The Pivotal Role of Ethylene in Plant Growth

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

The endophytic mutualism of plants with microorganisms often leads to several benefits to its host including plant health and survival under extreme environments. Arnebia euchroma is an endangered medicinal plant that grows naturally in extreme cold and arid environments in the Himalayas. The present study was conducted to decipher the cultivable endophytic diversity associated with the leaf and root tissues of A. euchroma. A total of 60 bacteria and 33 fungi including nine yeasts were isolated and characterized at the molecular level. Among these, Proteobacteria was the most abundant bacterial phylum with the abundance of Gammaproteobacteria (76.67%) and genus Pseudomonas. Ascomycota was the most abundant phylum (72.73%) dominated by class Eurotiales (42.42%) and genus Penicillium among isolated fungal endophytes. Leaf tissues showed a higher richness (S_chao1) of both bacterial and fungal communities as compared to root tissues. The abilities of endophytes to display plant growth promotion (PGP) through phosphorus (P) and potassium (K) solubilization and production of ACC deaminase (ACCD), indole acetic acid (IAA), and siderophores were also investigated under in vitro conditions. Of all the endophytes, 21.51% produced ACCD, 89.25% solubilized P, 43.01% solubilized K, 68.82% produced IAA, and 76.34% produced siderophores. Six bacteria and one fungal endophyte displayed all the five PGP traits. The study demonstrated that A. euchroma is a promising source of beneficial endophytes with multiple growth-promoting traits. These endophytes can be used for improving stress tolerance in plants under nutrient-deficient and cold/arid conditions.

Density Dependence Influences the Efficacy of Wastewater Remediation by Lemna minor

As part of a circular economy (CE) approach to food production systems, Lemnaceae, i.e., duckweed species, can be used to remediate wastewater due to rapid nutrient assimilation and tolerance of non-optimal growing conditions. Further, given rapid growth rates and high protein content, duckweed species are a valuable biomass. An important consideration for duckweed-mediated remediation is the density at which the plants grow on the surface of the wastewater, i.e., how much of the surface of the medium they cover. Higher duckweed density is known to have a negative effect on duckweed growth, which has implications for the development of duckweed-based remediation systems. In the present study, the effects of density (10-80% plant surface coverage) on Lemna minor growth, chlorophyll fluorescence and nutrient remediation of synthetic dairy processing wastewater were assessed in stationary (100 mL) and re-circulating non-axenic (11.7 L) remediation systems. Overall, L. minor growth, and TN and TP removal rates decreased as density increased. However, in the stationary system, absolute TN and TP removal were greater at higher densities (50-80% coverage). The exact cause of density related growth reduction in duckweed is unclear, especially at densities well below 100% surface coverage. A further experiment comparing duckweed grown at 'low' and 'high' density conditions with the same biomass and media volume conditions, showed that photosynthetic yield, Y(II), is reduced at high density despite the same nutrient availability at both densities, and arguably similar shading. The results demonstrate a negative effect of high density on duckweed growth and nutrient uptake, and point towards signals from neighbouring duckweed colonies as the possible cause.

Effects of 1-MCP treatment on sprouting and preservation of ginger rhizomes during storage at room temperature

The purpose of this study was to explore the effects of 1-MCP on the sprouting and preservation of ginger rhizomes during storage at room temperature. Ginger rhizomes were treated with 1 µL L-1 1-methylcyclopropene (1-MCP) and stored at 23 ± 0.2 °C. Our data showed that application of 1-MCP reduced the rate of sprouting during storage compared with the control rhizome. Respiration rate and the reducing sugar content were also reduced following 1-MCP treatment, while the starch content increased. 1-MCP treatment increased the total phenol content and inhibited polyphenol oxidase (PPO) activity. 1-MCP treatment was also associated with a higher ascorbic acid content but a reduced crude fiber content. The generation of superoxide anion free radicals (O2-), hydrogen peroxide (H2O2) and malondialdehyde (MDA) was lower following 1-MCP treatment, while the activities of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) were higher compared with the controls. These results suggested that application of 1-MCP could reduce sprouting rates, decrease the accumulation of ROS, and maintain the quality of ginger rhizomes during storage at room temperature. It would be useful to further explore the role and mechanisms of action of ethylene in regulating the sprouting of ginger rhizomes.

Ultrasonic treatment suppresses ethylene signaling and prolongs the freshness of spinach

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Ultrasonication revives and prolongs freshness of spinach.

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Ultrasonication induces stomatal closure in spinach leaves.

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Ultrasonication stimulates EBF1/EBF2 expression and suppresses ethylene signaling.

There have been many studies investigating the application of ultrasonic treatment in vegetables and fruits to eliminate surface contaminants including dirt, microbes, and chemicals such as pesticides. Using a jet ultrasonic washer developed by us to wash food materials, we found that ultrasonic treatment prolonged the freshness of spinach. The stomata closed in the ultrasonicated spinach leaves, whereas those in spinach soaked in water remained open during 24-h storage. Transcriptome analysis revealed that the expression of Ethylene-insensitive 3 Binding F-box protein 1 and 2 (EBF1 and EBF2), which inhibit ethylene signaling, was remarkably increased by ultrasonic treatment, suggesting that the suppression of ethylene signaling allowed stomatal closure in response to abscisic acid signals in the ultrasonicated leaves. Although the precise mechanism of the induction of EBF1 and EBF2 expression by ultrasonic treatment needs to be addressed in further studies, our findings suggest that ultrasonic treatment can be applied to revive and prolong the freshness of leaf vegetables, as well as for their cleaning.

The RING E3 ligase SDIR1 destabilizes EBF1/EBF2 and modulates the ethylene response to ambient temperature fluctuations in Arabidopsis

The gaseous phytohormone ethylene mediates numerous aspects of plant growth and development as well as stress responses. The F-box proteins EIN3-binding F-box protein 1 (EBF1) and EBF2 are key components that ubiquitinate and degrade the master transcription factors ethylene insensitive 3 (EIN3) and EIN3-like 1 (EIL1) in the ethylene response pathway. Notably, EBF1 and EBF2 themselves undergo the 26S proteasome-mediated proteolysis induced by ethylene and other stress signals. However, despite their importance, little is known about the mechanisms regulating the degradation of these proteins. Here, we show that a really interesting new gene (RING)-type E3 ligase, salt- and drought-induced ring finger 1 (SDIR1), positively regulates the ethylene response and promotes the accumulation of EIN3. Further analyses indicate that SDIR1 directly interacts with EBF1/EBF2 and targets them for ubiquitination and proteasome-dependent degradation. We show that SDIR1 is required for the fine tuning of the ethylene response to ambient temperature changes by mediating temperature-induced EBF1/EBF2 degradation and EIN3 accumulation. Thus, our work demonstrates that SDIR1 functions as an important modulator of ethylene signaling in response to ambient temperature changes, thereby enabling plant adaptation under fluctuating environmental conditions.

