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Auxin regulates many aspects of plant development and behavior, including the initiation of new outgrowth, patterning of vascular systems, control of branching, and responses to the environment. Computational models have complemented experimental studies of these processes. We review these models from two perspectives. First, we consider cellular and tissue-level models of interaction between auxin and its transporters in shoots. These models form a coherent body of results exploring different hypotheses pertinent to the patterning of new outgrowth and vascular strands. Second, we consider models operating at the level of plant organs and entire plants. We highlight techniques used to reduce the complexity of these models, which provide a path to capturing the essence of studied phenomena while running simulations efficiently.

Auxin signaling regulates growth and developmental processes in plants. The core of nuclear auxin signaling relies on just three components: TIR1/AFBs, Aux/IAAs, and ARFs. Each component is itself made up of several domains, all of which contribute to the regulation of auxin signaling. Studies of the structural aspects of these three core signaling components have deepened our understanding of auxin signaling dynamics and regulation. In addition to the structured domains of these components, intrinsically disordered regions within the proteins also impact auxin signaling outcomes. New research is beginning to uncover the role intrinsic disorder plays in auxin-regulated degradation and subcellular localization. Structured and intrinsically disordered domains affect auxin perception, protein degradation dynamics, and DNA binding. Taken together, subtle differences within the domains and motifs of each class of auxin signaling component affect signaling outcomes and specificity.

Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.

Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit. During the ripening process of tomato fruit, flavor and aroma metabolites, color, texture and plant hormones undergo significant changes. However, low temperatures delayed the ripening process of tomato fruit, inhibiting flavor compounds and ethylene production. Metabolomics and transcriptomics analyses of tomato fruit stored under low temperature (LT, 5°C) and room temperature (RT, 25°C) were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after harvest. The results of transcriptomics changes revealed that the differentially expressed genes (DEGs) involved in tomato fruit ripening, including several kinds of transcription factors (TFs) (TCP, WRKY, MYB and bZIP), enzymes involved in cell wall metabolism [beta-galactosidase (β-GAL), pectinesterase (PE) and pectate lyase (PL), cellulose and cellulose synthase (CESA)], enzymes associated with fruit flavor and aroma [acetyltransferase (AT), malic enzyme (ME), lipoxygenase(LOX), aldehyde dehydrogenase (ALDH), alcohol dehydrogenase (ADH) and hexokinase (HK)], genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1 (ERF1), Auxin/indoleacetic acids protein (AUX/IAA), gibberellin regulated protein. Based on the above results, we constructed a regulatory network model of the effects of different temperatures during the fruit ripening process. According to the analysis of the metabolomics results, it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature, including, organic acids (L-tartaric acid, a-hydroxyisobutyric acid and 4-acetamidobutyric acid), sugars (melezitose, beta-D-lactose, D-sedoheptulose 7-phosphate, 2-deoxyribose 1-phosphate and raffinose) and phenols (coniferin, curcumin and feruloylputrescine). This study revealed the effects of storage temperature on postharvest tomato fruit and provided a basis for further understanding of the molecular biology and biochemistry of fruit ripening.

Soil microbes promote plant growth through several mechanisms such as secretion of chemical compounds including plant growth hormones. Among the phytohormones, auxins, ethylene, cytokinins, abscisic acid and gibberellins are the best understood compounds. Gibberellins were first isolated in 1935 from the fungus Gibberella fujikuroi and are synthesized by several soil microbes. The effect of gibberellins on plant growth and development has been studied, as has the biosynthesis pathways, enzymes, genes and their regulation. This review revisits the history of gibberellin research highlighting microbial gibberellins and their effects on plant health with an emphasis on the early discoveries and current advances that can find vital applications in agricultural practices.

The development of a hook-like structure at the apical part of the soil-emerging organs has fascinated botanists for centuries, but how it is initiated remains unclear. Here, we demonstrate with high-throughput infrared imaging and 2-D clinostat treatment that, when gravity-induced root bending is absent, apical hook formation still takes place. In such scenarios, hook formation begins with a de novo growth asymmetry at the apical part of a straightly elongating hypocotyl. Remarkably, such de novo asymmetric growth, but not the following hook enlargement, precedes the establishment of a detectable auxin response asymmetry, and is largely independent of auxin biosynthesis, transport and signaling. Moreover, we found that functional cortical microtubule array is essential for the following enlargement of hook curvature. When microtubule array was disrupted by oryzalin, the polar localization of PIN proteins and the formation of an auxin maximum became impaired at the to-be-hook region. Taken together, we propose a more comprehensive model for apical hook initiation, in which the microtubule-dependent polar localization of PINs may mediate the instruction of growth asymmetry that is either stochastically took place, induced by gravitropic response, or both, to generate a significant auxin gradient that drives the full development of apical hook. This article is protected by copyright. All rights reserved.

The bioprocess methodology for the enhanced production of phytochemicals using plant cultures predominantly depends on the elicitors and precursors. The drug L-DOPA (anti-Parkinson's drug) (L-3, 4-dihydroxyphenylalanine) has been chiefly isolated from the popular medicinal plant species Mucuna. The present study has been carried out to enhance the production of L-DOPA and other secondary metabolites in the presence of the optimized concentration of growth promoters, elicitors and precursor's in vitro callus culture of Mucuna imbricata. Results revealed that there is a positive influence of Methyl Jasmonate (MJC) and Salicylic Acid (SAC) on the accumulation of L-DOPA and other secondary metabolites (Nutritional and anti-nutritional factors), which enhances their production by more than two folds. The highest accumulation of L-DOPA was noticed in the elicitation of 1 mM MJC (4.3 ± 0.4 %) followed by 1 mM SAC (3.4 ± 0.08 %) on 45th and 30th days respectively. Results also illustrated a significant increase of callus biomass (dry and moist weight) as well as total phenolics, flavonoids and antioxidants values in the elicited callus from day 30th to day 45th of explant inoculation which indicates a synergistic interaction of auxin, cytokinins with elicitors and precursors respectively. Additionally, results revealed that improved accumulation of carbohydrates was positively correlated with an increase in L-DOPA content in the elicited callus. Hence the protocol formulated delivers an effective alternative for mass production of L-DOPA from callus culture with improved metabolite content.

