage of carbon. However, the complex mechanisms underlying the promotion of xylem formation remain to be elucidated. Here, we found that overexpression of Auxin-Regulated Gene involved in Organ Size (ARGOS) in hybrid poplar 84 K (Populus alba × Populus tremula var. glandulosa) enlarged organ size. In particular, PagARGOS promoted secondary growth of stems with increased xylem formation. To gain further insight into how PagARGOS regulates xylem development, we further carried out yeast two-hybrid screening and identified that the auxin transporter WALLS ARE THIN1 (WAT1) interacts with PagARGOS. Overexpression of PagARGOS up-regulated WAT1, activating a downstream auxin response promoting cambial cell division and xylem differentiation for wood formation. Moreover, overexpressing PagARGOS caused not only higher wood yield but also lower lignin content compared with wild-type controls. PagARGOS is therefore a potential candidate gene for engineering fast-growing and low-lignin trees with improved biomass production.

IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato (Solanum tuberosum L.)

Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L-1. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato.

The hormone regulatory mechanism underlying parthenocarpic fruit formation in tomato

Parthenocarpic fruits, known for their superior taste and reliable yields in adverse conditions, develop without the need for fertilization or pollination. Exploring the physiological and molecular mechanisms behind parthenocarpic fruit development holds both theoretical and practical significance, making it a crucial area of study. This review examines how plant hormones and MADS-box transcription factors control parthenocarpic fruit formation. It delves into various aspects of plant hormones-including auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid-ranging from external application to biosynthesis, metabolism, signaling pathways, and their interplay in influencing parthenocarpic fruit development. The review also explores the involvement of MADS family gene functions in these processes. Lastly, we highlight existing knowledge gaps and propose directions for future research on parthenocarpy.

Biosynthesis and signal transduction of plant growth regulators and their effects on bioactive compound production in Salvia miltiorrhiza (Danshen)

Plant growth regulators (PGRs) are involved in multiple aspects of plant life, including plant growth, development, and response to environmental stimuli. They are also vital for the formation of secondary metabolites in various plants. Salvia miltiorrhiza is a famous herbal medicine and has been used commonly for > 2000 years in China, as well as widely used in many other countries. S. miltiorrhiza is extensively used to treat cardiovascular and cerebrovascular diseases in clinical practices and has specific merit against various diseases. Owing to its outstanding medicinal and commercial potential, S. miltiorrhiza has been extensively investigated as an ideal model system for medicinal plant biology. Tanshinones and phenolic acids are primary pharmacological constituents of S. miltiorrhiza. As the growing market for S. miltiorrhiza, the enhancement of its bioactive compounds has become a research hotspot. S. miltiorrhiza exhibits a significant response to various PGRs in the production of phenolic acids and tanshinones. Here, we briefly review the biosynthesis and signal transduction of PGRs in plants. The effects and mechanisms of PGRs on bioactive compound production in S. miltiorrhiza are systematically summarized and future research is discussed. This article provides a scientific basis for further research, cultivation, and metabolic engineering in S. miltiorrhiza.

Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration

Elucidating gene regulatory networks is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. Here, we integrated 46 co-expression networks, 283 protein-DNA interaction (PDI) assays, and 16 million SNPs used to identify expression quantitative trait loci (eQTL) to construct TF-target networks. In total, we analyzed ∼4.6M interactions to generate four distinct types of TF-target networks: co-expression, PDI, trans -eQTL, and cis -eQTL combined with PDIs. To functionally annotate TFs based on their target genes, we implemented three different network integration strategies. We evaluated the effectiveness of each strategy through TF loss-of function mutant inspection and random network analyses. The multi-network integration allowed us to identify transcriptional regulators of several biological processes. Using the topological properties of the fully integrated network, we identified potential functionally redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.

GRAPHICAL ABSTRACT

Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways

Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.

Plant Hormone Pathway Is Involved in Regulating the Embryo Development Mechanism of the Hydrangea macrophylla Hybrid

The research is aimed to elucidate the role of plant hormones in regulating the development of hybrid embryos in Hydrangea macrophylla. Fruits from the intraspecific cross of H. macrophylla 'Otaksa' × 'Coerulea' were selected at the globular, heart, and torpedo stages of embryo development. Transcriptome sequencing and differential gene expression analysis were conducted. The results showed that fruit growth followed a single "S-shaped growth curve, with globular, heart, and torpedo embryos appearing at 30, 40, and 50 d post-pollination, respectively, and the embryo maintaining the torpedo shape from 60 to 90 d. A total of 12,933 genes was quantified across the three developmental stages, with 3359, 3803, and 3106 DEGs in the S1_vs_S2, S1_vs_S3, and S2_vs_S3 comparisons, respectively. Among these, 133 genes related to plant hormone biosynthesis and metabolism were differentially expressed, regulating the synthesis and metabolism of eight types of plant hormones, including cytokinin, auxin, gibberellin, abscisic acid, and jasmonic acid. The pathways with the most differentially expressed genes were cytokinin, auxin, and gibberellin, suggesting these hormones may play crucial roles in embryo development. In the cytokinin pathway, CKX (Hma1.2p1_0579F.1_g182670.gene, Hma1.2p1_1194F.1_g265700.gene, and NewGene_12164) genes were highly expressed during the globular embryo stage, promoting rapid cell division in the embryo. In the auxin pathway, YUC (Hma1.2p1_0271F.1_g109005.gene and Hma1.2p1_0271F.1_g109020.gene) genes were progressively up-regulated during embryo growth; the early response factor AUX/IAA (Hma1.2p1_0760F.1_g214260.gene) was down-regulated, while the later transcriptional activator ARF (NewGene_21460, NewGene_21461, and Hma1.2p1_0209F.1_g089090.gene) was up-regulated, sustaining auxin synthesis and possibly preventing the embryo from transitioning to maturity. In the gibberellin pathway, GA3ox (Hma1.2p1_0129F.1_g060100.gene) expression peaked during the heart embryo stage and then declined, while the negative regulator GA2ox (Hma1.2p1_0020F.1_g013915.gene) showed the opposite trend; and the gibberellin signaling repressor DELLA (Hma1.2p1_1054F.1_g252590.gene) increased over time, potentially inhibiting embryo development and maintaining the torpedo shape until fruit maturity. These findings preliminarily uncover the factors affecting the development of hybrid H. macrophylla embryos, laying a foundation for further research into the regulatory mechanisms of H. macrophylla hybrid embryo development.