Arbuscular Mycorrhiza-Mediated Regulation of Polyamines and Aquaporins During Abiotic Stress: Deep Insights on the Recondite Players

Environmental stresses of (a)biotic origin induce the production of multitudinous compounds (metabolites and proteins) as protective defense mechanisms in plants. On account of the regulation of some of these compounds, arbuscular mycorrhizal fungi (AMF) reinforce the inherent tolerance of plants toward the stress of different origins and kind. This article reviews two specific fundamental mechanisms that are categorically associated with mycorrhiza in alleviating major abiotic stresses, salt, drought, and heavy metal (HM) toxicity. It puts emphasis on aquaporins (AQPs), the conduits of water and stress signals; and polyamines (PAs), the primordial stress molecules, which are regulated by AMF to assure water, nutrient, ion, and redox homeostasis. Under stressful conditions, AMF-mediated host AQP responses register distinct patterns: an upregulation to encourage water and nutrient uptake; a downregulation to restrict water loss and HM uptake; or no alterations. The patterns thereof are apparently an integrative outcome of the duration, intensity, and type of stress, AMF species, the interaction of fungal AQPs with that of plants, and the host type. However, the cellular and molecular bases of mycorrhizal influence on host AQPs are largely unexplored. The roles of PAs in augmenting the antioxidant defense system and improving the tolerance against oxidative stress are well-evident. However, the precise mechanism by which mycorrhiza accords stress tolerance by influencing the PA metabolism per se is abstruse and broadly variable under different stresses and plant species. This review comprehensively analyzes the current state-of-art of the involvement of AMF in "PA and AQP modulation" under abiotic stress and identifies the lesser-explored landscapes, gaps in understanding, and the accompanying challenges. Finally, this review outlines the prospects of AMF in realizing sustainable agriculture and provides insights into potential thrust areas of research on AMF and abiotic stress.

Temperature regulation of plant hormone signaling during stress and development

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview of known temperature-sensitive or temperature-reinforced molecular hubs in hormone biosynthesis, homeostasis, signaling and downstream responses. These include recent advances on temperature regulation at the genomic, transcriptional, post-transcriptional and post-translational levels - directly linking some plant hormone pathways to known thermosensing mechanisms. Where applicable, diverse plant species and various temperature ranges will be presented, along with emerging principles and themes. It is anticipated that a grand unifying synthesis of current and future fundamental outlooks on how fluctuating temperatures regulate important plant hormone signaling pathways can be leveraged towards forward-thinking solutions to develop climate-smart crops amidst our dynamically changing world.

Elevated Temperature Induced Adaptive Responses of Two Lupine Species at Early Seedling Phase

This study aimed to investigate the impact of climate warming on hormonal traits of invasive and non-invasive plants at the early developmental stage. Two different lupine species—invasive Lupinus polyphyllus Lindl. and non-invasive Lupinus luteus L.—were used in this study. Plants were grown in climate chambers under optimal (25 °C) and simulated climate warming conditions (30 °C). The content of phytohormone indole-3-acetic acid (IAA), ethylene production and the adaptive growth of both species were studied in four-day-old seedlings. A higher content of total IAA, especially of IAA-amides and transportable IAA, as well as higher ethylene emission, was determined to be characteristic for invasive lupine both under optimal and simulated warming conditions. It should be noted that IAA-L-alanine was detected entirely in the invasive plants under both growth temperatures. Further, the ethylene emission values increased significantly in invasive lupine hypocotyls under 30 °C. Invasive plants showed plasticity in their response by reducing growth in a timely manner and adapting to the rise in temperature. Based on the data of the current study, it can be suggested that the invasiveness of both species may be altered under climate warming conditions.

Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis

Gene expression profile or transcriptome can represent cellular states, thus understanding gene regulation mechanisms can help understand how cells respond to external stress. Interaction between transcription factor (TF) and target gene (TG) is one of the representative regulatory mechanisms in cells. In this paper, we present a novel computational method to construct condition-specific transcriptional networks from transcriptome data. Regulatory interaction between TFs and TGs is very complex, specifically multiple-to-multiple relations. Experimental data from TF Chromatin Immunoprecipitation sequencing is useful but produces one-to-multiple relations between TF and TGs. On the other hand, co-expression networks of genes can be useful for constructing condition transcriptional networks, but there are many false positive relations in co-expression networks. In this paper, we propose a novel method to construct a condition-specific and combinatorial transcriptional network, applying kernel canonical correlation analysis (kernel CCA) to identify multiple-to-multiple TF-TG relations in certain biological condition. Kernel CCA is a well-established statistical method for computing the correlation of a group of features vs. another group of features. We, therefore, employed kernel CCA to embed TFs and TGs into a new space where the correlation of TFs and TGs are reflected. To demonstrate the usefulness of our network construction method, we used the blood transcriptome data for the investigation on the response to high fat diet in a human and an arabidopsis data set for the investigation on the response to cold/heat stress. Our method detected not only important regulatory interactions reported in previous studies but also novel TF-TG relations where a module of TF is regulating a module of TGs upon specific stress.

Mycorrhizal-Bacterial Amelioration of Plant Abiotic and Biotic Stress

Soil microbiota plays an important role in the sustainable production of the different types of agrosystems. Among the members of the plant microbiota, mycorrhizal fungi (MF) and plant growth-promoting bacteria (PGPB) interact in rhizospheric environments leading to additive and/or synergistic effects on plant growth and heath. In this manuscript, the main mechanisms used by MF and PGPB to facilitate plant growth are reviewed, including the improvement of nutrient uptake, and the reduction of ethylene levels or biocontrol of potential pathogens, under both normal and stressful conditions due to abiotic or biotic factors. Finally, it is necessary to expand both research and field use of bioinoculants based on these components and take advantage of their beneficial interactions with plants to alleviate plant stress and improve plant growth and production to satisfy the demand for food for an ever-increasing human population.

Rhizosphere plant-microbe interactions under water stress

Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.

Essential Roles of the Linker Sequence Between Tetratricopeptide Repeat Motifs of Ethylene Overproduction 1 in Ethylene Biosynthesis

Ethylene Overproduction 1 (ETO1) is a negative regulator of ethylene biosynthesis. However, the regulation mechanism of ETO1 remains largely unclear. Here, a novel eto1 allele (eto1-16) was isolated with typical triple phenotypes due to an amino acid substitution of G480C in the uncharacterized linker sequence between the TPR1 and TPR2 motifs. Further genetic and biochemical experiments confirmed the eto1-16 mutation site. Sequence analysis revealed that G480 is conserved not only in two paralogs, EOL1 and EOL2, in Arabidopsis, but also in the homologous protein in other species. The glycine mutations (eto1-11, eto1-12, and eto1-16) do not influence the mRNA abundance of ETO1, which is reflected by the mRNA secondary structure similar to that of WT. According to the protein-protein interaction analysis, the abnormal root phenotype of eto1-16 might be caused by the disruption of the interaction with type 2 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACSs) proteins. Overall, these data suggest that the linker sequence between tetratricopeptide repeat (TPR) motifs and the glycine in TPR motifs or the linker region are essential for ETO1 to bind with downstream mediators, which strengthens our knowledge of ETO1 regulation in balancing ACSs.

