As above, so below: Auxin's role in lateral organ development

DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins

Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.

Hormonal involvement in boosting the vegetative vigour underlying caffeine-related improvements in lentil production

Previous studies have shown that caffeine (1,3,7-trimethylxanthine) has some potential for its use as a biostimulant ingredient for boosting lentil production at suboptimal temperatures. However, some limitations to its use include its potential side effects as an emerging contaminant and the current lack of knowledge of its mechanism of action. Here, we aimed to study the mechanisms underlying improved lentil production upon caffeine application. Greenhouse-grown plants treated with caffeine (at 10-5 M, 10-4 M, and 10-3 M) were compared to an untreated, control treatment, and both reproductive and vegetative vigour were evaluated in parallel with endogenous foliar concentrations of phytohormones, including both stress and growth-related hormones. Results showed an enhanced lentil production at the highest caffeine concentration (10-3 M) which might be attributed, at least in part, to a greater vegetative vigour. The hormonal profiling revealed a dual effect. Firstly, there was a specific increase in jasmonoyl-isoleucine (JA-Ile) in the short term, which may provide a priming effect. Secondly, abscisic acid (ABA) content kept at low levels and the active cytokinin (CK) isopentenyl adenine (2-iP) increased and persisted at high levels throughout the reproductive stage. Cytokinin-mediated effects on growth, and more specifically the high CK/ABA ratios in leaves, appeared to mediate caffeine-related effects in boosting vegetative vigour. In conclusion, caffeine emerges as a compelling alkaloid for integration into biostimulant formulations due to its favorable effect in boosting lentil production through an improvement of vegetative vigour. These outcomes appear to be modulated by phytohormones, most notably jasmonates, priming plants for improved performance under suboptimal temperatures, and cytokinins, alongside ABA and its associated ratios, collectively enhancing plant growth and reproductive vigour in challenging conditions.

Mutant IAA21 genes from Dendrocalamus sinicus Chia et J. L. Sun inhibit stem and root growth in transgenic tobacco by interacting with ARF5

Woody bamboos are important resource of industrial fibres. Auxin signaling plays a key role in multiple plant developmental processes, as yet the role of auxin/indole acetic acid (Aux/IAA) in culm development of woody bamboos has not been previously characterized. Dendrocalamus sinicus Chia et J. L. Sun is the largest woody bamboo documented in the world. Here, we identified two alleles of DsIAA21 gene (sIAA21 and bIAA21) from the straight- and bent-culm variants of D. sinicus, respectively, and studied how the domains I, i, and II of DsIAA21 affect the gene transcriptional repression. The results showed that bIAA21 expression was rapidly induced by exogenous auxin in D. sinicus. In transgenic tobacco, sIAA21 and bIAA21 mutated in domains i, and II significantly regulated plant architecture and root development. Stem cross sections revealed that parenchyma cells were smaller in transgenic plants than that in wild type plants. Domain i mutation changed the leucine and proline at position 45 to proline and leucine (siaa21L45P and biaa21P45L) strongly repressed cell expansion and root elongation by reducing the gravitropic response. Substitution of isoleucine with valine in domain II of the full length DsIAA21 resulted in dwarf stature in transgenic tobacco plants. Furthermore, the DsIAA21 interacted with auxin response factor 5 (ARF5) in transgenic tobacco plants, suggesting that DsIAA21 might inhibit stem and root elongation via interacting with ARF5. Taken together, our data indicated that DsIAA21 was a negative regulator of plant development and suggested that amino acid differences in domain i of sIAA21 versus bIAA21 affected their response to auxin, and might play a key role in the formation of the bent culm variant in D. sinicus. Our results not only shed a light on the morphogenetic mechanism in D. sinicus, but also provided new insights into versatile function of Aux/IAAs in plants.

Is auxin enough? Cytokinins and margin patterning in simple leaves

The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.

Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops

Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.

Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize

Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize

Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

Plant growth-promoting rhizobacteria Shewanella putrefaciens and Cronobacter dublinensis enhance drought tolerance of pearl millet by modulating hormones and stress-responsive genes

Drought is a major abiotic stress that affects crop productivity. Endophytic bacteria have been found to alleviate the adverse effects of drought on plants. In the present study, we evaluated the effects of two endophytic bacteria Shewanella putrefaciens strain MCL-1 and Cronobacter dublinensis strain MKS-1 on pearl millet (Pennisetum glaucum (L.) R. Br.) under drought stress conditions. Pearl millet plants were grown under three water levels: field capacity (FC), mild drought stress (MD), and severe drought stress (SD). The effects of inoculation on plant growth, physiological attributes, phytohormone content, and drought stress-responsive genes were assessed. The inoculation of pearl millet seeds with endophytes significantly improved shoot and root dry weight and root architecture of plants grown under FC and drought stress conditions. There was a significant increase in relative water content and proline accumulation in the inoculated plants. Among the phytohormones analyzed, the content of ABA and IAA was significantly higher in endophyte-treated plants under all moisture regimes than in uninoculated plants. C. dublinensis-inoculated plants had higher GA content than uninoculated plants under all moisture regimes. The expression level of genes involved in phytohormone biosynthesis (SbNCED, SbGA20oX, and SbYUC) and coding drought-responsive transcription factors (SbAP2, SbSNAC1 and PgDREB2A) was significantly higher under SD in endophyte-inoculated plants than in uninoculated plants. Thus, these endophytic bacteria presumably enhanced the tolerance of pearl millet to drought stress by modulating root growth, plant hormones, physiology and the expression of genes involved in drought tolerance.

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F7 derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.

Endogenous indole-3-acetic acid and nitric oxide are required for calcium-mediated alleviation of copper oxide nanoparticles toxicity in wheat seedlings

The action of nanoparticles is increasingly being studied in recent years to minimize their toxic impacts. Besides this, efforts are also being made to minimize their toxicity in crop plants by using various chemicals, i.e. nutrients, donors of signaling molecules, plant hormones, and so on. However, associated alleviatory mechanisms are still not well known. Therefore, in the present study, we have investigated the toxicity of CuONPs and its mitigation by exogenously applied calcium (Ca). The focus was on whether indole-3-acetic acid (IAA) or endogenous nitric oxide (NO) has any role in accomplishing this task. CuONPs declined wheat growth due to increased accumulation of Cu and oxidative stress markers such as superoxide radicals, hydrogen peroxide, and lipid peroxidation (malondialdehyde) and it was also accompanied by a decline in endogenous NO. CuONPs also altered the redox status of ascorbate and glutathione by inhibiting the activity of their regenerating enzymes. This collectively leads to cell death in wheat seedlings. However, exogenous supplementation of Ca mitigated toxic effects of CuONPs by reducing the excess accumulation of Cu, which caused remarkable enhancement in growth, protein contents, photosynthetic pigments, and endogenous NO; altogether protecting wheat roots from cell death. Interestingly, addition of 2,3,5-triiodobenzoic acid (TIBA) further increased CuONPs toxicity even in the presence of Ca, but the addition of IAA rescued this effect of TIBA. These results clearly show that Ca mitigates CuONPs toxicity in wheat seedlings by involving IAA. Further, the results also showed that endogenous NO has a positive and indispensable role in Ca-mediated mitigation of CuONPs toxicity in wheat seedlings.

An Essential Function for Auxin in Embryo Development

Embryogenesis in seed plants is the process during which a single cell develops into a mature multicellular embryo that encloses all the modules and primary patterns necessary to build the architecture of the new plant after germination. This process involves a series of cell divisions and coordinated cell fate determinations resulting in the formation of an embryonic pattern with a shoot-root axis and cotyledon(s). The phytohormone auxin profoundly controls pattern formation during embryogenesis. Auxin functions in the embryo through its maxima/minima distribution, which acts as an instructive signal for tissue specification and organ initiation. In this review, we describe how disruptions of auxin biosynthesis, transport, and response severely affect embryo development. Also, the mechanism of auxin action in the development of the shoot-root axis and the three-tissue system is discussed with recent findings. Biological tools that can be implemented to study the auxin function during embryo development are presented, as they may be of interest to the reader.

An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.

SAUR15 Promotes Lateral and Adventitious Root Development via Activating H+-ATPases and Auxin Biosynthesis