Graphical abstract, Highlights • Functional ABA biosynthesis genes show specific roles for ABA accumulation at different stages of seed development and seedling establishment. • De novo ABA biosynthesis during embryogenesis is required for late seed development, maturation, and induction of primary dormancy. • ABA plays multiple roles with the key LAFL hub to regulate various downstream signaling genes in seed and seedling development. • Key ABA signaling genes ABI3, ABI4, and ABI5 play important multiple functions with various cofactors during seed development such as de-greening, desiccation tolerance, maturation, dormancy, and seed vigor. • The crosstalk between ABA and other phytohormones are complicated and important for seed development and seedling establishment., Background Seed is vital for plant survival and dispersion, however, its development and germination are influenced by various internal and external factors. Abscisic acid (ABA) is one of the most important phytohormones that influence seed development and germination. Until now, impressive progresses in ABA metabolism and signaling pathways during seed development and germination have been achieved. At the molecular level, ABA biosynthesis, degradation, and signaling genes were identified to play important roles in seed development and germination. Additionally, the crosstalk between ABA and other hormones such as gibberellins (GA), ethylene (ET), Brassinolide (BR), and auxin also play critical roles. Although these studies explored some actions and mechanisms by which ABA-related factors regulate seed morphogenesis, dormancy, and germination, the complete network of ABA in seed traits is still unclear. Aim of review Presently, seed faces challenges in survival and viability. Due to the vital positive roles in dormancy induction and maintenance, as well as a vibrant negative role in the seed germination of ABA, there is a need to understand the mechanisms of various ABA regulators that are involved in seed dormancy and germination with the updated knowledge and draw a better network for the underlying mechanisms of the ABA, which would advance the understanding and artificial modification of the seed vigor and longevity regulation. Key scientific concept of review Here, we review functions and mechanisms of ABA in different seed development stages and seed germination, discuss the current progresses especially on the crosstalk between ABA and other hormones and signaling molecules, address novel points and key challenges (e.g., exploring more regulators, more cofactors involved in the crosstalk between ABA and other phytohormones, and visualization of active ABA in the plant), and outline future perspectives for ABA regulating seed associated traits.

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.

Polycyclic aromatic hydrocarbon (PAH) contamination has a negative impact on ecosystems. PAHs are a large group of toxins with two or more benzene rings that are persistent in the environment. Some PAHs can be cytotoxic, teratogenic, and/or carcinogenic. In the bacterium Pseudomonas, PAHs can be modified by dioxygenases, which increase the reactivity of PAHs. We hypothesize that some plant dioxygenases are capable of PAH biodegradation. Herein, we investigate the involvement of Arabidopsis thaliana At1g14130 in the degradation of phenanthrene, our model PAH. The At1g14130 gene encodes Dioxygenase For Auxin Oxidation 1 (AtDAO1), an enzyme involved in the oxidative inactivation of the hormone auxin. Expression analysis using a β-glucuronidase (GUS) reporter revealed that At1g14130 is prominently expressed in new leaves of plants exposed to media with phenanthrene. Analysis of the oxidative state of gain-of-function mutants showed elevated levels of H2O2 after phenanthrene treatments, probably due to an increase in the oxidation of phenanthrene by AtDAO1. Biochemical assays with purified AtDAO1 and phenanthrene suggest an enzymatic activity towards the PAH. Thus, data presented in this study support the hypothesis that an auxin dioxygenase, AtDAO1, from Arabidopsis thaliana contributes to the degradation of phenanthrene and that there is possible toxic metabolite accumulation after PAH exposure.

Members of the auxin/indoleacetic acid (Aux/IAA) gene family in plants are primary auxin-responsive genes that play important roles in many aspects of plant development and in responses to abiotic stress. Recently, 33 Aux/IAA have been identified in the apple genome. The biological responses of MdIAAs to salt stress are still unknown. In this study, Malus zumi, Malus baccata, and Malus × domestica 'Fuji' plantlets were subjected to salt stress by supplementing hydroponic media with NaCl at various concentrations. M. zumi showed the strongest salt resistance, followed by 'Fuji', and M. baccata was the most sensitive to salt stress. Tissue-specific expression profiles of MdIAAs were determined by quantitative real-time polymerase chain reaction. When apple plantlets were subjected to salt stress, most of salt-responsive MdIAAs were up-regulated by 1 h, 3 h, and 6 h in roots, shoot tips, and leaves, respectively. Highly expressed MdIAAs in roots, especially for M. zumi, consisted with the salt tolerance of apple rootstocks. Transgenic apple calli were tolerant to salt stress when over-expressed salt-responsive genes, MdIAA8, -9, and -25. These results provide clues about salt resistance in these three Malus species, which helps apple breeding of salt tolerance by genetic transformation.

The interaction of plant roots with bacteria is influenced by chemical signaling, where auxins play a critical role. Auxins exert positive or negative influences on the plant traits responsible of root architecture configuration such as root elongation and branching and root hair formation, but how bacteria that modify the plant auxin response promote or repress growth, as well as root structure, remains unknown. Here, we isolated and identified via molecular and electronic microscopy analysis a Micrococcus luteus LS570 strain as a plant growth promoter that halts primary root elongation in Arabidopsis seedlings and strongly triggers root branching and absorptive potential. The root biomass was exacerbated following root contact with bacterial streaks, and this correlated with inducible expression of auxin-related gene markers DR5:GUS and DR5:GFP. Cellular and structural analyses of root growth zones indicated that the bacterium inhibits both cell division and elongation within primary root tips, disrupting apical dominance, and as a consequence differentiation programs at the pericycle and epidermis, respectively, triggers the formation of longer and denser lateral roots and root hairs. Using Arabidopsis mutants defective on auxin signaling elements, our study uncovers a critical role of the auxin response factors ARF7 and ARF19, and canonical auxin receptors in mediating both the primary root and lateral root response to M. luteus LS570. Our report provides very basic information into how actinobacteria interact with plants and direct evidence that the bacterial genus Micrococcus influences the cellular and physiological plant programs ultimately responsible of biomass partitioning.