Pinus pinaster Early Hormonal Defence Responses to Pinewood Nematode (Bursaphelenchus xylophilus) Infection

The pinewood nematode (PWN) is the causal agent of pine wilt disease, a pathology that affects conifer forests, mainly Pinus spp. PWN infection can induce the expression of phytohormone-related genes; however, changes at the early phytohormone level have not yet been explored. Phytohormones are low-abundance metabolites, and thus, difficult to quantify. Moreover, most methodologies focus mainly on Arabidopsis or crop species. This work aimed to validate a fast (run time 6.6 min) liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS) analytical method to quantify 14 phytohormones in Pinus pinaster stem tissues. This method was further applied to evaluate, for the first time, early phytohormone changes in susceptible and resistant phenotypes of P. pinaster 24, 48 and 72 h after inoculation (HAI) with PWN. A significant increase in salicylic acid (SA, 48 and 72 HAI) and jasmonic acid methyl ester (JA-ME, 72 HAI) was observed in susceptible phenotypes. Results indicate that the higher susceptibility of P. pinaster to PWN infection might result from an inefficient trigger of hypersensitive responses, with the involvement of JA and SA pathways. This work provides an important update in forest research, and adds to the current knowledge of Pinus spp. defence responses to PWN infection.

Ethylene activation of carotenoid biosynthesis by a novel transcription factor CsERF061

Chromoplast-specific lycopene β-cyclase (LCYb2) is a critical carotenogenic enzyme, which controls the massive accumulation of downstream carotenoids, especially provitamin A carotenoids, in citrus. Its regulatory metabolism is largely unknown. Here, we identified a group I ethylene response factor, CsERF061, in citrus by yeast one-hybrid screen with the promoter of LCYb2. The expression of CsERF061 was induced by ethylene. Transcript and protein levels of CsERF061 were increased during fruit development and coloration. CsERF061 is a nucleus-localized transcriptional activator, which directly binds to the promoter of LCYb2 and activates its expression. Overexpression of CsERF061 in citrus calli and tomato fruits enhanced carotenoid accumulation by increasing the expression of key carotenoid pathway genes, and increased the number of chromoplasts needed to sequester the elevated concentrations of carotenoids, which was accompanied by changes in the concentrations of abscisic acid and gibberellin. Electrophoretic mobility shift and dual-luciferase assays verified that CsERF061 activates the promoters of nine other key carotenoid pathway genes, PSY1, PDS, CRTISO, LCYb1, BCH, ZEP, NCED3, CCD1, and CCD4, revealing the multitargeted regulation of CsERF061. Collectively, our findings decipher a novel regulatory network of carotenoid enhancement by CsERF061, induced by ethylene, which will be useful for manipulating carotenoid accumulation in citrus and other plants.

Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz)

The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F₁ population was constructed. The genetic map had a total size of 5,484.07 centimorgan (cM), containing 5,956 single nucleotide polymorphisms (SNPs) based on Specific Length Amplified Fragment sequencing. Six fast-growing related stable QTL were identified on six chromosomes, and five stable QTL were identified by a principal component analysis (PCA). By combining the RNA-seq analysis for the two parents and two progenies with the qRT-PCR analysis, four candidate genes, annotated as DnaJ, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), Caffeic acid 3-O-methyltransferase 1 (COMT1), and Dirigent protein 6 (DIR6), that may regulate height growth were identified. Several lignin biosynthesis-related genes that may take part in height growth were detected. In addition, 21 hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of TH and DBH.

Effects of Increased 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity in Bradyrhizobium sp. SUTN9-2 on Mung Bean Symbiosis under Water Deficit Conditions

Bacteria exhibiting 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, which inhibits the biosynthesis of ethylene in higher plants, promote plant growth through the degradation of ethylene precursors, such as ACC. ACC deaminase activity in Bradyrhizobium sp. SUTN9-2 was enhanced by genetic engineering and adaptive laboratory evolution (ALE)-based methods. The transferal of a plasmid containing the acdR and acdS genes into SUTN9-2 was genetic engineering improved, while the ALE method was performed based on the accumulation of an adaptive bacterial population that continuously grew under specified growth conditions for a long time. ACC deaminase enzyme activity was 8.9–fold higher in SUTN9-2:pMG103::acdRS and 1.4–fold higher in SUTN9-2 (ACCDadap) than in the wild-type strain. The effects of increased activity were examined in the host plant (Vigna radiata (L.) R.Wilczek SUT1). The improved strains enhanced nodulation in early stage of plant growth. SUTN9-2:pMG103::acdRS also maintained nitrogen fixation under water deficit conditions and increased the plant biomass after rehydration. Changes in nucleotides and amino acids in the AcdS protein of SUTN9-2 (ACCDadap) were then investigated. Some nucleotides predicted to be located in the ACC-binding site were mutated. These mutations may have increased ACC deaminase activity, which enhanced both symbiotic interactions and drought tolerance and promoted recovery after rehydration more than lower ACC deaminase activity. Adaptive evolution represents a promising strategy for further applications in the field.

Host-produced ethylene is required for marked cell expansion and endoreduplication in dodder search hyphae

The genus Cuscuta comprises stem holoparasitic plant species with wide geographic distribution. Cuscuta spp. obtain water, nutrients, proteins, and mRNA from their host plants via a parasitic organ called the haustorium. As the haustorium penetrates into the host tissue, search hyphae elongate within the host tissue and finally connect with the host's vascular system. Invasion by Cuscuta spp. evokes various reactions within the host plant's tissues. Here, we show that, when Arabidopsis (Arabidopsis thaliana) is invaded by Cuscuta campestris, ethylene biosynthesis by the host plant promotes elongation of the parasite's search hyphae. The expression of genes encoding 1-aminocylclopropane-1-carboxylic acid (ACC) synthases, ACC SYNTHASE2 (AtACS2) and ACC SYNTHASE6 (AtACS6), was activated in the stem of Arabidopsis plants upon invasion by C. campestris. When the ethylene-deficient Arabidopsis acs octuple mutant was invaded by C. campestris, cell elongation and endoreduplication of the search hyphae were significantly reduced, and the inhibition of search hyphae growth was complemented by exogenous application of ACC. In contrast, in the C. campestris-infected Arabidopsis ethylene-insensitive mutant etr1-3, no growth inhibition of search hyphae was observed, indicating that ETHYLENE RESPONSE1-mediated ethylene signaling in the host plant is not essential for parasitism by C. campestris. Overall, our results suggest that C. campestris recognizes host-produced ethylene as a stimulatory signal for successful invasion.