SMALL AUXIN-UP RNAs (SAURs) comprise the largest family of early auxin response genes. Some SAURs have been reported to play important roles in plant growth and development, but their functional relationships with auxin signaling remain unestablished. Here, we report Arabidopsis (Arabidopsis thaliana) SAUR15 acts downstream of the auxin response factors ARF6,8 and ARF7,19 to regulate auxin signaling-mediated lateral root (LR) and adventitious root (AR) formation. The loss-of-function mutant saur15-1 exhibits fewer LRs and ARs. By contrast, plants overexpressing SAUR15 exhibit more LRs and ARs. We find that the SAUR15 promoter contains four tandem auxin-responsive elements, which are directly bound by ARF6 and ARF7 and are essential for SAUR15 expression. LR and AR impairment in arf6 and arf7 mutants is partially reduced by ectopic expression of SAUR15 Additionally, we demonstrate that the ARF6,7-upregulated SAUR15 promotes LR and AR development using two mechanisms. On the one hand, SAUR15 interacts with PP2C-D subfamily type 2C protein phosphatases to inhibit their activities, thereby stimulating plasma membrane H+-ATPases, which drives cell expansion and facilitates LR and AR formation. On the other hand, SAUR15 promotes auxin accumulation, potentially by inducing the expression of auxin biosynthesis genes. A resulting increase in free auxin concentration likely triggers LR and AR formation, forming a feedback loop. Our study provides insights and a better understanding of how SAURs function at the molecular level in regulating auxin-mediated LR and AR development.

Genetic dissection of the auxin response network

The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.

An Enzymatically Hydrolyzed Animal Protein-Based Biostimulant (Pepton) Increases Salicylic Acid and Promotes Growth of Tomato Roots Under Temperature and Nutrient Stress

Biostimulants may be particularly interesting for application in agricultural and horticultural crops since they can exert a growth-promoting effect on roots. This may be important for promoting longitudinal and lateral root growth and therefore increasing belowground vegetative growth, which may in turn lead to improved aboveground vegetative growth and increased yields. Here, we examined the effects and mechanism of action of an enzymatically hydrolyzed animal protein-based biostimulant (Pepton) on the root growth of tomato plants, with an emphasis on its possible role on chorismate-derived hormones (auxin, salicylic acid, and melatonin). Tomato plants growing in hydroponic systems were exposed to either nutrient stress conditions (experiment 1) or suboptimal temperatures (experiment 2) in a greenhouse, and the concentration of auxin, salicylic acid, and melatonin in roots were measured just prior and after the application of the biostimulant. Results showed that the application of Pepton exerted a growth-promoting effect on roots in plants growing under suboptimal conditions, which might be associated with enhanced salicylic acid levels in roots. The extent of effects of this enzymatically hydrolyzed animal protein-based biostimulant might strongly depend on the growth conditions and stage of root system development. It is concluded that an enzymatically hydrolyzed animal protein-based biostimulant (Pepton) may exert a positive effect enhancing primary and lateral root growth of tomato plants growing under suboptimal conditions, by stimulating the biosynthesis of specific hormonal pathways, such as salicylic acid under stress.

Lateral Leaflet Suppression 1 (LLS1), encoding the MtYUCCA1 protein, regulates lateral leaflet development in Medicago truncatula

In species with compound leaves, the positions of leaflet primordium initiation are associated with local peaks of auxin accumulation. However, the role of auxin during the late developmental stages and outgrowth of compound leaves remains largely unknown. Using genome resequencing approaches, we identified insertion sites at four alleles of the LATERAL LEAFLET SUPPRESSION1 (LLS1) gene, encoding the auxin biosynthetic enzyme YUCCA1 in Medicago truncatula. Linkage analysis and complementation tests showed that the lls1 mutant phenotypes were caused by the Tnt1 insertions that disrupted the LLS1 gene. The transcripts of LLS1 can be detected in primordia at early stages of leaf initiation and later in the basal regions of leaflets, and finally in vein tissues at late leaf developmental stages. Vein numbers and auxin content are reduced in the lls1-1 mutant. Analysis of the lls1 sgl1 and lls1 palm1 double mutants revealed that SGL1 is epistatic to LLS1, and LLS1 works with PALM1 in an independent pathway to regulate the growth of lateral leaflets. Our work demonstrates that the YUCCA1/YUCCA4 subgroup plays very important roles in the outgrowth of lateral leaflets during compound leaf development of M. truncatula, in addition to leaf venation.

Aspergillus alliaceus infection fatally shifts Orobanche hormones and phenolic metabolism

In this study, the physio pathological effects of Aspergillus alliaceus (Aa, fungi, biocontrol agent) on Orobanche (parasitic plant) were investigated by hormone and phenolic substance tests. In experimental group, Orobanches were treated with the fungi, considering control group was fungus-free. Based on the hormonal tests, in the experimental group, salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA) levels significantly decreased, and only indole acetic acid (IAA) hormone levels were fairly higher than the control group. According to phenolic substance tests, it was found that only gallic acid, syringic acid and caffeic acid values significantly increased compared with control, and catechin and p-coumaric acid values were significantly lower. Consequently, it was determined that Aa pathogenesis (1) considerably reduces the effects of all defence hormones (JA, ABA, SA), (2) operates an inadequate defence based solely on the IAA hormone and several phenolic substances (gallic acid, syringic acid and caffeic acid), (3) and inevitably the fungi lead the Orobanche to a slow and continuous death. The results were evaluated in detail in the light of similar recent article and current literature in terms of biocontrol and pathology.