A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root

The interaction between auxin and cytokinin is important in many aspects of plant development. Experimental measurements of both auxin and cytokinin concentration and reporter gene expression clearly show the coexistence of auxin and cytokinin concentration patterning in Arabidopsis root development. However, in the context of crosstalk among auxin, cytokinin, and ethylene, little is known about how auxin and cytokinin concentration patterns simultaneously emerge and how they regulate each other in the Arabidopsis root. This work utilizes a wide range of experimental observations to propose a mechanism for simultaneous patterning of auxin and cytokinin concentrations. In addition to revealing the regulatory relationships between auxin and cytokinin, this mechanism shows that ethylene signaling is an important factor in achieving simultaneous auxin and cytokinin patterning, while also predicting other experimental observations. Combining the mechanism with a realistic in silico root model reproduces experimental observations of both auxin and cytokinin patterning. Predictions made by the mechanism can be compared with a variety of experimental observations, including those obtained by our group and other independent experiments reported by other groups. Examples of these predictions include patterning of auxin biosynthesis rate, changes in PIN1 and PIN2 patterns in pin3,4,7 mutants, changes in cytokinin patterning in the pls mutant, PLS patterning, and various trends in different mutants. This research reveals a plausible mechanism for simultaneous patterning of auxin and cytokinin concentrations in Arabidopsis root development and suggests a key role for ethylene pattern integration.

Space, the final frontier: The spatial component of phytoplankton-bacterial interactions

Microscale interactions between marine phytoplankton and bacteria shape the microenvironment of individual cells, impacting their physiology and ultimately influencing global-scale biogeochemical processes like carbon and nutrient cycling. In dilute environments such as the ocean water column, metabolic exchange between microorganisms likely requires close proximity between partners. However, the biological strategies to achieve this physical proximity remain an understudied aspect of phytoplankton-bacterial associations. Understanding the mechanisms by which these microorganisms establish and sustain spatial relationships and the extent to which spatial proximity is necessary for interactions to occur, is critical to learning how spatial associations influence the ecology of phytoplankton and bacterial communities. Here, we provide an overview of current knowledge on the role of space in shaping interactions among ocean microorganisms, encompassing behavioural and metabolic evidence. We propose that characterising phytoplankton-bacterial interactions from a spatial perspective can contribute to a mechanistic understanding of the establishment and maintenance of these associations and, consequently, an enhanced ability to predict the impact of microscale processes on ecosystem-wide phenomena.

Optimisation of indole acetic acid production by Neopestalotiopsis aotearoa endophyte isolated from Thymus vulgaris and its impact on seed germination of Ocimum basilicum

BACKGROUND

Microbial growth during plant tissue culture is a common problem that causes significant losses in the plant micro-propagation system. Most of these endophytic microbes have the ability to propagate through horizontal and vertical transmission. On the one hand, these microbes provide a rich source of several beneficial metabolites.

RESULTS

The present study reports on the isolation of fungal species from different in vitro medicinal plants (i.e., Breynia disticha major, Breynia disticha, Duranta plumieri, Thymus vulgaris, Salvia officinalis, Rosmarinus officinalis, and Ocimum basilicum l) cultures. These species were tested for their indole acetic acid (IAA) production capability. The most effective species for IAA production was that isolated from Thymus vulgaris plant (11.16 µg/mL) followed by that isolated from sweet basil plant (8.78 µg/mL). On screening for maximum IAA productivity, medium, "MOS + tryptophan" was chosen that gave 18.02 μg/mL. The macroscopic, microscopic examination and the 18S rRNA sequence analysis indicated that the isolate that given code T4 was identified as Neopestalotiopsis aotearoa (T4). The production of IAA by N. aotearoa was statistically modeled using the Box-Behnken design and optimized for maximum level, reaching 63.13 µg/mL. Also, IAA extract was administered to sweet basil seeds in vitro to determine its effect on plant growth traits. All concentrations of IAA extract boosted germination parameters as compared to controls, and 100 ppm of IAA extract exhibited a significant growth promotion effect for all seed germination measurements.

CONCLUSIONS

The IAA produced from N. aotearoa (T4) demonstrated an essential role in the enhancement of sweet basil (Ocimum basilicum) growth, suggesting that it can be employed to promote the plant development while lowering the deleterious effect of using synthetic compounds in the environment.