Early transcriptome changes induced by the Geminivirus C4 oncoprotein: setting the stage for oncogenesis

BACKGROUND

The Beet curly top virus C4 oncoprotein is a pathogenic determinant capable of inducing extensive developmental abnormalities. No studies to date have investigated how the transcriptional profiles differ between plants expressing or not expressing the C4 oncoprotein.

RESULTS

We investigated early transcriptional changes in Arabidopsis associated with expression of the Beet curly top virus C4 protein that represent initial events in pathogenesis via a comparative transcriptional analysis of mRNAs and small RNAs. We identified 48 and 94 differentially expressed genes at 6- and 12-h post-induction versus control plants. These early time points were selected to focus on direct regulatory effects of C4 expression. Since previous evidence suggested that the C4 protein regulated the brassinosteroid (BR)-signaling pathway, differentially expressed genes could be divided into two groups: those responsive to alterations in the BR-signaling pathway and those uniquely responsive to C4. Early transcriptional changes that disrupted hormone homeostasis, 18 and 19 differentially expressed genes at both 6- and 12-hpi, respectively, were responsive to C4-induced regulation of the BR-signaling pathway. Other C4-induced differentially expressed genes appeared independent of the BR-signaling pathway at 12-hpi, including changes that could alter cell development (4 genes), cell wall homeostasis (5 genes), redox homeostasis (11 genes) and lipid transport (4 genes). Minimal effects were observed on expression of small RNAs.

CONCLUSION

This work identifies initial events in genetic regulation induced by a geminivirus C4 oncoprotein. We provide evidence suggesting the C4 protein regulates multiple regulatory pathways and provides valuable insights into the role of the C4 protein in regulating initial events in pathogenesis.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

GENOMES UNCOUPLED1-independent retrograde signaling targets the ethylene pathway to repress photomorphogenesis

When germinating in the light, Arabidopsis (Arabidopsis thaliana) seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening, and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrograde signals are not yet fully known. Here, we show that lincomycin-treated seedlings (which lack developed chloroplasts) show strong phenotypic similarities to seedlings treated with ethylene (ET) precursor 1-aminocyclopropane-1-carboxylic acid, as both signals inhibit cotyledon separation in the light. We show that the lincomycin-induced phenotype partly requires a functioning ET signaling pathway, but could not detect increased ET emissions in response to the lincomycin treatment. The two treatments show overlap in upregulated gene transcripts, downstream of transcription factors ETHYLENE INSENSITIVE3 and EIN3-LIKE1. The induction of the ET signaling pathway is triggered by an unknown retrograde signal acting independently of GENOMES UNCOUPLED1. Our data show how two apparently different stress responses converge to optimize photomorphogenesis.

A Conceptual Framework for Incorporation of Composting in Closed-Loop Urban Controlled Environment Agriculture

Controlled environment agriculture (CEA), specifically advanced greenhouses, plant factories, and vertical farms, has a significant role to play in the urban agri-food landscape through provision of fresh and nutritious food for urban populations. With the push towards improving sustainability of these systems, a circular or closed-loop approach for managing resources is desirable. These crop production systems generate biowaste in the form of crop and growing substrate residues, the disposal of which not only impacts the immediate environment, but also represents a loss of valuable resources. Closing the resource loop through composting of crop residues and urban biowaste is presented. Composting allows for the recovery of carbon dioxide and plant nutrients that can be reused as inputs for crop production, while also providing a mechanism for managing and valorizing biowastes. A conceptual framework for integrating carbon dioxide and nutrient recovery through composting in a CEA system is described along with potential environmental benefits over conventional inputs. Challenges involved in the recovery and reuse of each component, as well as possible solutions, are discussed. Supplementary technologies such as biofiltration, bioponics, ozonation, and electrochemical oxidation are presented as means to overcome some operational challenges. Gaps in research are identified and future research directions are proposed.

Gene expression patterns in shoots of Camelina sativa with enhanced salinity tolerance provided by plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase or expression of the corresponding acdS gene

Growth of plants in soil inoculated with plant growth promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase or expression of the corresponding acdS gene in transgenic lines reduces the decline in shoot length, shoot weight and photosynthetic capacity triggered by salt stress in Camelina sativa. Reducing the levels of ethylene attenuated the salt stress response as inferred from decreases in the expression of genes involved in development, senescence, chlorosis and leaf abscission that are highly induced by salt to levels that may otherwise have a negative effect on plant growth and productivity. Growing plants in soil treated with Pseudomonas migulae 8R6 negatively affected ethylene signaling, auxin and JA biosynthesis and signalling, but had a positive effect on the regulation of genes involved in GA signaling. In plants expressing acdS, the expression of the genes involved in auxin signalling was positively affected, while the expression of genes involved in cytokinin degradation and ethylene biosynthesis were negatively affected. Moreover, fine-tuning of ABA signaling appears to result from the application of ACC deaminase in response to salt treatment. Moderate expression of acdS under the control of the root specific rolD promoter or growing plants in soil treated with P. migulae 8R6 were more effective in reducing the expression of the genes involved in ethylene production and/or signaling than expression of acdS under the more active Cauliflower Mosaic Virus 35S promoter.

Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

BES1 negatively regulates the expression of ACC oxidase 2 to control the endogenous level of ethylene in Arabidopsis thaliana

Quantitative reverse transcription PCR (qRT-PCR) analysis and ProACO2::GUS expression showed that ACO2 was highly expressed in the shoots of Arabidopsis seedlings under light conditions. Exogenously applied aminocyclopropane-1-carboxylic acid (ACC) enhanced the expression of ACO2, whereas Co²⁺ ions suppressed its expression. In comparison with wild-type seedlings, the ACO2 knockdown mutant aco2-1 produced less ethylene, which resulted in the inhibited growth of Arabidopsis seedlings. Exogenously applied brassinolide reduced the expression of ACO2. ACO2 expression was increased in det2, a brassinosteroid (BR)-deficient mutant; however, it was decreased in bes1-D, a brassinosteroid insensitive 1-EMS-suppressor 1 (BES1)-dominant mutant. In the putative promoter region of ACO2, 11 E-box sequences for BES1 binding but not BR regulatory element sequences for brassinazole-resistant 1 (BZR1) binding were found. Chromatin immunoprecipitation assay showed that BES1 could directly bind to the E-boxes located in the putative promoter region of ACO4. Less ethylene was produced in bes1-D seedlings compared with wild-type seedlings, suggesting that the direct binding of BES1 to the ACO2 promoter may negatively regulate ACO2 expression to control the endogenous level of ethylene in Arabidopsis seedlings.