Endophytic fungus Falciphora oryzae promotes lateral root growth by producing indole derivatives after sensing plant signals

The endophytic fungus Falciphora oryzae was initially isolated from wild rice (Oryza granulata) and colonizes many crop species and promotes plant growth. However, the molecular mechanisms underlying F. oryzae-mediated growth promotion are still unknown. We found that F. oryzae was able to colonize Arabidopsis thaliana. The most dramatic change after F. oryzae inoculation was observed in the root architecture, as evidenced by increased lateral root growth but reduced primary root length, similar to the effect of auxin, a significant plant growth hormone. The expression of genes responsible for auxin biosynthesis, transport, and signalling was regulated in Arabidopsis roots after F. oryzae cocultivation. Indole derivatives were detected at significantly higher levels in liquid media after cocultivation compared with separate cultivation of Arabidopsis and F. oryzae. Consistently, the expression of indole biosynthetic genes was highly upregulated in F. oryzae upon treatment with Arabidopsis exudates. Global analysis of Arabidopsis gene expression at the early stage after F. oryzae cocultivation suggested that signals were exchanged to initiate Arabidopsis-F. oryzae interactions. All these results suggest that signalling molecules from Arabidopsis roots are perceived by F. oryzae and induce the biosynthesis of indole derivatives in F. oryzae, consequently stimulating Arabidopsis lateral root growth.

Mepiquat chloride promotes cotton lateral root formation by modulating plant hormone homeostasis

BACKGROUND

Mepiquat chloride (MC), a plant growth regulator, enhances root growth by promoting lateral root formation in cotton. However, the underlying molecular mechanisms of this phenomenon is still unknown.

METHODS

In this study, we used 10 cotton (Gossypium hirsutum Linn.) cultivars to perform a seed treatment with MC to investigate lateral root formation, and selected a MC sensitive cotton cultivar for dynamic monitor of root growth and transcriptome analysis during lateral root development upon MC seed treatment.

RESULTS

The results showed that MC treated seeds promotes the lateral root formation in a dosage-depended manner and the effective promotion region is within 5 cm from the base of primary root. MC treated seeds induce endogenous auxin level by altering gene expression of both gibberellin (GA) biosynthesis and signaling and abscisic acid (ABA) signaling. Meanwhile, MC treated seeds differentially express genes involved in indole acetic acid (IAA) synthesis and transport. Furthermore, MC-induced IAA regulates the expression of genes related to cell cycle and division for lateral root development.

CONCLUSIONS

Our data suggest that MC orchestrates GA and ABA metabolism and signaling, which further regulates auxin biosynthesis, transport, and signaling to promote the cell division responsible for lateral root formation.

Growth dynamics of the Arabidopsis fruit is mediated by cell expansion

Fruit have evolved a sophisticated tissue and cellular architecture to secure plant reproductive success. Postfertilization growth is perhaps the most dramatic event during fruit morphogenesis. Several studies have proposed that fertilized ovules and developing seeds initiate signaling cascades to coordinate and promote the growth of the accompanying fruit tissues. This dynamic process allows the fruit to conspicuously increase its size and acquire its final shape and means for seed dispersal. All these features are key for plant survival and crop yield. Despite its importance, we lack a high-resolution spatiotemporal map of how postfertilization fruit growth proceeds at the cellular level. In this study, we have combined live imaging, mutant backgrounds in which fertilization can be controlled, and computational modeling to monitor and predict postfertilization fruit growth in Arabidopsis We have uncovered that, unlike leaves, sepals, or roots, fruit do not exhibit a spatial separation of cell division and expansion domains; instead, there is a separation into temporal stages with fertilization as the trigger for transitioning to cell expansion, which drives postfertilization fruit growth. We quantified the coordination between fertilization and fruit growth by imaging no transmitting tract (ntt) mutants, in which fertilization fails in the bottom half of the fruit. By combining our experimental data with computational modeling, we delineated the mobility properties of the seed-derived signaling cascades promoting growth in the fruit. Our study provides the basis for generating a comprehensive understanding of the molecular and cellular mechanisms governing fruit growth and shape.