PbARF19-mediated auxin signaling regulates lignification in pear fruit stone cells

The stone cells in pear fruits cause rough flesh and low juice, seriously affecting the taste. Lignin has been demonstrated as the main component of stone cells. Auxin, one of the most important plant hormone, regulates most physiological processes in plants including lignification. However, the concentration effect and regulators of auxin on pear fruits stone cell formation remains unclear. Here, endogenous indole-3-acetic acid (IAA) and stone cells were found to be co-localized in lignified cells by immunofluorescence localization analysis. The exogenous treatment of different concentrations of IAA demonstrated that the application of 200 µM IAA significantly reduced stone cell content, while concentrations greater than 500 µM significantly increased stone cell content. Besides, 31 auxin response factors (ARFs) were identified in pear genome. Putative ARFs were predicted as critical regulators involved in the lignification of pear flesh cells by phylogenetic relationship and expression analysis. Furthermore, the negative regulation of PbARF19 on stone cell formation in pear fruit was demonstrated by overexpression in pear fruitlets and Arabidopsis. These results illustrated that the PbARF19-mediated auxin signal plays a critical role in the lignification of pear stone cell by regulating lignin biosynthetic genes. This study provides theoretical and practical guidance for improving fruit quality in pear production.

The development of yellow lupin anthers depends on the relationship between jasmonic acid and indole-3-acetic acid

The main purpose of this study was to demonstrate that the course of anther development, including post-meiotic maturation, dehiscence and senescence, is ensured by the interdependencies between jasmonic acid (JA) and indole-3-acetic acid (IAA) in yellow lupin (Lupinus luteus L.). The concentration of JA peaked during anther dehiscence when IAA level was low, whereas the inverse relationship was specific to anther senescence. Cellular and tissue localization of JA and IAA, in conjunction with broad expression profile for genes involved in biosynthesis, signalling, response, and homeostasis under different conditions, allowed to complete and define the role of studied phytohormones during late anther development, as well as predict events triggered by them. The development/degeneration of septum and anther wall cells, dehydration of epidermis, and rupture of stomium may involve JA signalling, while the formation of secondary thickening in endothecial cell walls is rather JA independent. The IAA is involved in programmed cell death (PCD)-associated processes during anther senescence but does not exclude its participation in the anther dehiscence processes, mainly related to cell disintegration and degeneration. A detailed understanding of these multistage processes, especially at the level of phytohormonal interplay, can contribute to the effective control of male fertility, potentially revolutionizing the breeding of L. luteus.

PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons

Directional auxin transport and formation of auxin maxima are critical for embryogenesis, organogenesis, pattern formation, and growth coordination in plants, but the mechanisms underpinning the initiation and establishment of these auxin dynamics are not fully understood. Here we show that a self-initiating and -terminating transient auxin flow along the marginal cells (MCs) contributes to the formation of an auxin maximum at the tip of Arabidopsis cotyledon that globally coordinates the interdigitation of puzzle-shaped pavement cells in the cotyledon epidermis. Prior to the interdigitation, indole butyric acid (IBA) is converted to indole acetic acid (IAA) to induce PIN2 accumulation and polarization in the marginal cells, leading to auxin flow toward and accumulation at the cotyledon tip. When IAA levels at the cotyledon tip reaches a maximum, it activates pavement cell interdigitation as well as the accumulation of the IBA transporter TOB1 in MCs, which sequesters IBA to the vacuole and reduces IBA availability and IAA levels. The reduction of IAA levels results in PIN2 down-regulation and cessation of the auxin flow. Hence, our results elucidate a self-activating and self-terminating transient polar auxin transport system in cotyledons, contributing to the formation of localized auxin maxima that spatiotemporally coordinate pavement cell interdigitation.

Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching

The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.

Bioprospecting endophytic fungi for bioactive metabolites with seed germination promoting potentials

There is an urgent need for new bioactive molecules with unique mechanisms of action and chemistry to address the issue of incorrect use of chemical fertilizers and pesticides, which hurts both the environment and the health of humans. In light of this, research was done for this work to isolate, identify, and evaluate the germination-promoting potential of various plant species' fungal endophytes. Zea mays L. (maize) seed germination was examined using spore suspension of 75 different endophytic strains that were identified. Three promising strains were identified through screening to possess the ability mentioned above. These strains Alternaria alternate, Aspergilus flavus, and Aspergillus terreus were isolated from the stem of Tecoma stans, Delonix regia, and Ricinus communis, respectively. The ability of the three endophytic fungal strains to produce siderophore and indole acetic acid (IAA) was also examined. Compared to both Aspergillus flavus as well as Aspergillus terreus, Alternaria alternata recorded the greatest rates of IAA, according to the data that was gathered. On CAS agar versus blue media, all three strains failed to produce siderophores. Moreover, the antioxidant and antifungal potentials of extracts from these fungi were tested against different plant pathogens. The obtained results indicated the antioxidant and antifungal activities of the three fungal strains. GC-Mass studies were carried out to determine the principal components in extracts of all three strains of fungi. The three strains' fungus extracts included both well-known and previously unidentified bioactive compounds. These results may aid in the development of novel plant growth promoters by suggesting three different fungal strains as sources of compounds that may improve seed germination. According to the study that has been given, as unexplored sources of bioactive compounds, fungal endophytes have great potential.

Molecular and genetic regulation of petal number variation

Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.