Ethylene, not ABA, is closely linked to the recovery of gas exchange after drought in four Caragana species

Drought is a cyclical phenomenon in natural environments. During dehydration, stomatal closure is mainly regulated by abscisic acid (ABA) dynamics that limit transpiration in seed plants, but following rehydration, the mechanism of gas exchange recovery is still not clear. In this study, leaf water potential (ψ_leaf ), stomatal conductance (g_s ), leaf hydraulic conductance (K_leaf ), foliar ABA level, ethylene emission rate in response to dehydration and rehydration were investigated in four Caragana species with isohydric (Caragana spinosa and C. pruinosa) and anisohydric (C. intermedia and C. microphylla) traits. Two isohydric species with ABA-induced stomatal closure exhibited more sensitive g_s and K_leaf to decreasing ψ_leaf than two anisohydric species which exhibited a switch from ABA to water potential-driven stomatal closure during dehydration. Following rehydration, the recovery of gas exchange was not associated with a decrease in ABA level but was strongly limited by the degradation of the ethylene emission rate in all species. Furthermore, two anisohydric species with low drought-induced ethylene production exhibited more rapid recovery in gas exchange upon rehydration. Our results indicated that ethylene is a key factor regulating the drought-recovery ability in terms of gas exchange, which may shape species adaptation to drought and potential species distribution.

Comparative Study of Several Fe Deficiency Responses in the Arabidopsis thaliana Ethylene Insensitive Mutants ein2-1 and ein2-5

Iron (Fe) is an essential micronutrient for plants since it participates in essential processes such as photosynthesis, respiration and nitrogen assimilation. Fe is an abundant element in most soils, but its availability for plants is low, especially in calcareous soils. Fe deficiency causes Fe chlorosis, which can affect the productivity of the affected crops. Plants favor Fe acquisition by developing morphological and physiological responses in their roots. Ethylene (ET) and nitric oxide (NO) have been involved in the induction of Fe deficiency responses in dicot (Strategy I) plants, such as Arabidopsis. In this work, we have conducted a comparative study on the development of subapical root hairs, of the expression of the main Fe acquisition genes FRO2 and IRT1, and of the master transcription factor FIT, in two Arabidopsis thaliana ET insensitive mutants, ein2-1 and ein2-5, affected in EIN2, a critical component of the ET transduction pathway. The results obtained show that both mutants do not induce subapical root hairs either under Fe deficiency or upon treatments with the ET precursor 1-aminocyclopropane-1-carboxylate (ACC) and the NO donor S-nitrosoglutathione (GSNO). By contrast, both of them upregulate the Fe acquisition genes FRO2 and IRT1 (and FIT) under Fe deficiency. However, the upregulation was different when the mutants were exposed to ET [ACC and cobalt (Co), an ET synthesis inhibitor] and GSNO treatments. All these results clearly support the participation of ET and NO, through EIN2, in the regulation of subapical root hairs and Fe acquisition genes. The results will be discussed, taking into account the role of both ET and NO in the regulation of Fe deficiency responses.

Rhizobia as a Source of Plant Growth-Promoting Molecules: Potential Applications and Possible Operational Mechanisms

The symbiotic interaction between rhizobia and legumes that leads to nodule formation is a complex chemical conversation involving plant release of nod-gene inducing signal molecules and bacterial secretion of lipo-chito-oligossacharide nodulation factors. During this process, the rhizobia and their legume hosts can synthesize and release various phytohormones, such as IAA, lumichrome, riboflavin, lipo-chito-oligossacharide Nod factors, rhizobitoxine, gibberellins, jasmonates, brassinosteroids, ethylene, cytokinins and the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase that can directly or indirectly stimulate plant growth. Whereas these attributes may promote plant adaptation to various edapho-climatic stresses including the limitations in nutrient elements required for plant growth promotion, tapping their full potential requires understanding of the mechanisms involved in their action. In this regard, several N2-fixing rhizobia have been cited for plant growth promotion by solubilizing soil-bound P in the rhizosphere via the synthesis of gluconic acid under the control of pyrroloquinoline quinone (PQQ) genes, just as others are known for the synthesis and release of siderophores for enhanced Fe nutrition in plants, the chelation of heavy metals in the reclamation of contaminated soils, and as biocontrol agents against diseases. Some of these metabolites can enhance plant growth via the suppression of the deleterious effects of other antagonistic molecules, as exemplified by the reduction in the deleterious effect of ethylene by ACC deaminase synthesized by rhizobia. Although symbiotic rhizobia are capable of triggering biological outcomes with direct and indirect effects on plant mineral nutrition, insect pest and disease resistance, a greater understanding of the mechanisms involved remains a challenge in tapping the maximum benefits of the molecules involved. Rather than the effects of individual rhizobial or plant metabolites however, a deeper understanding of their synergistic interactions may be useful in alleviating the effects of multiple plant stress factors for increased growth and productivity.

Targeted plant hologenome editing for plant trait enhancement

Breeding better crops is a cornerstone of global food security. While efforts in plant genetic improvement show promise, it is increasingly becoming apparent that the plant phenotype should be treated as a function of the holobiont, in which plant and microbial traits are deeply intertwined. Using a minimal holobiont model, we track ethylene production and plant nutritional value in response to alterations in plant ethylene synthesis (KO mutation in ETO1), which induces 1-aminocyclopropane-1-carboxylic acid (ACC) synthase 5 (ACS5), or microbial degradation of ACC (KO mutation in microbial acdS), preventing the breakdown of the plant ACC pool, the product of ACS5. We demonstrate that similar plant phenotypes can be generated by either specific mutations of plant-associated microbes or alterations in the plant genome. Specifically, we could equally increase plant nutritional value by either altering the plant ethylene synthesis gene ETO1, or the microbial gene acdS. Both mutations yielded a similar plant phenotype with increased ethylene production and higher shoot micronutrient concentrations. Restoring bacterial AcdS enzyme activity also rescued the plant wild-t8yp phenotype in an eto1 background. Plant and bacterial genes build an integrated plant-microbe regulatory network amenable to genetic improvement from both the plant and microbial sides.

Bioregulators: unlocking their potential role in regulation of the plant oxidative defense system

Plant bioregulators play an important role in managing oxidative stress tolerance in plants. Utilizing their ability in stress sensitive crops through genetic engineering will be a meaningful approach to manage food production under the threat of climate change. Exploitation of the plant defense system against oxidative stress to engineer tolerant plants in the climate change scenario is a sustainable and meaningful strategy. Plant bioregulators (PBRs), which are important biotic factors, are known to play a vital role not only in the development of plants, but also in inducing tolerance in plants against various environmental extremes. These bioregulators include auxins, gibberellins, cytokinins, abscisic acid, brassinosteroids, polyamines, strigolactones, and ascorbic acid and provide protection against the oxidative stress-associated reactive oxygen species through modulation or activation of a plant's antioxidant system. Therefore, exploitation of their functioning and accumulation is of considerable significance for the development of plants more tolerant of harsh environmental conditions in order to tackle the issue of food security under the threat of climate change. Therefore, this review summarizes a new line of evidence that how PBRs act as inducers of oxidative stress resistance in plants and how they could be modulated in transgenic crops via introgression of genes. Reactive oxygen species production during oxidative stress events and their neutralization through an efficient antioxidants system is comprehensively detailed. Further, the use of exogenously applied PBRs in the induction of oxidative stress resistance is discussed. Recent advances in engineering transgenic plants with modified PBR gene expression to exploit the plant defense system against oxidative stress are discussed from an agricultural perspective.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