Growth promotion induced by the endosymbiont Piriformospora indica has been observed in various plants; however, except growth phytohormones, specific functional metabolites involved in P. indica-mediated growth promotion are unknown. Here, we used a gas chromatography-mass spectrometry-based untargeted metabolite analysis to identify tomato (Solanum lycopersicum) metabolites whose levels were altered during P. indica-mediated growth promotion. Metabolomic multivariate analysis revealed several primary metabolites with altered levels, with putrescine (Put) induced most significantly in roots during the interaction. Further, our results indicated that P. indica modulates the arginine decarboxylase (ADC)-mediated Put biosynthesis pathway via induction of SlADC1 in tomato. Piriformospora indica did not promote growth in Sladc1-(virus-induced gene silencing of SlADC1) lines of tomato and showed less colonization. Furthermore, using LC–MS/MS we showed that Put promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4 and GA7) levels in tomato. In Arabidopsis (Arabidopsis thaliana) adc knockout mutants, P. indica colonization also decreased and showed no plant growth promotion, and this response was rescued upon exogenous application of Put. Put is also important for hyphal growth of P. indica, indicating that it is co-adapted by both host and microbe. Taken together, we conclude that Put is an essential metabolite and its biosynthesis in plants is crucial for P. indica-mediated plant growth promotion and fungal growth.

In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.

During plant development, a precise balance of cytokinin is crucial for correct growth and patterning, but it remains unclear how this is achieved across different cell types and in the context of a growing organ. Here we show that in the root apical meristem, the TMO5/LHW complex increases active cytokinin levels via two cooperatively acting enzymes. By profiling the transcriptomic changes of increased cytokinin at single-cell level, we further show that this effect is counteracted by a tissue-specific increase in CYTOKININ OXIDASE 3 expression via direct activation of the mobile transcription factor SHORTROOT. In summary, we show that within the root meristem, xylem cells act as a local organizer of vascular development by non-autonomously regulating cytokinin levels in neighbouring procambium cells via sequential induction and repression modules.

Under tropical and subtropical environments, citrus leaves are exposed to excess sunlight, inducing photoinhibition. Huanglongbing (HLB, citrus greening), a devastating phloem-limited disease putatively caused by Candidatus Liberibacter asiaticus, exacerbates this challenge with additional photosynthetic loss and excessive starch accumulation. A combined metabolomics and physiological approach was used to elucidate whether shade alleviates the deleterious effects of HLB in field-grown citrus trees, and to understand the underlying metabolic mechanisms related to shade-induced morpho-physiological changes in citrus. Using metabolite profiling and multinomial logistic regression, we identified pivotal metabolites altered in response to shade. A core metabolic network associated with shade conditions was identified through pathway enrichment analysis and metabolite mapping. We measured physio-biochemical responses and growth and yield characteristics. With these, the relationships between metabolic network and the variables measured above were investigated. We found that moderate-shade alleviates sink limitation by preventing excessive starch accumulation and increasing foliar sucrose levels. Increased growth and fruit yield in shaded compared with non-shaded trees were associated with increased photosystem II efficiency and leaf carbon fixation pathway metabolites. Our study also shows that, in HLB-affected trees under shade, the signaling of plant hormones (auxins and cytokinins) and nitrogen supply were downregulated with reducing new shoot production likely due to diminished needs of cell damage repair and tissue regeneration under shade. Overall, our findings provide the first glimpse of the complex dynamics between cellular metabolites and leaf physiological functions in citrus HLB pathosystem under shade, and reveal the mechanistic basis of how shade ameliorates HLB disease.

The tea plant, Camellia sinensis (L.) O. Kuntze, is an economically important, perennial woody plant rich in catechins. Although catechins have been reported to play an important role in plant defences against microbes, their roles in the defence of tea plants against herbivores remain unknown. In this study, we allowed the larvae of Ectropis grisescens, a leaf-feeding pest, to feed on the plants, and alternatively, we wounded the plants and then treated them with E. grisescens oral secretions (WOS). Both approaches triggered jasmonic acid-, ethylene- and auxin-mediated signalling pathways; as a result, plants accumulated three catechin compounds: (+)-catechin, epicatechin and epigallocatechin. Not only was the mass of E. grisescens larvae fed on plants previously infested with E. grisescens or treated with WOS significantly lower than that of larvae fed on controls, but also artificial diet supplemented with epicatechin, (+)-catechin or epigallocatechin gallate reduced larval growth rates. In addition, the exogenous application of jasmonic acid, ethylene or auxin induced the biosynthesis of the three catechins, which, in turn, enhanced the resistance of tea plants to E. grisescens, leading to the coordination of the three signalling pathways. Our results suggest that the three catechins play an important role in the defences of tea plants against E. grisescens.

PIN-FORMED (PIN)-dependent directional auxin transport is crucial for plant development. Although the redistribution of auxin mediated by the polarization of PIN3 plays key roles in modulating hypocotyl cell expansion, how PIN3 becomes repolarized to the proper sites within hypocotyl cells is poorly understood. We previously generated the clathrin light chain clc2-1 clc3-1 double mutant in Arabidopsis thaliana and found that it has an elongated hypocotyl phenotype compared to the wild type. Here, we performed genetic, cell biology, and pharmacological analyses combined with live-cell imaging to elucidate the molecular mechanism underlying the role of clathrin light chains in hypocotyl elongation. Our analyses indicated that the defects of the double mutant enhanced auxin maxima in epidermal cells, thus, promoting hypocotyl elongation. PIN3 relocated to the lateral sides of hypocotyl endodermal cells in clc2-1 clc3-1 mutants to redirect auxin toward the epidermal cell layers. Moreover, the loss of function of PIN3 largely suppressed the long hypocotyl phenotype of the clc2-1 clc3-1 double mutant, as did treatment with auxin transport inhibitors. Based on these data, we propose that clathrin modulates PIN3 abundance and polarity to direct auxin flux and inhibit cell elongation in the hypocotyl, providing novel insights into the regulation of hypocotyl elongation. This article is protected by copyright. All rights reserved.