Phytochrome-interacting factors play shared and distinct roles in regulating shade avoidance responses in Populus trees

Plants adjust their growth and development in response to changing light caused by canopy shade. The molecular mechanisms underlying shade avoidance responses have been widely studied in Arabidopsis and annual crop species, yet the shade avoidance signalling in woody perennial trees remains poorly understood. Here, we first showed that PtophyB1/2 photoreceptors serve conserved roles in attenuating the shade avoidance syndrome (SAS) in poplars. Next, we conducted a systematic identification and characterization of eight PtoPIF genes in Populus tomentosa. Knocking out different PtoPIFs led to attenuated shade responses to varying extents, whereas overexpression of PtoPIFs, particularly PtoPIF3.1 and PtoPIF3.2, led to constitutive SAS phenotypes under normal light and enhanced SAS responses under simulated shade. Notably, our results revealed that distinct from Arabidopsis PIF4 and PIF5, which are major regulators of SAS, the Populus homologues PtoPIF4.1 and PtoPIF4.2 seem to play a minor role in controlling shade responses. Moreover, we showed that PtoPIF3.1/3.2 could directly activate the expression of the auxin biosynthetic gene PtoYUC8 in response to shade, suggesting a conserved PIF-YUC-auxin pathway in modulating SAS in tree. Overall, our study provides insights into shared and divergent functions of PtoPIF members in regulating various aspects of the SAS in Populus.

Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation

The root system plays an essential role in plant growth and adaptation to the surrounding environment. The root clock periodically specifies lateral root prebranch sites (PBS), where a group of pericycle founder cells (FC) is primed to become lateral root founder cells and eventually give rise to lateral root primordia or lateral roots (LRs). This clock-driven organ formation process is tightly controlled by modulation of auxin content and signaling. Auxin perception entails the physical interaction of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or AUXIN SIGNALING F-BOX (AFBs) proteins with AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to form a co-receptor system. Despite the apparent simplicity, the understanding of how specific auxin co-receptors are assembled remains unclear. We identified the compound bis-methyl auxin conjugated with N-glucoside, or BiAux, in Arabidopsis (Arabidopsis thaliana) that specifically induces the formation of PBS and the emergence of LR, with a slight effect on root elongation. Docking analyses indicated that BiAux binds to F-box proteins, and we showed that BiAux function depends on TIR1 and AFB2 F-box proteins and AUXIN RESPONSE FACTOR 7 activity, which is involved in FC specification and LR formation. Finally, using a yeast (Saccharomyces cerevisiae) heterologous expression system, we showed that BiAux favors the assemblage of specific co-receptors subunits involved in LR formation and enhances AUXIN/INDOLE-3-ACETIC ACID 28 protein degradation. These results indicate that BiAux acts as an allosteric modulator of specific auxin co-receptors. Therefore, BiAux exerts a fine-tune regulation of auxin signaling aimed to the specific formation of LR among the many development processes regulated by auxin.

ENHANCER OF SHOOT REGENERATION1 promotes de novo root organogenesis after wounding in Arabidopsis leaf explants

Plants have an astonishing ability to regenerate new organs after wounding. Here, we report that the wound-inducible transcription factor ENHANCER OF SHOOT REGENERATION1 (ESR1) has a dual mode of action in activating ANTHRANILATE SYNTHASE ALPHA SUBUNIT1 (ASA1) expression to ensure auxin-dependent de novo root organogenesis locally at wound sites of Arabidopsis (Arabidopsis thaliana) leaf explants. In the first mode, ESR1 interacts with HISTONE DEACETYLASE6 (HDA6), and the ESR1-HDA6 complex directly binds to the JASMONATE-ZIM DOMAIN5 (JAZ5) locus, inhibiting JAZ5 expression through histone H3 deacetylation. As JAZ5 interferes with the action of ETHYLENE RESPONSE FACTOR109 (ERF109), the transcriptional repression of JAZ5 at the wound site allows ERF109 to activate ASA1 expression. In the second mode, the ESR1 transcriptional activator directly binds to the ASA1 promoter to enhance its expression. Overall, our findings indicate that the dual biochemical function of ESR1, which specifically occurs near wound sites of leaf explants, maximizes local auxin biosynthesis and de novo root organogenesis in Arabidopsis.

Maternal nitric oxide homeostasis impacts female gametophyte development under optimal and stress conditions

In adverse environments, the number of fertilizable female gametophytes (FGs) in plants is reduced, leading to increased survival of the remaining offspring. How the maternal plant perceives internal growth cues and external stress conditions to alter FG development remains largely unknown. We report that homeostasis of the stress signaling molecule nitric oxide (NO) plays a key role in controlling FG development under both optimal and stress conditions. NO homeostasis is precisely regulated by S-nitrosoglutathione reductase (GSNOR). Prior to fertilization, GSNOR protein is exclusively accumulated in sporophytic tissues and indirectly controls FG development in Arabidopsis (Arabidopsis thaliana). In GSNOR null mutants, NO species accumulated in the degenerating sporophytic nucellus, and auxin efflux into the developing FG was restricted, which inhibited FG development, resulting in reduced fertility. Importantly, restoring GSNOR expression in maternal, but not gametophytic tissues, or increasing auxin efflux substrate significantly increased the proportion of normal FGs and fertility. Furthermore, GSNOR overexpression or added auxin efflux substrate increased fertility under drought and salt stress. These data indicate that NO homeostasis is critical to normal auxin transport and maternal control of FG development, which in turn determine seed yield. Understanding this aspect of fertility control could contribute to mediating yield loss under adverse conditions.