Influence of Ethylene Signaling in the Crosstalk Between Fe, S, and P Deficiency Responses in Arabidopsis thaliana

To cope with P, S, or Fe deficiency, dicot plants, like Arabidopsis, develop several responses (mainly in their roots) aimed to facilitate the mobilization and uptake of the deficient nutrient. Within these responses are the modification of root morphology, an increased number of transporters, augmented synthesis-release of nutrient solubilizing compounds and the enhancement of some enzymatic activities, like ferric reductase activity (FRA) or phosphatase activity (PA). Once a nutrient has been acquired in enough quantity, these responses should be switched off to minimize energy costs and toxicity. This implies that they are tightly regulated. Although the responses to each deficiency are induced in a rather specific manner, crosstalk between them is frequent and in such a way that P, S, or Fe deficiency can induce responses related to the other two nutrients. The regulation of the responses is not totally known but some hormones and signaling substances have been involved, either as activators [ethylene (ET), auxin, nitric oxide (NO)], or repressors [cytokinins (CKs)]. The plant hormone ET is involved in the regulation of responses to P, S, or Fe deficiency, and this could partly explain the crosstalk between them. In spite of these crosslinks, it can be hypothesized that, to confer the maximum specificity to the responses of each deficiency, ET should act in conjunction with other signals and/or through different transduction pathways. To study this latter possibility, several responses to P, S, or Fe deficiency have been studied in the Arabidopis wild-type cultivar (WT) Columbia and in some of its ethylene signaling mutants (ctr1, ein2-1, ein3eil1) subjected to the three deficiencies. Results show that key elements of the ET transduction pathway, like CTR1, EIN2, and EIN3/EIL1, can play a role in the crosstalk among nutrient deficiency responses.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

Peptides composed of a short chain of amino acids can play significant roles in plant growth, development, and stress responses. Most of these functional peptides are derived by either processing precursor proteins or direct translation of small open reading frames present in the genome and sometimes located in the untranslated region sequence of a messenger RNA. Generally, canonical peptides serve as local signal molecules mediating short- or long-distance intercellular communication. Also, they are commonly used as ligands perceived by an associated receptor, triggering cellular signaling transduction. In recent years, increasing pieces of evidence from studies in both plants and animals have revealed that peptides are also encoded by RNAs currently defined as non-coding RNAs (ncRNAs), including long ncRNAs, circular RNAs, and primary microRNAs. Primary microRNAs (miRNAs) have been reported to encode regulatory peptides in Arabidopsis, grapevine, soybean, and Medicago, called miRNA-encoded peptides (miPEPs). Remarkably, overexpression or exogenous applications of miPEPs specifically increase the expression level of their corresponding miRNAs by enhancing the transcription of the MIRNA (MIR) genes. Here, we first outline the current knowledge regarding the coding of putative ncRNAs. Notably, we review in detail the limited studies available regarding the translation of miPEPs and their relevant regulatory mechanisms. Furthermore, we discuss the potential cellular and molecular mechanisms in which miPEPs might be involved in plants and raise problems that needed to be solved.

Phosphoproteomic Analysis of Thermomorphogenic Responses in Arabidopsis

Plants rapidly adapt to elevated ambient temperature by adjusting their growth and developmental programs. To date, a number of experiments have been carried out to understand how plants sense and respond to warm temperatures. However, how warm temperature signals are relayed from thermosensors to transcriptional regulators is largely unknown. To identify new early regulators of plant thermo-responsiveness, we performed phosphoproteomic analysis using TMT (Tandem Mass Tags) labeling and phosphopeptide enrichment with Arabidopsis etiolated seedlings treated with or without 3h of warm temperatures (29°C). In total, we identified 13,160 phosphopeptides in 5,125 proteins with 10,700 quantifiable phosphorylation sites. Among them, 200 sites (180 proteins) were upregulated, while 120 sites (87 proteins) were downregulated by elevated temperature. GO (Gene Ontology) analysis indicated that phosphorelay-related molecular function was enriched among the differentially phosphorylated proteins. We selected ATL6 (ARABIDOPSIS TOXICOS EN LEVADURA 6) from them and expressed its native and phosphorylation-site mutated (S343A S357A) forms in Arabidopsis and found that the mutated form of ATL6 was less stable than that of the native form both in vivo and in cell-free degradation assays. Taken together, our data revealed extensive protein phosphorylation during thermo-responsiveness, providing new candidate proteins/genes for studying plant thermomorphogenesis in the future.

Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply

Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.

Signal Integration in Plant Abiotic Stress Responses via Multistep Phosphorelay Signaling

Plants growing in any particular geographical location are exposed to variable and diverse environmental conditions throughout their lifespan. The multifactorial environmental pressure resulted into evolution of plant adaptation and survival strategies requiring ability to integrate multiple signals that combine to yield specific responses. These adaptive responses enable plants to maintain their growth and development while acquiring tolerance to a variety of environmental conditions. An essential signaling cascade that incorporates a wide range of exogenous as well as endogenous stimuli is multistep phosphorelay (MSP). MSP mediates the signaling of essential plant hormones that balance growth, development, and environmental adaptation. Nevertheless, the mechanisms by which specific signals are recognized by a commonly-occurring pathway are not yet clearly understood. Here we summarize our knowledge on the latest model of multistep phosphorelay signaling in plants and the molecular mechanisms underlying the integration of multiple inputs including both hormonal (cytokinins, ethylene and abscisic acid) and environmental (light and temperature) signals into a common pathway. We provide an overview of abiotic stress responses mediated via MSP signaling that are both hormone-dependent and independent. We highlight the mutual interactions of key players such as sensor kinases of various substrate specificities including their downstream targets. These constitute a tightly interconnected signaling network, enabling timely adaptation by the plant to an ever-changing environment. Finally, we propose possible future directions in stress-oriented research on MSP signaling and highlight its potential importance for targeted crop breeding.

Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes

Plant roots are built of concentric cell layers that are thought to respond to microbial infections by employing specific, genetically defined programs. Yet, the functional impact of this radial organization remains elusive, particularly due to the lack of genome-wide techniques for monitoring expression at a cell-layer resolution. Here, cell-type-specific expression of tagged ribosomes enabled the isolation of ribosome-bound mRNA to obtain cell-layer translatomes (TRAP-seq, translating ribosome affinity purification and RNA sequencing). After inoculation with the vascular pathogen Verticillium longisporum, pathogenic oomycete Phytophthora parasitica, or mutualistic endophyte Serendipita indica, root cell-layer responses reflected the fundamentally different colonization strategies of these microbes. Notably, V. longisporum specifically suppressed the endodermal barrier, which restricts fungal progression, allowing microbial access to the root central cylinder. Moreover, localized biosynthesis of antimicrobial compounds and ethylene differed in response to pathogens and mutualists. These examples highlight the power of this resource to gain insights into root-microbe interactions and to develop strategies in crop improvement.