Co-suppression of NbClpC1 and NbClpC2 alters plant morphology with changed hormone levels in Nicotiana benthamiana

KEY MESSAGE

Co-suppression of chaperonic ClpC1 and ClpC2 in Nicotiana benthamiana significantly affect the development and exogenous application of gibberellin partially rescue the developmental defects. Over the past decade, the Clp protease complex has been identified as being implicated in plastid protein quality control in plant cells. CLPC1 and CLPC2 proteins form the chaperone subunits of the Clp protease complex and unfold protein substrates to thread them into the ClpP complex. Here, using the technique of virus-induced gene silencing (VIGS), we suppressed both Nicotiana benthamiana ClpC1 and ClpC2 (NbClpC1/C2) functioning as chaperone subunits in the protease complex. Co-suppression of NbClpC1/C2 caused chlorosis and retarded-growth phenotype with no seed formation and significantly reduced root length. We found that co-suppression of NbClpC1/C2 also affected stomata and trichome formation and vascular bundle differentiation and patterning. Analysis of phytohormones revealed significant alteration and imbalance of major hormones in the leaves of NbClpC1/C2 co-suppressed plant. We also found that application of gibberellin (GA3) partially rescued the developmental defects. Co-suppression of NbClpC1/C2 significantly affected the development of N. benthamiana and exogenous application of GA3 partially rescued the developmental defects. Overall, our findings demonstrate that CLPC1 and CLPC2 proteins have a pivotal role in plant growth and development.

TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture

Developmental processes that control root system architecture are critical for soil exploration by plants, allowing for uptake of water and nutrients. Conversion of the auxin precursor indole-3-butyric acid (IBA) to active auxin (indole-3-acetic acid; IAA) modulates lateral root formation. However, mechanisms governing IBA-to-IAA conversion have yet to be elucidated. We identified TRANSPORTER OF IBA1 (TOB1) as a vacuolar IBA transporter that limits lateral root formation. Moreover, TOB1, which is transcriptionally regulated by the phytohormone cytokinin, is necessary for the ability of cytokinin to exert inhibitory effects on lateral root production. The increased production of lateral roots in tob1 mutants, TOB1 transport of IBA into the vacuole, and cytokinin-regulated TOB1 expression provide a mechanism linking cytokinin signaling and IBA contribution to the auxin pool to tune root system architecture.

The Systems Biology of Lateral Root Formation: Connecting the Dots

The root system is a major determinant of a plant's access to water and nutrients. The architecture of the root system to a large extent depends on the repeated formation of new lateral roots. In this review, we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions. Moreover, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. In addition, we analyze how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. Finally, we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation, and how one stage drives the transition to the next.

Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits

Climacteric and non-climacteric fruits are differentiated by the ripening process, in particular by the involvement of ethylene, high respiration rates and the nature of the process, being autocatalytic or not, respectively. Here, we focus on the biosynthesis, metabolism and function of three compounds (auxin, salicylic acid and melatonin) sharing not only a common precursor (chorismate), but also regulatory functions in plants, and therefore in fruits. Aside from describing their biosynthesis in plants, with a particular emphasis on common precursors and points of metabolic diversion, we will discuss recent advances on their role in fruit ripening and the regulation of bioactive compounds accumulation, both in climacteric and non-climacteric fruits.

MiR393 and miR390 synergistically regulate lateral root growth in rice under different conditions

BACKGROUND

Plants have evolved excellent ability of flexibly regulating the growth of organs to adapt to changing environment, for example, the modulation of lateral root development in response to environmental stresses. Despite of fundamental discovery that some microRNAs are involved in this process, the molecular mechanisms of how these microRNAs work together are still largely unknown.

RESULTS

Here we show that miR390 induced by auxin promotes lateral root growth in rice. However, this promotion can be suppressed by miR393, which is induced by various stresses and ABA (Abscisic Acid). Results that miR393 responded to ABA stronger and earlier than other stresses implied that ABA likely is authentic factor for inducing miR393. The transgenic lines respectively over-expressing miR393 and OsTAS3a (Oryza sativa Trans-Acting Short RNA precursor 3a) displayed opposite phenotypes in lateral root growth. MiR390 was found to be dominantly expressed at lateral root primordia and roots tips while miR393 mainly expressed in the base part of roots at very low level. When miR393 was up-regulated by various stresses, miR390 expression level fell down. However, the risen expression level of miR390 induced by auxin didn't affect the expression of miR393 and its target OsTIR1 (Transport Inhibitor Response 1). Together with analysis of the two transgenic lines, we provide a model of how the growth of lateral roots in rice is regulated distinctively by the 2 microRNAs.