Background Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established. Results In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism. Conclusions Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

Inactivation of the phytohormone auxin plays important roles in plant development, and several enzymes have been implicated in auxin inactivation. In this study, we show that the predominant natural auxin, indole-3-acetic acid (IAA), is mainly inactivated via the GH3-ILR1-DAO pathway. IAA is first converted to IAA-amino acid conjugates by GH3 IAA-amidosynthetases. The IAA-amino acid conjugates IAA-aspartate (IAA-Asp) and IAA-glutamate (IAA-Glu) are storage forms of IAA and can be converted back to IAA by ILR1/ILL amidohydrolases. We further show that DAO1 dioxygenase irreversibly oxidizes IAA-Asp and IAA-Glu into 2-oxindole-3-acetic acid-aspartate (oxIAA-Asp) and oxIAA-Glu, which are subsequently hydrolyzed by ILR1 to release inactive oxIAA. This work established a complete pathway for the oxidative inactivation of auxin and defines the roles played by auxin homeostasis in plant development.

Background Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants. Results A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416. Conclusion So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.

The leading purpose of this work is the development of efficient culture conditions to induce calli from cabbage (Brassica oleracea var. capitata L.) under in vitro conditions. The mature seeds were surface sterilized with combinations of different concentrations of ethanol and NaOCl in different time durations and were germinated on MS basal medium. The results revealed that the best sterilization method of cabbage seeds was by using 70% ethanol for one minute, followed by 15 min in 2% (NaOCl). Seedlings were used as donor sources for hypocotyls, cotyledon leaves, true leaves, and shoot tip explants. These explants were cultured on different combinations of cytokinins (TDZ, BAP, Ad) and auxins (IAA, NAA, 2, 4-D) then implanted in Murashige and Skoog (MS) media. 4 weeks after culturing, a significant difference was found among the explants in response to plant hormones. The maximum percentage of callus induction (100%) was using the combinations of 1 BAP + 1 2, 4-D, 1 BAP + 1 NAA, and 1 BAP + 2 2,4-D mg. l-1. In addition, explants responses varied and the hypocotyls showed a superior result (85.71 %) as compared to other explants. For callus fresh weight, the combination of 0.22 TDZ + 79.9 Ad mg. l-1 had a significant effect, causing the highest fresh weight (0.2745g), while control treatment gave the lowest mean of 0.0066 g. Data showed that cotyledon explants were significantly superior in giving highest callus fresh weight with the mean of 0.1723 g. On the other hand, hypocotyl explants gave the lowest mean, reaching 0.1542 g.

Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin., A vector system and flow cell set-up allow long-term imaging of both gene expression and anatomy in Arabidopsis primary and lateral roots.

Microbial plant biostimulants (MPBs) are capable of improving the productivity and quality of crops by activating plant physiological and molecular processes, representing an efficient tool in sustainable agriculture. Through phytohormone production, MPBs are capable of regulating plant physiological processes, increasing the productivity and quality of crops, in addition to being an efficient alternative in the industrial production of phytohormones. Bacillus is a bacterial genus with various species on the market being used as biopesticides, due to their ability to produce antimicrobial, nematicidal and insecticidal compounds. The capability of Bacillus species to protect plants against pests and/or pathogens also entails the triggering or increase of plant defense responses. Furthermore, a relevant number of species from the genus Bacillus provoke plant growth promotion by different mechanisms such as increasing the tolerance of their host plants under abiotic stress conditions or improving plant nutrition. In several cases, the plant response is mediated by the bacterial production of phytohormones. In the present work, all studies from recent decades where the production of phytohormones by Bacillus species are reported, highlighting their role in host plants and the mechanisms by which they are capable of increasing plant growth, promoting their development, and improving their response to different stresses. KEY POINTS: • Different Bacillus-species are known as agricultural biopesticides. • Bacillus role as biostimulants is being increasingly addressed. • Bacillus represents a good source of phytohormones of agricultural interest.

How plants balance growth and stress adaptation is a long-standing topic in plant biology. Abscisic acid (ABA) induces the expression of the stress-responsive Asparagine Rich Protein (NRP), which promotes the vacuolar degradation of PP6 phosphatase FyPP3, releasing ABI5 transcription factor to initiate transcription. Whether NRP is required for growth remains unknown. We generated an nrp1 nrp2 double mutant, which had a dwarf phenotype that can be rescued by inhibiting auxin transport. Insufficient auxin in the transition zone and over-accumulation of auxin at the root tip was responsible for the short elongation zone and short-root phenotype of nrp1 nrp2. The auxin efflux carrier PIN2 over-accumulated in nrp1 nrp2 and became de-polarized at the plasma membrane, leading to slower root basipetal auxin transport. Knock-out of PIN2 suppressed the dwarf phenotype of nrp1 nrp2. Furthermore, ABA can induce NRP-dependent vacuolar degradation of PIN2 to inhibit primary root elongation. FyPP3 also is required for NRP-mediated PIN2 turnover. In summary, in growth condition, NRP promotes PIN2 vacuolar degradation to help maintain PIN2 protein concentration and polarity, facilitating the establishment of the elongation zone and primary root elongation. When stressed, ABA employs this pathway to inhibit root elongation for stress adaptation.

Endosperm transfer cells function as the nutrient transporter, antimicrobic barrier, and signal mediator between filial and maternal tissues. Sugar supply of maternal tissues, sugar demand of filial tissues, and requirement for defence against pathogens are three elemental factors inducing differentiation of endosperm transfer cells. Epigenetic factors, especially MEG1, moderate the key genetic factor ZmMRP-1 to activate endosperm transfer cell-specific genes that control the flange wall ingrowth formation and defensin-like protein secretion in maize. Auxin and cytokinin are primary hormones involved in development of maize endosperm transfer cells. Crosstalk between glucose and hormone signaling regulates endosperm transfer cell development via modifying ZmMRP-1 expression. This review summarizes the current knowledge on maize endosperm transfer cell development, and discusses its potential molecular mechanisms. It is expected to strengthen the theoretical basis for structural and functional optimization of endosperm transfer cells, and yield improvement of kernels in maize.