Versatile Roles of Aquaporins in Plant Growth and Development

Aquaporins (AQPs) are universal membrane integrated water channel proteins that selectively and reversibly facilitate the movement of water, gases, metalloids, and other small neutral solutes across cellular membranes in living organisms. Compared with other organisms, plants have the largest number of AQP members with diverse characteristics, subcellular localizations and substrate permeabilities. AQPs play important roles in plant water relations, cell turgor pressure maintenance, the hydraulic regulation of roots and leaves, and in leaf transpiration, root water uptake, and plant responses to multiple biotic and abiotic stresses. They are also required for plant growth and development. In this review, we comprehensively summarize the expression and roles of diverse AQPs in the growth and development of various vegetative and reproductive organs in plants. The functions of AQPs in the intracellular translocation of hydrogen peroxide are also discussed.

A Tour of TOR Complex Signaling in Plants

To identify the appropriate times for growth and development, organisms must sense and process information about the availability of nutrients, energy status, and environmental cues. For sessile eukaryotes such as plants, integrating such information can be critical in life or death decisions. For nearly 30 years, the conserved phosphatidylinositol 3-kinase-related protein kinases (PIKKs) target of rapamycin (TOR) has been established as a central hub for integrating external and internal metabolic cues. Despite the functional conservation across eukaryotes, the TOR complex has evolved specific functional and mechanistic features in plants. Here, we present recent findings on the plant TOR complex that highlight the conserved and unique nature of this critical growth regulator and its role in multiple aspects of plant life.

Preservation of Agaricus bisporus freshness with using innovative ethylene manipulating active packaging paper

Agaricus bisporus produces substantial ethylene during storage and transportation, which accelerates ripening and senescence, thereby shortening the shelf-life. In this study, a novel food packaging material with ethylene removal property was prepared to increase storage time of Agaricus bisporus. 1-Methylcyclopropen and molecular sieves loaded with potassium permanganate were used as ethylene scavengers to coat the fresh-keeping paper. SEM, FT-IR and DSC analyses proved that these functional components were successfully coated on the fresh-keeping paper. The qualities of the mushrooms packed by prepared functional paper were then determined. The results showed that this prepared functional paper could delay the softening, browning and weight loss of mushrooms during storage by inhibiting ethylene synthesis-related enzymes and gene expression in the mushroom fruiting body, and continuous adsorption and removal of the exogenous ethylene. Consequently, the functional paper could reduce the biochemical and physicochemical quality loss of Agaricus bisporus, thus prolonging its shelf-life.

Determination of complex type free, non-conjugated oligosaccharide glucose unit values in tomato xylem sap for early detection of nutrient deficiency

Although knowledge on glycan biosynthesis and processing is continuously maturing, there are still a limited number of studies that examine biological functions of N-glycan structures in plants, which remain virtually unknown. Here, the statistical correlation between nutrient (nitrogen) deficiency symptoms of crops and changes in 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled complex type free oligosaccharides is reported. While deficiency symptoms are predicted by multispectral images and Kjeldahl digestion, APTS-labeled complex type free oligosaccharides are identified by their glucose unit (GU) values in tomato xylem sap, using capillary electrophoresis with laser induced fluorescence detection (CE-LIF). Given the limited number of structures obtained from plants, archived in the literature, in the future, it is intended to create an open access database of promising indicators, namely, glycan structures that are presumably responsible for the nutrient deficiency caused stress in plants (http://glycoplants.org).

Transcriptomic and proteomic responses to brown plant hopper (Nilaparvata lugens) in cultivated and Bt-transgenic rice (Oryza sativa) and wild rice (O. rufipogon)

Strategies are still employed to reduce insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with foreign genes' insertion. Cultivated and Bt-transgenic rice (Oryza sativa) and two ecotypes of wild rice (O. rufipogon) were treated by a 72 h feeding of brown plant hopper (Nilaparvata lugens). Under the feeding of N. lugens, compared with the cultivated rice (568 and 4), more differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) were identified in transgenic rice (2098 and 11) and two wild ecotypes (1990, 39 and 1932, 25, respectively). The iTRAQ analysis showed 79 DAPs and confirmed the results of RNA-seq, which showed the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. DAPs significantly enriched two GO terms that are related with Bph14 and Bph33 genes in rice. Most of DEGs and DAPs were related to plant biological processes of plant-pathogen interaction and plant hormone signal transduction, and hormone signaling and transcription factors regulate the immune response of rice to BPH. Our results demonstrated the similarity in the wild rice and Bt-transgenic rice for their transcriptomic and proteomic response to herbivory, while cultivated rice lacked enough pathways in response to herbivory. STATEMENT OF SIGNIFICANCE OF THE STUDY: The iTRAQ analysis and RNA-seq were employed 39 to identify differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) in seedlings of cultivated, Bt-transgenic and two wild rice ecotypes under feeding of brown plant hopper. Wild rice showed DEGs and DAPs related to biochemical pathways of plant pathogen interactions and plant hormone signal transductions, while cultivated rice lacked enough pathways in response to herbivory. Crop domestication weakened the response of plants to herbivory, while the insertion of Bt gene might promote the response of plants to herbivory. Growing environment plays an important role in regulating gene networks of plant response to herbivory. Our results highlighted the importance of conservation of crop wild species. SIGNIFICANCE: Insect damage is one of main factors in reducing agricultural production, and technologies and methods were employed to control insect pests in agricultural systems. Transgenic technology is developed to produce insect-resistant crops, but receive concerns on biosafety risks. Alternatively, crop wild species are important genetic resource in crop breeding to produce trait-specific varieties. Here, we investigated the molecular mechanisms of plant response to herbivory in wild, Bt-transgenic and cultivated rice, and found crop domestication weakened the response of plants to herbivory. The insertion of foreign Bt gene may promote the expression of other genes. In addition, our results showed growing environment plays an important role in regulating gene networks of plant response to herbivory. These results highlight the importance of wild species conservation, with the strategy of in situ conservation.

Maize endophytic microbial-communities revealed by removing PCR and 16S rRNA sequencing and their synthetic applications to suppress maize banded leaf and sheath blight

Endophytic microbial-communities have specific beneficial functions and are considered key drivers for host plant health. The removing-PCR (R-PCR) is a simple culture-independent cost-effective method to identify endophytic microbial-communities. Microbial communities from maize plant grown in different soil types were identified and characterized via the R-PCR and 16S rRNA sequencing. Culture-dependent microbial community identified through 16S rRNA gene sequencing, further these bacterial communities screened for antagonistic assay against Rhizoctonia solani WH1, in vitro compatibility tests, plant-growth-promoting traits and BIOLOG identification. After that, synthetic-communities (SycomA and SycomB) were prepared by mixing different compatible bacterial-strains to use as an inoculant to suppress pathogens of maize. We identified 167 bacterial operational taxonomic units (OTUs) and unexpected 8 fungal OTUs through the R-PCR, whereas, 95 bacterial OTUs via 16S rRNA sequencing from maize leaves and roots. SycomA and SycomB treatments suppressed the disease level and promoted growth attributes more effectively as compare to the single bacterial-strain and control treatments. This study establishes an efficient approach to isolate, identify and characterize diverse endophytic microbial-community assembly in maize leaves and roots, to successfully apply particular microbes to improve crop growth in soils affected by soil-borne-pathogens.