CONCLUSION

We propose that miR390 induced by auxin triggers the lateral root growth under normal growth conditions, meanwhile miR393 just lurks as a potentially regulative role; Once plants suffer from stresses, miR393 will be induced to negatively regulate miR390-mediated growth of lateral roots in rice.

Lateral root growth in Arabidopsis is controlled by short and long distance signaling through the LRR RLKs XIP1/CEPR1 and CEPR2

Plants rely on lateral roots to explore their soil environment and to maximize their uptake of essential minerals and water. Here we present evidence that the receptor kinases XIP1/CEPR1 and CEPR2 regulate both the initiation of lateral root primordia and emergence of lateral roots locally in the root, while also controlling lateral root extension in response to shoot-derived sucrose in Arabidopsis plants. In addition, mutation of both of these receptors prevents seedlings from responding to sucrose in the media, resulting in longer lateral roots. These results, combined with previous data, establish XIP1/CEPR1 and CEPR2-dependent roles in short- and long-distance pathways regulating different stages of lateral root growth.

Immediate vs. evolutionary consequences of polyploidy on clonal reproduction in an autopolyploid plant

Background and Aims

Clonal reproduction in polyploids is expected to exceed that in diploids, due to either the immediate direct effects of whole-genome duplication (WGD) or selection during establishment. The timing of polyploidy effects on clonality are largely unknown despite its hypothesized influence on polyploid success. This study tests the direction and timing of divergence in clonal traits in diploid and polyploid Chamerion angustifolium.

Methods

Root bud production and biomass allocation patterns were compared between diploids and synthesized tetraploids (neotetraploids), and between neotetraploids and naturally occurring tetraploids grown in a common environment.

Key Results

Neotetraploids produced more root buds and fewer sexual structures than diploids and natural tetraploids; diploids and natural tetraploids had similar root bud numbers and sexual investment. The root bud:inflorescence biomass ratio was 71 % higher in neotetraploids than in natural tetraploids. Root bud location suggests that ramet density in neotetraploid genets could be higher than in diploid genets.

Conclusions

WGD immediately increases investment in asexual vs. sexual reproduction in C. angustifolium, potentially promoting within-cytotype mating and establishment for neopolyploids. However, evolutionary change after the polyploidization event negates the direct effects of WGD. Natural polyploids and diploids have similar root bud production and biomass allocation patterns, probably resulting from habitat- and ploidy-mediated selection on polyploids to become more like diploids. These results highlight the value of studying the effects of polyploidization in young vs. established polyploids.

Auxin production as an integrator of environmental cues for developmental growth regulation

Being sessile organisms, plants have evolved mechanisms allowing them to control their growth and development in response to environmental changes. This occurs by means of complex interacting signalling networks that integrate diverse environmental cues into co-ordinated and highly regulated responses. Auxin is an essential phytohormone that functions as a signalling molecule, driving both growth and developmental processes. It is involved in numerous biological processes ranging from control of cell expansion and cell division to tissue specification, embryogenesis, and organ development. All these processes require the formation of auxin gradients established and maintained through the combined processes of biosynthesis, metabolism, and inter- and intracellular directional transport. Environmental conditions can profoundly affect the plant developmental programme, and the co-ordinated shoot and root growth ought to be fine-tuned to environmental challenges such as temperature, light, and nutrient and water content. The key role of auxin as an integrator of environmental signals has become clear in recent years, and emerging evidence implicates auxin biosynthesis as an essential component of the overall mechanisms of plants tolerance to stress. In this review, we provide an account of auxin's role as an integrator of environmental signals and, in particular, we highlight the effect of these signals on the control of auxin production.

The plant hormone auxin beats the time for oscillating, light-regulated lateral root induction

The molecular mechanism underlying the periodic induction of lateral roots, a paradigmatic example of clock-driven organ formation in plant development, is presently a matter of ongoing, controversial debate. Here we provide experimental evidence that this clock is frequency-modulated by light and that auxin serves as a mediator for translating continuous light signals into discontinuous gene activation signals preceding the initiation of lateral roots in Arabidopsis seedlings. Based on this evidence, we propose a molecular model of an ultradian biological clock involving auxin-dependent degradation of an AUX/IAA-type transcription repressor as a flexible, frequency-controlling delay element. This model widens the bandwidth of biological clocks by adding a new type that allows the pace of organ formation to adapt to the changing environmental demands of the growing plant.

Control of Endogenous Auxin Levels in Plant Root Development

In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.