Background and Aims Initiation of cluster roots in white lupin (Lupinus albus) under phosphorus (P) deficiency requires auxin signalling, whereas flavonoids inhibit auxin transport. However, little information is available about the interactions between P deficiency and flavonoids in terms of cluster-root formation in white lupin. Methods Hydroponic and aeroponic systems were used to investigate the role of flavonoids in cluster-root formation, with or without 75 μm P supply. Key Results Phosphorus-deficiency-induced flavonoid accumulation in cluster roots depended on developmental stage, based on in situ determination of fluorescence of flavonoids and flavonoid concentration. LaCHS8, which codes for a chalcone synthase isoform, was highly expressed in cluster roots, and silencing LaCHS8 reduced flavonoid production and rootlet density. Exogenous flavonoids suppressed cluster-root formation. Tissue-specific distribution of flavonoids in roots was altered by P deficiency, suggesting that P deficiency induced flavonoid accumulation, thus fine-tuning the effect of flavonoids on cluster-root formation. Furthermore, naringenin inhibited expression of an auxin-responsive DR5:GUS marker, suggesting an interaction of flavonoids and auxin in regulating cluster-root formation. Conclusions Phosphorus deficiency triggered cluster-root formation through the regulation of flavonoid distribution, which fine-tuned an auxin response in the early stages of cluster-root development. These findings provide valuable insights into the mechanisms of cluster-root formation under P deficiency.

Micropropagation through nodal explants was attempted for a rare and endemic taxon Corynandra chelidonii var. pallae (Cleomaceae) in view of its medicinal uses, bioactive compounds, declining natural populations due to intermittent sterility, low seed set and erratic seed germination. Multiple shoots were regenerated directly from the nodal explants on Murashige and Skoog’s medium containing different concentrations and combinations of cytokinins and auxins. High-frequency multiple shoots of 8.15 ± 0.249 with 1.63 ± 0.031 shoot length (cm) were obtained on MS medium augmented with the combination of 0.5 mg/L of thidiazuron and 1.0 mg/L of indole-3-acetic acid. Directly regenerated shoots were rooted with 95% root induction on a half-strength MS medium supplemented with 1.0 mg/L of indole-3 butyric acid. The in vitro raised plantlets were hardened in plastic pots and acclimatized initially in the greenhouse conditions and later transferred to the field conditions with a 78% of survival rate. The genetic fidelity of in vitro generated and field transferred plantlets with that of the mother plant was checked by carrying ISSR marker-based polymerase chain reaction method. This protocol on direct organogenesis and genetic fidelity analysis in Corynadra chellidonii var. pallae can be successfully employed for large-scale multiplication and conservation.

Auxin is the major hormone involved in the shade-avoidance response in plants. Auxin-induced elongation of the stem is accompanied by the restraint of leaf blade expansion. The auxin transportation inhibitor, 1-N-naphthylphthalamic acid (NPA), is widely used in auxin functional studies, while the effects of NPA on soybean leaf expansion under shade conditions is still not known. This study assessed the effect of NPA on hormone content and cell dynamics variations during leaf expansion of soybeans under shade conditions. The results revealed that the inhibition of soybean leaf area under shade conditions was caused by a reduction in the cell number at the early stages of leaf expansion. The application of NPA under shade conditions inhibited leaf expansion by reducing the cell number. Auxin levels showed an increasing trend during the leaf expansion under shade, while cytokinin was significantly reduced. The application of NPA also reduced cytokinin levels. Cell flow cytometry revealed that reduction of the cell mitotic index by shade and NPA were caused by decreasing cell division at the early stages of leaf expansion. The shade-tolerant variety had a relative larger leaf area than the shade-sensitive variety due to higher cell division. In conclusion, the application of NPA caused a cytokinin reduction at the early stages of leaf expansion, leading to a lower cell division and cell number and inhibiting the leaf area in soybeans under shade. Future works of the function of cytokinin on cell division for selecting a higher leaf area may increase shade tolerance.

The development of secondary vascular tissue enhances the transport capacity and mechanical strength of plant bodies, while contributing a huge proportion of the world’s biomass in the form of wood. Cell divisions in the cambium, which constitutes the vascular meristem, provide progenitors from which conductive xylem and phloem are derived. The cambium is a somewhat unusual stem cell population in two respects, making it an interesting subject for developmental research. Firstly, it arises post-germination, and thus represents a model for understanding stem cell initiation beyond embryogenesis. Secondly, xylem and phloem differentiate on opposing sides of cambial stem cells, making them bifacial in nature. Recent discoveries in Arabidopsis thaliana have provided insight into the molecular mechanisms that regulate the initiation, patterning, and maintenance of the cambium. In this review, the roles of intercellular signalling via mobile transcription factors, peptide–receptor modules, and phytohormones are described. Crosstalk between these regulatory pathways is becoming increasingly apparent, yet the underlying mechanisms are not fully understood. Future study of the interaction between multiple independently identified regulators, as well as the functions of their orthologues in trees, will deepen our understanding of radial growth in plants., We review the literature describing the molecular mechanisms by which the vascular cambium is initiated and maintained in Arabidopsis.

A highly efficient and reproducible in vitro plant regeneration method has been developed from shoot bud, half-shoot, and shoot slice explants of four genotypes of turmeric (Curcuma longa L.). The shoot slice explant produced the highest number of shoots (22.4 shoots explant−1) than half-shoot (18.6 shoots explant−1) and shoot bud explant (14.2 shoots explant−1) of Salem genotype on medium amended with 13.32 µM 6-benzylaminopurine (BAP) and 5.37 µM 1-naphthaleneacetic acid (NAA). Salem genotype was more efficient among the four genotypes tested, followed by Duggirala Red, Prathibha, and PCT-13 genotypes. Approximately 80% of shoots were induced spontaneous rooting on shoot induction media fortified with NAA. The complete plantlets were obtained after rooting the shoots on a medium augmented with 4.90 µM Indole-3-butyric acid (IBA). IBA was an efficient auxin to induce the maximum number of roots per shoot than Indole-3-acetic acid (IAA) and NAA. The plantlets were acclimatized under greenhouse conditions, and the survival rate was recorded as 96%. The plantlets obtained from all explants were morphologically similar to mother plants. Two genome-based molecular markers, namely inter simple sequence repeats (ISSR) and start codon targeted (SCoT) molecular markers, were employed to determine the genetic stability of plants obtained from the tissue culture of the Salem genotype. The DNA markers validated the genetic uniformity of the plants obtained from all three explants was similar to their mother plant. This plant regeneration procedure could be a helpful method for the genetic improvement of turmeric.

The KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) gene is highly expressed in flower and leaf abscission zones (AZs), and KD1 was reported to regulate tomato flower pedicel abscission via alteration of the auxin gradient and response in the flower AZ (FAZ). The present work was aimed to further examine how KD1 regulates signaling factors and regulatory genes involved in pedicel abscission, by using silenced KD1 lines and performing a large-scale transcriptome profiling of the FAZ before and after flower removal, using a customized AZ-specific microarray. The results highlighted a differential expression of regulatory genes in the FAZ of KD1-silenced plants compared to the wild-type. In the TAPG4::antisense KD1-silenced plants, KD1 gene expression decreased before flower removal, resulting in altered expression of regulatory genes, such as epigenetic modifiers, transcription factors, posttranslational regulators, and antioxidative defense factors occurring at zero time and before affecting auxin levels in the FAZ detected at 4 h after flower removal. The expression of additional regulatory genes was altered in the FAZ of KD1-silenced plants at 4-20 h after flower removal, thereby leading to an inhibited abscission phenotype, and downregulation of genes involved in abscission execution and defense processes. Our data suggest that KD1 is a master regulator of the abscission process, which promotes abscission of tomato flower pedicels. This suggestion is based on the inhibitory effect of KD1 silencing on flower pedicel abscission that operates via alteration of various regulatory pathways, which delay the competence acquisition of the FAZ cells to respond to ethylene signaling.

Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.

The in vitro development of a plant is controlled by factors that promote a series of plant responses, which interfere with tissue organogenesis and morphology. For plants of the family Lamiaceae, these factors remain unknown or poorly understood, hindering in vitro cultivation of these plants. The basil cultivar ‘Grecco a palla’ has attractive chemical properties for medicinal, pharmaceutical, and cosmetic industries; however, its production is limited due to the lack of appropriate cultivation conditions. Two types of explants of this species (nodal segments and stem apexes) were grown in culture media with auxin and cytokinin, and their development was followed for 60 days. During in vitro cultivation, both explants were subjected to higher concentrations of plant growth regulators (PGRs) produced only calluses, without induction of shoots. Small amounts of regulators favored hyperhydricity as nodal segments or stem apexes in the absence of PGRs produced plants with disturbances, including brittle, light green, and thick leaves. In this case, there was an increase in the cell layers of palisade parenchyma, which had large cell spaces and larger cells. This tissue also advanced to spongy parenchyma and compressed it. The stomatal density was low; however, the stomata were larger with additions mainly in the guard cells and the stomatic opening. Therefore, stem apexes in the absence of PGRs produced more vigorous plants, whereas nodal segments with low amounts of cytokinins and auxins developed a well-branched and abundant root system.

Background Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored. Results Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety. Conclusions Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Phytohormones play important roles in controlling leaf size and in the modulation of various stress responses, including drought. In this study, hormone profiling analyses by ultra high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UHPLC-MS/MS) was performed in leaves collected at three stages of active leaf growth to unravel which phytohormones modulate leaf size in sesame (Sesamum indicum L.) plants, an important oil-rich crop. Furthermore, endogenous contents of phytohormones were measured in parallel to various stress markers in sesame plants exposed to mild water deficit conditions by withholding water in potted plants for one week. Results revealed a major role of cytokinins and auxin in the modulation of leaf growth in sesame plants (which increased by 21.5 and 2.1-fold, respectively, with leaf growth), as well as a putative antagonistic response between jasmonic acid and salicylic acid during leaf development. Furthermore, growth arrest during water deficit stress appeared to be modulated by cytokinins, the endogenous contents of which decreased (by 48%) in parallel with ABA increases (by 59%). Reductions in the contents of the active cytokinin trans-zeatin occurred in parallel with increases in isopentenyladenine contents under drought, which suggests a partial metabolic limitation in cytokinin biosynthesis in leaves upon water deficit stress. These results provide useful information for the hormonal modulation of leaf size and the improvement of leaf growth and production in sesame plants through manipulation of the levels of key regulatory phytohormones.

Aim: This study evaluated efficient culture media for the regeneration of elite material through somatic embryogenesis from oil palm zygotic embryos. Methodology: For callus induction, zygotic embryos of four elite genotypes (G1-264T, G2-238DX17P, G3-37DX17P and G4-237T) were cultured on three basal media (Y3, MS and N6) with different auxin 2 mg l-1 (Picloram, 2,4-D and Dicamba) combinations. Subculture was made every month for three passages. It evaluated various callus characters. The embryogenic calli from callus induction media were transferred to the embryo maturation medium and subcultured until the polyembryoids formed. For shoot and root formation, somatic embryo clumps were transferred into regeneration media. In-vitro plantlets with well-grown roots were hardened in pots for six weeks and assessed clonal fidelity using polymorphic SSR primers. Results: Among the treatments, calli from N6+2,4-D, Y3+2,4-D and N6+Picloram showed the highest embryogenic callus potential. G4-237T induced more embryogenic calli (32.982) among genotypes, which was on par with G1-264T (24.196). Embryogenic calli grown on N6 media with Dicamba showed the highest proliferation rate (1.141). After 60 days of culture on regeneration media, the highest number of plantlets per somatic embryogenic clump was obtained from G1-264T on N6 media supplemented with Dicamba. Interpretation: Culture media salt concentration showed a significant difference among media by causing perturbations of auxin flow during somatic embryogenesis affecting callus induction, proliferation and plantlet regeneration. This may be useful for standardizing the genotype-specific regeneration media in oil palm.

Investigation of the biochemical and molecular changes during rooting in woody species can reveal how specific molecules are involved in adventitious root (AR) induction. We investigated the effects of indole butyric acid (IBA) and inhibitors of polar auxin transport and auxin signaling on ex vitro rooting of micropropagated shoots of Cedrela fissilis and evaluated the proteomic profile and endogenous contents of indole acetic acid (IAA) during AR initiation. We observed that exogenous IBA was not necessary for ex vitro rooting, and root induction was significantly reduced by auxin signaling (p-chlorophenoxyisobutyric acid—PCIB) and polar auxin transport (triiodobenzoic acid—TIBA) inhibitors. The presence of meristematic cells and the formation of meristematic centers in the base of shoot cuttings at 3 days of rooting are necessary for AR formation. The accumulation of cell division- and auxin-related proteins and the presence of unique proteins related to cell wall modification in shoot cuttings at 3 days of rooting were associated with higher IAA contents and AR initiation. In addition, an accumulation of proteins related to dephosphorylation, glycolytic and tricarboxylic acid cycle pathways and a reduction in the accumulation of proteins from isoflavonoid metabolism were associated with the promotion of AR initiation. These results show the relevance of these proteins for AR initiation in this species. This is the first study showing the involvement of protein accumulation and endogenous IAA contents in adventitious rooting initiation in C. fissilis, an easily rooted endangered woody species from the Brazilian rainforest. Auxin contents and proteomic analyses during adventitious rooting of in vitro propagated Cedrela fissilis shoots.