The additive function of YIGE2 and YIGE1 in regulating maize ear length

Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement.

Plant-Entomopathogenic Fungi Interaction: Recent Progress and Future Prospects on Endophytism-Mediated Growth Promotion and Biocontrol

Entomopathogenic fungi, often acknowledged primarily for their insecticidal properties, fulfill diverse roles within ecosystems. These roles encompass endophytism, antagonism against plant diseases, promotion of the growth of plants, and inhabitation of the rhizosphere, occurring both naturally and upon artificial inoculation, as substantiated by a growing body of contemporary research. Numerous studies have highlighted the beneficial aspects of endophytic colonization. This review aims to systematically organize information concerning the direct (nutrient acquisition and production of phytohormones) and indirect (resistance induction, antibiotic and secondary metabolite production, siderophore production, and mitigation of abiotic and biotic stresses) implications of endophytic colonization. Furthermore, a thorough discussion of these mechanisms is provided. Several challenges, including isolation complexities, classification of novel strains, and the impact of terrestrial location, vegetation type, and anthropogenic reluctance to use fungal entomopathogens, have been recognized as hurdles. However, recent advancements in biotechnology within microbial research hold promising solutions to many of these challenges. Ultimately, the current constraints delineate potential future avenues for leveraging endophytic fungal entomopathogens as dual microbial control agents.

Exogenous indole-3-acetic acid promotes the plant growth and accumulation of selenium in grapevine under selenium stress

To alleviate the selenium (Se) stress in fruit trees and improve its accumulation, the effects of exogenous indole-3-acetic acid (IAA) on the growth and Se accumulation of grapevine under Se stress were studied. The application of exogenous IAA increased the biomass of grapevine, and the concentration of exogenous IAA had a regression relationship with the biomass. The root and shoot biomass were the maximum at 60 mg L- 1 IAA, increasing by 15.61% and 23.95%, respectively, compared with the control. Exogenous IAA also increased the photosynthetic pigments and the activities of superoxide dismutase and peroxidase in grapevine. Moreover, exogenous IAA increased the contents of total Se, organic Se, and inorganic Se, and the concentration of exogenous IAA had a regression relationship with the total Se content. The highest contents of root total Se and shoot total Se were accumulated at 90 mg L- 1 IAA, increasing by 29.94% and 55.77% respectively,. In addition, the correlation and path analyses revealed that the carotenoid content and root total Se content were closely associated with the shoot total Se content. Therefore, the application of exogenous IAA can alleviate the stress of Se to grape and promote its uptake and the most effective amount for the uptake of Se is 90 mg L- 1 IAA.

IAA-producing plant growth promoting rhizobacteria from Ceanothus velutinus enhance cutting propagation efficiency and Arabidopsis biomass

Climate-induced drought impacts plant growth and development. Recurring droughts increase the demand for water for food production and landscaping. Native plants in the Intermountain West region of the US are of keen interest in low water use landscaping as they are acclimatized to dry and cold environments. These native plants do very well at their native locations but are difficult to propagate in landscape. One of the possible reasons is the lack of associated microbiome in the landscaping. Microbiome in the soil contributes to soil health and impacts plant growth and development. Here, we used the bulk soil from the native plant Ceanothus velutinus (snowbrush ceanothus) as inoculant to enhance its propagation. Snowbrush ceanothus is an ornamental plant for low-water landscaping that is hard to propagate asexually. Using 50% native bulk soil as inoculant in the potting mix significantly improved the survival rate of the cuttings compared to no-treated cuttings. Twenty-four plant growth-promoting rhizobacteria (PGPR) producing indole acetic acid (IAA) were isolated from the rhizosphere and roots of the survived snowbrush. Seventeen isolates had more than 10µg/mL of IAA were shortlisted and tested for seven different plant growth-promoting (PGP) traits; 76% showed nitrogen-fixing ability on Norris Glucose Nitrogen free media,70% showed phosphate solubilization activity, 76% showed siderophore production, 36% showed protease activity, 94% showed ACC deaminase activity on DF-ACC media, 76% produced catalase and all of isolates produced ammonia. Eight of seventeen isolates, CK-6, CK-22, CK-41, CK-44, CK-47, CK-50, CK-53, and CK-55, showed an increase in shoot biomass in Arabidopsis thaliana. Seven out of eight isolates were identified as Pseudomonas, except CK-55, identified as Sphingobium based on 16S rRNA gene sequencing. The shortlisted isolates are being tested on different grain and vegetable crops to mitigate drought stress and promote plant growth.

Transcriptome and Metabolome Reveal Key Genes from the Plant Hormone Signal Transduction Pathway Regulating Plant Height and Leaf Size in Capsicum baccatum

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.

Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns

In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.

Phenylboronic Acid-Functionalized Micelles Dual-Targeting Boronic Acid Transporter and Polysaccharides for siRNA Delivery into Brown Algae

Brown algae play essential roles ecologically, practically, and evolutionarily because they maintain coastal areas, capture carbon dioxide, and produce valuable chemicals such as therapeutic drugs. To unlock their full potential, understanding the unique molecular biology of brown algae is imperative. Genetic engineering tools that regulate homeostasis in brown algae are essential for determining their biological mechanisms in detail. However, few methodologies have been developed to control gene expression due to the robust structural barriers of brown algae. To address this issue, we designed peptide-based, small interfering RNA (siRNA)-loaded micelles decorated with phenylboronic acid (PBA) ligands. The PBA ligands facilitated the cellular uptake of the micelles into a model brown alga, Ectocarpus siliculosus (E. Siliculosus), through chemical interaction with polysaccharides in the cell wall and biological recognition by boronic acid transporters on the plasma membrane. The micelles, featuring "kill two birds with one stone" ligands, effectively induced gene silencing related to auxin biosynthesis. As a result, the growth of E. siliculosus was temporarily inhibited without persistent genome editing. This study demonstrated the potential for exploring the characteristics of brown algae through a simple yet effective approach and presented a feasible system for delivering siRNA in brown algae.