The AP2/ERF Transcription Factor DRNL Modulates Gynoecium Development and Affects Its Response to Cytokinin

The gynoecium is the female reproductive system in flowering plants. It is a complex structure formed by different tissues, some that are essential for reproduction and others that facilitate the fertilization process and nurture and protect the developing seeds. The coordinated development of these different tissues during the formation of the gynoecium is important for reproductive success. Both hormones and genetic regulators guide the development of the different tissues. Auxin and cytokinin in particular have been found to play important roles in this process. On the other hand, the AP2/ERF2 transcription factor BOL/DRNL/ESR2/SOB is expressed at very early stages of aerial organ formation and has been proposed to be a marker for organ founder cells. In this work, we found that this gene is also expressed at later stages during gynoecium development, particularly at the lateral regions (the region related to the valves of the ovary). The loss of DRNL function affects gynoecium development. Some of the mutant phenotypes present similarities to those observed in plants treated with exogenous cytokinins, and AHP6 has been previously proposed to be a target of DRNL. Therefore, we explored the response of drnl-2 developing gynoecia to cytokinins, and found that the loss of DRNL function affects the response of the gynoecium to exogenously applied cytokinins in a developmental-stage-dependent manner. In summary, this gene participates during gynoecium development, possibly through the dynamic modulation of cytokinin homeostasis and response.

Plants under Stress: Involvement of Auxin and Cytokinin

Plant growth and development are critically influenced by unpredictable abiotic factors. To survive fluctuating changes in their environments, plants have had to develop robust adaptive mechanisms. The dynamic and complementary actions of the auxin and cytokinin pathways regulate a plethora of developmental processes, and their ability to crosstalk makes them ideal candidates for mediating stress-adaptation responses. Other crucial signaling molecules responsible for the tremendous plasticity observed in plant morphology and in response to abiotic stress are reactive oxygen species (ROS). Proper temporal and spatial distribution of ROS and hormone gradients is crucial for plant survival in response to unfavorable environments. In this regard, the convergence of ROS with phytohormone pathways acts as an integrator of external and developmental signals into systemic responses organized to adapt plants to their environments. Auxin and cytokinin signaling pathways have been studied extensively. Nevertheless, we do not yet understand the impact on plant stress tolerance of the sophisticated crosstalk between the two hormones. Here, we review current knowledge on the function of auxin and cytokinin in redirecting growth induced by abiotic stress in order to deduce their potential points of crosstalk.

Periodic Lateral Root Priming: What Makes It Tick?

Conditioning small groups of root pericycle cells for future lateral root formation has a major impact on overall plant root architecture. This priming of lateral roots occurs rhythmically, involving temporal oscillations in auxin response in the root tip. During growth, this process generates a spatial pattern of prebranch sites, an early stage in lateral root formation characterized by a stably maintained high auxin response. To date, the molecular mechanism behind this rhythmicity has remained elusive. Some data implicate a cell-autonomous oscillation in gene expression, while others strongly support the importance of tissue-level modulations in auxin fluxes. Here, we summarize the experimental data on periodic lateral root priming. We present a theoretical framework that distinguishes between a priming signal and its subsequent memorization and show how major roles for auxin fluxes and gene expression naturally emerge from this framework. We then discuss three mechanisms that could potentially induce oscillations of auxin response: cell-autonomous oscillations, Turing-type patterning, and tissue-level oscillations in auxin fluxes, along with specific properties of lateral root priming that may be used to discern which type of mechanism is most likely to drive lateral root patterning. We conclude with suggestions for future experiments and modeling studies.

The vascular plants: open system of growth

What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom. One of the foundations of their success relies on the plant-pollinator relationship, essentially unique to angiosperms that pushed large speciation in both plants and insects and on the presence of the carpel, the structure devoted to seed enclosure. A seed represents the main organ preserving the genetic information of a plant; during embryogenesis, the primary axis of development is established by two groups of pluripotent cells: the shoot apical meristem (SAM), responsible for gene rating all aboveground organs, and the root apical meristem (RAM), responsible for producing all underground organs. During postembryonic shoot development, axillary meristem (AM) initiation and outgrowth are responsible for producing all secondary axes of growth including inflorescence branches or flowers. The production of AMs is tightly linked to the production of leaves and their separation from SAM. As leaf primordia are formed on the flanks of the SAM, a region between the apex and the developing organ is established and referred to as boundary zone. Interaction between hormones and the gene network in the boundary zone is fundamental for AM initiation. AMs only develop at the adaxial base of the leaf; thus, AM initiation is also strictly associated with leaf polarity. AMs function as new SAMs: form axillary buds with a few leaves and then the buds can either stay dormant or develop into shoot branches to define a plant architecture, which in turn affects assimilate production and reproductive efficiency. Therefore, the radiation of angiosperms was accompanied by a huge diversification in growth forms that determine an enormous morphological plasticity helping plants to environmental changes. In this review, we focused on the developmental processes of AM initiation and outgrowth. In particular, we summarized the primary growth of SAM, the key role of positional signals for AM initiation, and the dissection of molecular players involved in AM initiation and outgrowth. Finally, the interaction between phytohormone signals and gene regulatory network controlling AM development was discussed.