BRASSINAZOLE-RESISTANT (BZR) genes are a family that has transcription factors that are particular to plants and are involved in the signal transduction of brassinosteroids. This study identified nine BZR genes in tomato using a computational approach. BZRs are hydrophilic proteins mostly located in the nucleus. The most common secondary structure of BZRs is random coil. The number of introns contained in the BZR family genes is between 1 and 9, and these genes are distributed in a disarrayed fashion across the chromosomes, while there were two pairs of duplicated gene fragments. Forty-four cis-elements were identified in the region of the gene promoter, all of which were associated with plant hormones, tissue specific expression, response to stress, and light response. The genes in this family mainly responded to plant hormones such as gibberellin, salicylic acid, abscisic acid, auxin, and methyl jasmonate (MeJa). Analysis of the expression profile demonstrated that SlBZR gene expression was significantly different in tissues and organs at different developmental stages of tomato, and some genes had tissue specific expression. The results of qRT-PCR demonstrated that all genes in the BZR family were involved in stress response (200 mmol/L SA, 200 mmol/L ABA, and 4 °C). The results lay the foundation to further study the functions of tomato BZR genes.

The shoot organ boundaries have important roles in plant growth and morphogenesis. It has been reported that a gene encoding a cysteine-rich secreted peptide of the EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family, EPFL2, is expressed in the boundary domain between the two cotyledon primordia of Arabidopsis thaliana embryo. However, its developmental functions remain unknown. This study aimed to analyze the role of EPFL2 during embryogenesis. We found that cotyledon growth was reduced in its loss-of-function mutants, and this phenotype was associated with the reduction of auxin response peaks at the tips of the primordia. The reduced cotyledon size of the mutant embryo recovered in germinating seedlings, indicating the presence of a factor that acted redundantly with EPFL2 to promote cotyledon growth in late embryogenesis. Our analysis suggests that the boundary domain between the cotyledon primordia acts as a signaling center that organizes auxin response peaks and promotes cotyledon growth.

Recalcitrant plants are difficult to handle in tissue culture, and this limits their accessibility for various studies. Novel strategies are being developed to compensate the restricted nature of these plants to make them more adapted to tissue culture applications. Sorghum is one of the most recalcitrant plants with decreased efficiency and non-standardized tissue culture protocols. The advances in embryogenic genes ease the somatic embryo formation and regeneration ability in sorghum. BABY BOOM (BBM) is the most prominent transcription factor involved in somatic embryogenesis, even without exogenous auxin application, the spontaneous somatic embryo formation could occur in plants, which makes this gene(s) an optimal target for recalcitrant plants. This study is designed to characterize SbBBM-like genes in sorghum. Two similar length of protein pairs, SbBBM-like 1 (XP_021313568.1) and SbBBM-like 2 (XP_002452443.1), were identified in cv. Aldari and cis-regulatory elements of these proteins were observed to be involved in particularly light response and hormonal regulation. The protein –protein interaction data indicated possible role in auxin mechanism. The expression data showed SbBBM-like was highly expressed in seedling root and embryogenic callus, however the expression was highest in embryogenic callus for SbBBM-like 2 with almost 200-fold increase, compared to other tissues.

Plants can detect the quorum sensing (QS) signaling molecules of microorganisms, such as amino acids, fat derivatives and diketopiperazines (DKPs), thus allowing the exchange information to promote plant growth and development. Here, we evaluated the effects of 12 synthesized DKPs on Arabidopsis thaliana roots and studied their underlying mechanisms of action. Results showed that, as QS signal molecules, the DKPs promoted lateral root development and root hair formation in A.thaliana to differing degrees. The DKPs enhanced the polar transport of the plant hormone auxin from the shoot to root and triggered the auxin-responsive protein IAA7/17 to decrease the auxin response factor, leading to the accumulation of auxin at the root tip and accelerated root growth. In addition, the DKPs induced the development of lateral roots and root hair in the A. thaliana root system architecture via interference with auxin receptor transporter inhibitor response protein 1 (TIR1). A series of TIR1 sites that potentially interact with DKPs were also predicted using molecular docking analysis. Mutations of these sites inhibited the phosphorylation of TIR1 after DKP treatment, thereby inhibiting lateral root formation, especially TIR1-1 site. This study identified several DKP signal molecules in the QS system that can promote the expression of auxin response factors ARF7/19 via interactions of TIR1 and IAA7/17 proteins, thus promoting plant growth and development.

Style length is a major determinant of breeding strategies in flowering plants and can vary dramatically between and within species. However, little is known about the genetic and developmental control of style elongation. We characterized the role of two classes of leaf adaxial-abaxial polarity factors, SUPPRESSOR OF GENE SILENCING3 (SGS3) and the YABBY family transcription factors, in the regulation of style elongation in Mimulus lewisii. We also examined the spatiotemporal patterns of auxin response during style development. Loss of SGS3 function led to reduced style length via limiting cell division, and downregulation of YABBY genes by RNA interference resulted in shorter styles by decreasing both cell division and cell elongation. We discovered an auxin response minimum between the stigma and ovary during the early stages of pistil development that marks style differentiation. Subsequent redistribution of auxin response to this region was correlated with style elongation. Auxin response was substantially altered when both SGS3 and YABBY functions were disrupted. We suggest that auxin signaling plays a central role in style elongation and that the way in which auxin signaling controls the different cell division and elongation patterns underpinning natural style length variation is a major question for future research.