Short De-Etiolation Increases the Rooting of VC801 Avocado Rootstock

Dark-grown (etiolated) branches of many recalcitrant plant species root better than their green counterparts. Here it was hypothesized that changes in cell-wall properties and hormones occurring during etiolation contribute to rooting efficiency. Measurements of chlorophyll, carbohydrate and auxin contents, as well as tissue compression, histological analysis and gene-expression profiles were determined in etiolated and de-etiolated branches of the avocado rootstock VC801. Differences in chlorophyll content and tissue rigidity, and changes in xyloglucan and pectin in cambium and parenchyma cells were found. Interestingly, lignin and sugar contents were similar, suggesting that de-etiolated branches resemble the etiolated ones in this respect. Surprisingly, the branches that underwent short de-etiolation rooted better than the etiolated ones, and only a slight difference in IAA content between the two was observed. Gene-expression profiles revealed an increase in ethylene-responsive transcripts in the etiolated branches, which correlated with enrichment in xyloglucan hydrolases. In contrast, transcripts encoding pectin methylesterase and pectolyases were enriched in the de-etiolated branches. Taken together, it seems that the short de-etiolation period led to fine tuning of the conditions favoring adventitious root formation in terms of auxin-ethylene balance and cell-wall properties.

New gene functions are involved in the thermotolerance of the wild wheat relative Aegilops umbellulata

Wheat is one of the most important food crops in the world for human consumption, like all plants it is exposed to environmental stresses including high temperatures. The deleterious effect of high temperatures negatively affects plant growth and development, leading to reduced viability and yield. These effects can be reduced by improvement of thermotolerance through innovative breeding strategies, based on the expansion of the genetic pool available, by exploring important genetic functions from wheat wild progenitors. Improving the genetic thermotolerance characteristics of wheat requires greater understanding of genetic bases of thermotolerance, through identification of high temperature stress related genes. A good source of new useful alleles is given by Aegilops species characterized by thermotolerant habits. In this study we have classified as thermotolerant or thermosensitive, on the basis of physiologic tests, some accessions of wheat wild relative species belonging to Aegilops and Triticum genera. A thermotolerant accession of Aegilops umbellulata (AUM5) was selected, subjected to different thermal treatments and analyzed at transcriptional level. By differential display reverse transcriptase polymerase chain reaction (DDRT-PCR), we investigated modulation of gene expression elicited by heat treatments. This approach allowed the identification of various transcript-derived fragments (TDFs) produced by AUM5 in response to different thermal treatments. The functions of the inducible unique genes in the molecular determination of thermotolerance process are discussed.

How Plant Hormones Mediate Salt Stress Responses

Salt stress is one of the major environmental stresses limiting plant growth and productivity. To adapt to salt stress, plants have developed various strategies to integrate exogenous salinity stress signals with endogenous developmental cues to optimize the balance of growth and stress responses. Accumulating evidence indicates that phytohormones, besides controlling plant growth and development under normal conditions, also mediate various environmental stresses, including salt stress, and thus regulate plant growth adaptation. In this review, we mainly discuss and summarize how plant hormones mediate salinity signals to regulate plant growth adaptation. We also highlight how, in response to salt stress, plants build a defense system by orchestrating the synthesis, signaling, and metabolism of various hormones via multiple crosstalks.

The Importance of Microbial Inoculants in a Climate-Changing Agriculture in Eastern Mediterranean Region

Climate change has gained importance due to its severe consequences for many aspects of life. Increasing temperature, drought and greenhouse gases affect directly or indirectly the productivity of agricultural and natural ecosystems as well as human health. The nutrient supply capacity of the soil is diminishing, while food requirements for the growing population are increasing. The ongoing application of agrochemicals results in adverse effects on ecosystem functioning and food chain. Now, more than ever, there is a need to mitigate the effects of agricultural activities on climate change using environmentally friendly techniques. The role of plant beneficial microorganisms on this global challenge is increasingly being explored, and there is strong evidence that could be important. The use of functional microbial guilds forms an alternative or even a supplementary approach to common agricultural practices, due to their ability to act as biofertilizers and promote plant growth. Application of microbial inocula has a significantly lower impact on the environment compared to chemical inputs, while the agricultural sector will financially benefit, and consumers will have access to quality products. Microbial inoculants could play an important role in agricultural stress management and ameliorate the negative impacts of climate change. This short review highlights the role of microbes in benefiting agricultural practices against climate-changing conditions. In particular, the main microbial plant growth-promoting functional traits that are related to climate change are presented and discussed. The importance of microbial inoculants’ multifunctionality is debated, while future needs and challenges are also highlighted.

Volatile-mediated defence regulation occurs in maize leaves but not in maize root

The above article was published in error by the publisher before a final editorial decision had been reached. It has therefore been removed temporarily while the editorial process concludes. The publisher apologizes for the inconvenience.

Comparative transcriptome analyses provide novel insights into etiolated shoot development of walnut (Juglans regia L.)

In general, genes promoting IAA, CTK GA and ethylene biosynthesis were upregulated, while genes participating in ABA, chlorophyll and starch biosynthesis pathways performed opposite tendency during etiolation. Etiolation as a method for rejuvenation plays an important role in the vegetative propagation of woody plants. However, the molecular mechanism of etiolated shoot development remains unclear. In this study, we investigated changes at different etiolation stages of Juglans regia. The histology and transcriptome of J. regia were analysed using etiolated stems, which were treated in darkness for 30, 60, 90 days. The results showed that the ratios of pith (Pi) diameter/stem diameter (D), cortex (Co) width/D, and phloem (Ph) width/D increased, while the ratio of xylem (Xy) width/D decreased after etiolation, and the difference in these ratios between etiolated stems and the control was more significant at 60 days than 90 days. Differentially expressed genes (DEGs) were significantly enriched in pathways such as plant hormone biosynthesis and signal transduction, chlorophyll biosynthesis and degradation, and starch and sucrose metabolism. The difference in the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), sugar and chlorophyll between etiolated stems and the control increased with increasing treatment duration; in contrast, the concentrations of gibberellin (GA), zeatin (ZT), and starch, as well as the difference between the etiolated stems and control were lowest at 60 days among the three stages. On the whole, the positive effect of etiolation on the rejuvenation of walnut stems changed as the treatment period increased. The present investigation lays a foundation for future studies on the effect of etiolation on rejuvenation and for promoting the efficiency of vegetative propagation.