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

Identifying key information in transcriptomic data is very important, especially when the "omic" study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrichment analysis, protein-protein interaction networks and gene visualization tools was employed. A total of 13,230 genes of the 12 studies were analyzed with functional data mining tools: 5,215 were upregulated, 8,015 were downregulated. Gene set enrichment analysis pointed out that photosynthesis was inhibited by Erwinia amylovora and fungal pathogens. Different hormonal crosstalk was linked with responses to different pathogens. Gibberellin-related pathways, ABA-related were mostly repressed by fungal pathogens. Relating to transcription factors, genes encoding MYBs and WRKY2 were downregulated by fungal pathogens and 12 WRKYs were commonly regulated by different biotic stresses The protein-protein interaction analysis discovered the presence of several proteins affected by more than one biotic stress including a WRKY40 and some highly interactive proteins such as heat shock proteins. This study represents a first preliminary curated meta-analysis of apple transcriptomic responses to biotic stresses.

Molecular cloning, phylogenetic analysis, and expression patterns of LATERAL SUPPRESSOR-LIKE and REGULATOR OF AXILLARY MERISTEM FORMATION-LIKE genes in sunflower (Helianthus annuus L.)

The wild sunflower (Helianthus annuus) plants develop a highly branched form with numerous small flowering heads. The origin of a no branched sunflower, producing a single large head, has been a key event in the domestication process of this species. The interaction between hormonal factors and several genes organizes the initiation and outgrowth of axillary meristems (AMs). From sunflower, we have isolated two genes putatively involved in this process, LATERAL SUPPRESSOR (LS)-LIKE (Ha-LSL) and REGULATOR OF AXILLARY MERISTEM FORMATION (ROX)-LIKE (Ha-ROXL), encoding for a GRAS and a bHLH transcription factor (TF), respectively. Typical amino acid residues and phylogenetic analyses suggest that Ha-LSL and Ha-ROXL are the orthologs of the branching regulator LS and ROX/LAX1, involved in the growth habit of both dicot and monocot species. qRT-PCR analyses revealed a high accumulation of Ha-LSL transcripts in roots, vegetative shoots, and inflorescence shoots. By contrast, in internodal stems and young leaves, a lower amount of Ha-LSL transcripts was observed. A comparison of transcription patterns between Ha-LSL and Ha-ROXL revealed some analogies but also remarkable differences; in fact, the gene Ha-ROXL displayed a low expression level in all organs analyzed. In situ hybridization (ISH) analysis showed that Ha-ROXL transcription was strongly restricted to a small domain within the boundary zone separating the shoot apical meristem (SAM) and the leaf primordia and in restricted regions of the inflorescence meristem, beforehand the separation of floral bracts from disc flower primordia. These results suggested that Ha-ROXL may be involved to establish a cell niche for the initiation of AMs as well as flower primordia. The accumulation of Ha-LSL transcripts was not restricted to the boundary zones in vegetative and inflorescence shoots, but the mRNA activity was expanded in other cellular domains of primary shoot apical meristem as well as AMs. In addition, Ha-LSL transcript accumulation was also detected in leaves and floral primordia at early stages of development. These results were corroborated by qRT-PCR analyses that evidenced high levels of Ha-LSL transcripts in very young leaves and disc flowers, suggesting a role of Ha-LSL for the early outgrowth of lateral primordia.

Genetic Control of Lateral Root Formation in Cereals

Cereals form complex root systems composed of different root types. Lateral root formation is a major determinant of root architecture and is instrumental for the efficient uptake of water and nutrients. Positioning and patterning of lateral roots and cell types involved in their formation are unique in monocot cereals. Recent discoveries advanced the molecular understanding of the intrinsic genetic control of initiation and elongation of lateral roots in cereals by distinct, in part root-type-specific genetic programs. Moreover, molecular networks modulating the plasticity of lateral root formation in response to water and nutrient availability and arbuscular mycorrhizal fungal colonization have been identified. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in cereals.