Fine mapping of TFL, a major gene regulating fruit length in snake gourd (Trichosanthes anguina L)

Fruit length is a crucial agronomic trait of snake gourd (Trichosanthes anguina L); however, genes associated with fruit length have not been characterised. In this study, F2 snake gourd populations were generated by crossing the inbred lines, S1 and S2 (fruit lengths: 110 and 20 cm, respectively). Subsequently, bulk segregant analysis, sequencing, and fine-mapping were performed on the F2 population to identify target genes. Our findings suggest that the fruit length of snake gourd is regulated by a major-effect regulatory gene. Mining of genes regulating fruit length in snake gourd to provide a basis for subsequent selection and breeding of new varieties. Genotype-phenotype association analysis was performed on the segregating F2 population comprising 6,000 plants; the results indicate that the target gene is located on Chr4 (61,846,126-61,865,087 bp, 18.9-kb interval), which only carries the annotated candidate gene, Tan0010544 (designated TFL). TFL belongs to the MADS-box family, one of the largest transcription factor families. Sequence analysis revealed a non-synonymous mutation of base C to G at position 202 in the coding sequence of TFL, resulting in the substitution of amino acid Gln to Glu at position 68 in the protein sequence. Subsequently, an InDel marker was developed to aid the marker-assisted selection of TFL. The TFL in the expression parents within the same period was analysed using quantitative real-time PCR; the TFL expression was significantly higher in short fruits than long fruits. Therefore, TFL can be a candidate gene for determining the fruit length in snake gourd. Collectively, these findings improve our understanding of the genetic components associated with fruit length in snake gourds, which could aid the development of enhanced breeding strategies for plant species.

Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response

Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.

MtTCP18 Regulates Plant Structure in Medicago truncatula

Plant structure has a large influence on crop yield formation, with branching and plant height being the important factors that make it up. We identified a gene, MtTCP18, encoding a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor highly conserved with Arabidopsis gene BRC1 (BRANCHED1) in Medicago truncatula. Sequence analysis revealed that MtTCP18 included a conserved basic helix-loop-helix (BHLH) motif and R domain. Expression analysis showed that MtTCP18 was expressed in all organs examined, with relatively higher expression in pods and axillary buds. Subcellular localization analysis showed that MtTCP18 was localized in the nucleus and exhibited transcriptional activation activity. These results supported its role as a transcription factor. Meanwhile, we identified a homozygous mutant line (NF14875) with a mutation caused by Tnt1 insertion into MtTCP18. Mutant analysis showed that the mutation of MtTCP18 altered plant structure, with increased plant height and branch number. Moreover, we found that the expression of auxin early response genes was modulated in the mutant. Therefore, MtTCP18 may be a promising candidate gene for breeders to optimize plant structure for crop improvement.

Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience

Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.

Histone dynamics responding to internal and external cues underlying plant development

Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.

Development of a stable genetic transformation system in Erigeron breviscapus: a case study with EbYUC2 in relation to leaf number and flowering time

MAIN CONCLUSION

A stable genetic transformation system for Erigeron breviscapus was developed. We cloned the EbYUC2 gene and genetically transformed it into Arabidopsis thaliana and E. breviscapus. The leaf number, YUC2 gene expression, and the endogenous auxin content in transgenic plants were significantly increased. Erigeron breviscapus is a prescription drug for the clinical treatment of cardiovascular and cerebrovascular diseases. The rosette leaves have the highest content of the major active compound scutellarin and are an important component in the yield of E. breviscapus. However, little is known about the genes related to the leaf number and flowering time of E. breviscapus. In our previous study, we identified three candidate genes related to the leaf number and flowering of E. breviscapus by combining resequencing data and genome-wide association study (GWAS). However, their specific functions remain to be characterized. In this study, we cloned and transformed the previously identified full-length EbYUC2 gene into Arabidopsis thaliana, developed the first stable genetic transformation system for E. breviscapus, and obtained the transgenic plants overexpressing EbYUC2. Compared with wild-type plants, the transgenic plants showed a significant increase in the number of leaves, which was correlated with the increased expression of EbYUC2. Consistently, the endogenous auxin content, particularly indole-3-acetic acid, in transgenic plants was also significantly increased. These results suggest that EbYUC2 may control the leaf number by regulating auxin biosynthesis, thereby laying a foundation for revealing the molecular mechanism governing the leaf number and flowering time of E. breviscapus.

Effect of arbuscular mycorrhizal symbiosis on growth and biochemical characteristics of Chinese fir (Cunninghamia lanceolata) seedlings under low phosphorus environment

Background

The continuous establishment of Chinese fir (Cunninghamia lanceolata) plantations across multiple generations has led to the limited impact of soil phosphorus (P) on tree growth. This challenge poses a significant obstacle in maintaining the sustainable management of Chinese fir.