Osmotic stress influences root system architecture, and polar auxin transport (PAT) is well established to regulate root growth and development. However, how PAT responds to osmotic stress at the molecular level remains poorly understood. In this study, we explored whether and how the auxin efflux carrier PIN-FORMED3 (PIN3) participates in osmotic stress-induced root growth inhibition in Arabidopsis (Arabidopsis thaliana). We observed that osmotic stress induces a HD-ZIP II transcription factor-encoding gene HOMEODOMAIN ARABIDOPSIS THALIANA2 (HAT2) expression in roots. The hat2 loss-of-function mutant is less sensitive to osmotic stress in terms of root meristem growth. Consistent with this phenotype, whereas the auxin response is downregulated in wild-type roots under osmotic stress, the inhibition of auxin response by osmotic stress was alleviated in hat2 roots. Conversely, transgenic lines overexpressing HAT2 (Pro35S::HAT2) had shorter roots and reduced auxin accumulation compared with wild-type plants. PIN3 expression was significantly reduced in the Pro35S::HAT2 lines. We determined that osmotic stress-mediated repression of PIN3 was alleviated in the hat2 mutant because HAT2 normally binds to the promoter of PIN3 and inhibits its expression. Taken together, our data revealed that osmotic stress inhibits root growth via HAT2, which regulates auxin activity by directly repressing PIN3 transcription.

As one of the main vegetable crops cultivated in the world, the tomato has advantages of high yield and economic benefits, and plays an important role in promoting farmers' income and social and economic growth. However, lateral branches during the growth process of tomato consume considerable nutrients and reduce the yield of tomato. Phytohormones such as strigolactone and auxin can inhibit the formation of lateral branches. However, the mechanism of their interaction is not particularly clear. To better understand the effects of exogenous strigolactone and auxin on tomato, proteome analyses of tomato shoots treated with exogenous GR24 and indole acetic acid were performed using an integrated approach involving tandem mass tag (TMT) labeling and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). We identified 6685 proteins, of which 5822 contained quantitative information. Many differentially expressed proteins (DEPs) were found in different comparisons, including 415, 148, and 130 DEPs in GR24 vs mock, IAA vs mock, and GR24 + IAA vs mock comparisons, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that ‘photosynthesis - antenna proteins’ were significantly enriched in three treatments. Our data can help reveal the interaction between strigolactone and auxin in tomato seedlings.

Alfalfa (Medicago sativa L.) has the advantages of high yield and nutritional value as a perennial forage. However, one of the drawbacks of alfalfa is its susceptibility to drought conditions, which is a global problem in agriculture. The purpose of this study was to reveal the effects of exogenous PopW, a harpin protein from Ralstonia solanacearum, treatment on growth parameters, physiological and biochemical mechanism of alfalfa under drought-stress conditions. Growth parameters, relative water content, free proline, leaf area, total chlorophyll, antioxidative enzymes, endogenous hormones including ABA, CTK, GA, JA, SA and IAA were determined in response to exogenous PopW treatment under drought stress in alfalfa cultivar (Victoria). Moreover, relative gene expressions of drought-related and leaf senescence genes were determined. Under drought stress, alfalfa plants had lower shoot dry weight, shoot length, relative water content, leaf area, and total chlorophyll content, compared to control (non-stressed). However, Exogenous PopW treatment significantly increased growth values, relative water content, free proline, leaf area, total chlorophyll content, catalase, glutathione reductase and superoxide dismutase under drought conditions, compared to control and drought stress alone. Moreover, exogenous PopW treatment significantly increased ABA, GA, JA, SA, IAA contents, up-regulated auxin- and drought-responsive genes, down-regulated leaf senescence genes. Exogenous PopW treatment enhanced drought stress tolerance of alfalfa due to changes of endogenous hormone contents and expression levels of drought stress and leaf senescence genes. The results of the study show that PopW treatment could be used to increase the forage yield of alfalfa on areas having drought problem.

Endophytes colonizing plant tissue play an essential role in plant growth, development, stress tolerance and plant protection from soil-borne diseases. In this study, we report the diversity of cultivable endophytic bacteria associated with marigold (Calendula officinalis L.) by using 16S rRNA gene analysis and their plant beneficial properties. A total of 42 bacterial isolates were obtained from plant tissues of marigold. They belonged to the genera Pantoea, Enterobacter, Pseudomonas, Achromobacter, Xanthomonas, Rathayibacter, Agrobacterium, Pseudoxanthomonas, and Beijerinckia. Among the bacterial strains, P. kilonensis FRT12, and P. rhizosphaerae FST5 showed moderate or vigorous inhibition against three tested plant pathogenic fungi, F. culmorum, F. solani and R. solani. They also demonstrated the capability to produce hydrolytic enzymes and indole-3-acetic acid (IAA). Five out of 16 isolates significantly stimulated shoot and root growth of marigold in a pot experiment. The present study reveals that more than half of the bacterial isolates associated with marigold (C. officinalis L.) provided antifungal activity against one or more plant pathogenic fungi. Our findings suggest that medicinal plants with antimicrobial activity could be a source for selecting microbes with antagonistic activity against fungal plant pathogens or with plant growth stimulating potential. These isolates might be considered as promising candidates for the improvement of plant health.

Bacillusspecies genomes are rich in plant growth-promoting genetic elements.Bacillus subtilisandBacillus velezensisare important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using tenBacillusspecies. From the analysis, pan-genome ofBacillus subtilisandBacillus velezensisare still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

The root phenotype is an important aspect of plant architecture and plays a critical role in plant facilitation of the extraction of water and nutrition from the soil. MicroRNAs (miRNAs) are classes of small RNAs with important roles in regulating endogenous gene expression at the post-transcriptional level that function in a range of plant development processes and in the response to abiotic stresses. However, little is known concerning the molecular mechanism of miRNAs in regulating the generation and development of plant root architecture. Herein, we demonstrated that potato miR160a/b acted as a critical regulator and affected plant root architecture by targeting the mRNA of StARF10 and StARF16 for cleavage. The miR160a/b precursor was cloned from potato. Quantitative PCR assays showed that the expression levels of miR160 and its targets were down- or up-regulated with the development of potato roots, respectively. Moreover, transgenic lines with suppressed stu-miR160 expression were established with the short tandem targets mimic (STTM), and the results showed that the ectopic expression of miR160a/b altered the levels of auxin and the expression of auxin signaling-related genes and caused drastic change in root architecture compared with that in control plants. Suppressing the expression of miR160 led to a severe reduction in root length, an increase in the number of lateral roots, and a decrease in fresh root weight in potato. Collectively, our data established a key role of miR160 in modulating plant root architecture in potato.