Methods

To investigate the effects of Arbuscular mycorrhizal fungi (AMF) on the growth and physiological characteristics of Chinese fir under different P supply treatments. We conducted an indoor pot simulation experiment in the greenhouse of the Forestry College of Fujian Agriculture and Forestry University with one-and-half-year-old seedlings of Chinese fir from March 2019 to June 2019, with the two P level treatment groups included a normal P supply treatment (1.0 mmol L-1 KH2PO4, P1) and a no P supply treatment (0 mmol L-1 KH2PO4, P0). P0 and P1 were inoculated with Funneliformis mosseae (F.m) or Rhizophagus intraradices (R.i) or not inoculated with AMF treatment. The AMF colonization rate in the root system, seedling height (SH), root collar diameter (RCD) growth, chlorophyll (Chl) photosynthetic characteristics, enzyme activities, and endogenous hormone contents of Chinese fir were estimated.

Results

The results showed that the colonization rate of F.m in the roots of Chinese fir seedlings was the highest at P0, up to 85.14%, which was 1.66 times that of P1. Under P0 and P1 treatment, root inoculation with either F.m or R.i promoted SH growth, the SH of R.i treatment was 1.38 times and 1.05 times that of F.m treatment, respectively. In the P1 treatment, root inoculation with either F.m or R.i inhibited RCD growth. R.i inhibited RCD growth more aggressively than F.m. In the P0 treatment, root inoculation with F.m and R.i reduced the inhibitory effect of phosphorus deficiency on RCD. At this time, there was no significant difference in RCD between F.m, R.i and CK treatments (p < 0.05). AMF inoculation increased Fm, Fv, Fv/Fm, and Fv/Fo during the chlorophyll fluorescence response in the tested Chinese fir seedlings. Under the two phosphorus supply levels, the trend of Fv and Fm of Chinese fir seedlings in different treatment groups was F.m > R.i > CK. Under P0 treatment, The values of Fv were 235.86, 221.86 and 147.71, respectively. The values of Fm were 287.57, 275.71 and 201.57, respectively. It increased the antioxidant enzyme activity and reduced the leaf's malondialdehyde (MDA) content to a certain extent.

Conclusion

It is concluded that AMF can enhance the photosynthetic capacity of the host, regulate the distribution of endogenous hormones in plants, and promote plant growth by increasing the activity of antioxidant enzymes. When the P supply is insufficient, AMF is more helpful to plants, and R.i is more effective than F.m in alleviating P starvation stress in Chinese fir.

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Integrative analysis of the transcriptome and metabolome reveals Bacillus atrophaeus WZYH01-mediated salt stress mechanism in maize (Zea mays L.)

Maize is an important food crop that is affected by salt stress during growth, which can hinder plant growth and result in a significant decrease in yield. The application of plant growth-promoting rhizobacteria can improve this situation to a certain extent. However, the gene network of rhizosphere-promoting bacteria regulating the response of maize to salt stress remains elusive. Here, we used metabolomics and transcriptomics techniques to elucidate potential gene networks and salt-response pathways in maize. Phenotypic analysis showed that the Bacillus atrophaeus treatment improved the plant height, leaf area, biomass, ion, nutrient and stomatal indicators of maize. Metabolomic analysis identified that differentially expressed metabolites (DEMs) were primarily concentrated in the arginine, proline and phytohormone signaling metabolic pathways. 4-Hydroxyphenylacetylglutamic acid, L-histidinol, oxoglutaric acid, L-glutamic acid, L-arginine, and L-tyrosine were significantly increased in the Bacillus atrophaeus treatment. Weighted gene coexpression network analysis (WGCNA) identified several hub genes associated with salt response: Zm00001eb155540 and Zm00001eb088790 (ABC transporter family), Zm00001eb419060 (extra-large GTP-binding protein family), Zm00001eb317200 (calcium-transporting ATPase), Zm00001eb384800 (aquaporin NIP1-4) and Zm00001eb339170 (cytochrome P450). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that genes related to plant hormone signal transduction and the MAPK signaling pathway were involved in the response to the effect of Bacillus atrophaeus under salt stress. In the plant hormone signal transduction pathway, 3 differentially expressed genes (DEGs) encoding EIN3/EILs protein, 3 DEGs encoding GH3, 1 DEG encoding PYR/PYL and 6 DEGs encoding PP2C were all upregulated in Bacillus atrophaeus treatment. In the MAPK signaling pathway, 2 DEGs encoding CAT1 and 2 DEGs encoding WRKY22/WRKY29 were significantly upregulated, and the expression of DEGs encoding RbohD was downregulated by the application of Bacillus atrophaeus. In conclusion, the application of Bacillus atrophaeus under salt stress regulated key physiological and molecular processes in plants, which could stimulate the expression of genes related to ion transport and nutrients in maize, alleviate salt stress and promote maize growth to some extent, deepening our understanding of the application of Bacillus atrophaeus under salt stress to improve the salt-response gene network of maize growth.

The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice

Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.

Unraveling the Role of AtSRT2 in Energy Metabolism, Stress Responses, and Gene Expression during Osmotic Stress in Arabidopsis thaliana

Sirtuins participate in chromatin remodeling and gene expression regulation during stress responses. They are the only deacetylases that couple the cellular NAD+-dependent energy metabolism with transcriptional regulation. They catalyze the production of nicotinamide, inhibiting sirtuin 2 (SIR2) activity in vivo. The SIR2 homolog, AtSRT2, deacetylates non-histone proteins associated with mitochondrial energy metabolism. To date, AtSRT2 mechanisms during stress responses in Arabidopsis thaliana remain unclear. The transduction of mitochondrial metabolic signals links the energy status to transcriptional regulation, growth, and stress responses. These signals induce changes by regulating nuclear gene expression. The present study aimed to determine the role of SRT2 and its product nicotinamide in the development of A. thaliana and the expression of osmotic stress-response genes. Leaf development was greater in srt2+ plants than in the wild type, indicating that SET2 plays a role in energy metabolism. Treatment with polyethylene glycol activated and inhibited gene expression in srt2- and srt2+ lines, respectively. Therefore, we concluded that SRT2-stimulated plant growth and repressed signaling are associated with osmotic stress.

Regulation of tissue growth in plants - A mathematical modeling study on shade avoidance response in Arabidopsis hypocotyls

Introduction

Plant growth is a plastic phenomenon controlled both by endogenous genetic programs and by environmental cues. The embryonic stem, the hypocotyl, is an ideal model system for the quantitative study of growth due to its relatively simple geometry and cellular organization, and to its essentially unidirectional growth pattern. The hypocotyl of Arabidopsis thaliana has been studied particularly well at the molecular-genetic level and at the cellular level, and it is the model of choice for analysis of the shade avoidance syndrome (SAS), a growth reaction that allows plants to compete with neighboring plants for light. During SAS, hypocotyl growth is controlled primarily by the growth hormone auxin, which stimulates cell expansion without the involvement of cell division.

Methods

We assessed hypocotyl growth at cellular resolution in Arabidopsis mutants defective in auxin transport and biosynthesis and we designed a mathematical auxin transport model based on known polar and non-polar auxin transporters (ABCB1, ABCB19, and PINs) and on factors that control auxin homeostasis in the hypocotyl. In addition, we introduced into the model biophysical properties of the cell types based on precise cell wall measurements.

Results and Discussion

Our model can generate the observed cellular growth patterns based on auxin distribution along the hypocotyl resulting from production in the cotyledons, transport along the hypocotyl, and general turnover of auxin. These principles, which resemble the features of mathematical models of animal morphogen gradients, allow to generate robust shallow auxin gradients as they are expected to exist in tissues that exhibit quantitative auxin-driven tissue growth, as opposed to the sharp auxin maxima generated by patterning mechanisms in plant development.

Auxin resistant 1 gene (AUX1) mediates auxin effect on Arabidopsis thaliana callus growth by regulating its content and distribution pattern

Callus sustained growth relies heavily on auxin, which is supplied to the culture medium. Surprisingly, there is a noticeable absence of information regarding the involvement of carrier-mediated auxin polar transport gene in callus growth regulation. Here, we delve into the role of the AUXIN RESISTANT 1 (AUX1) influx transporter in the regulation of callus growth, comparing the effects under conditions of light versus darkness. It was observed that callus growth was significantly enhanced under light illumination. This growth-stimulatory effect was accompanied by a decrease in the levels of free auxin within the callus cells when compared to conditions of darkness. In the aux1-22 mutant callus, which lacks functional AUX1, there was a substantial reduction in IAA levels. Nonetheless, the mutant callus exhibited markedly higher growth rates compared to the wild type. This suggests that the reduction in exogenous auxin uptake through the AUX1-dependent pathway may prevent the overaccumulation of growth-restricting hormone concentrations. The growth-stimulatory effect of AUX1 deficiency was counteracted by nonspecific auxin influx transport inhibitors. This finding shows that other auxin influx carriers likely play a role in facilitating the diffusion of auxin from the culture medium to sustain high growth rates. AUX1 was primarily localized in the plasma membranes of the two outermost cell layers of the callus clump and the parenchyma cells adjacent to tracheary elements. Significantly, these locations coincided with the regions of maximal auxin concentration. Consequently, it can be inferred that AUX1 mediates the auxin distribution within the callus.

Humic acid improves wheat growth by modulating auxin and cytokinin biosynthesis pathways

Humic acids have been widely used for centuries to enhance plant growth and productivity. The beneficial effects of humic acids have been attributed to different functional groups and phytohormone-like compounds enclosed in macrostructure. However, the mechanisms underlying the plant growth-promoting effects of humic acids are only partially understood. We hypothesize that the bio-stimulatory effect of humic acids is mainly due to the modulation of innate pathways of auxin and cytokinin biosynthesis in treated plants. A physiological investigation along with molecular characterization was carried out to understand the mechanism of bio-stimulatory effects of humic acid. A gene expression analysis was performed for the genes involved in auxin and cytokinin biosynthesis pathways in wheat seedlings. Furthermore, Arabidopsis thaliana transgenic lines generated by fusing the auxin-responsive DR5 and cytokinin-responsive ARR5 promoter to ß-glucuronidase (GUS) reporter were used to study the GUS expression analysis in humic acid treated seedlings. This study demonstrates that humic acid treatment improved the shoot and root growth of wheat seedlings. The expression of several genes involved in auxin (Tryptophan Aminotransferase of Arabidopsis and Gretchen Hagen 3.2) and cytokinin (Lonely Guy3) biosynthesis pathways were up-regulated in humic acid-treated seedlings compared to the control. Furthermore, GUS expression analysis showed that bioactive compounds of humic acid stimulate endogenous auxin and cytokinin-like activities. This study is the first report in which using ARR5:GUS lines we demonstrate the biostimulants activity of humic acid.

FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry

Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.