The Pivotal Role of Ethylene in Plant Growth

Recent Advances in Fluorescent Probe for Detecting Biorelevant Analytes during Stress in Plants

Plants are constantly exposed to various stressors that can severely hinder their growth and threaten agricultural productivity. Recent advancements in plant imaging using fluorescent probes have opened new avenues for exploring the intricate processes involved in plant stress perception and signaling. This review represents the comprehensive effort to consolidate recent advances in fluorescent probe technologies, encompassing small-molecule probes, nanoprobes, and genetically encoded indicators, as revolutionary tools for deciphering stress-induced physiological dynamics. We present a comprehensive classification of fluorescent probes designed for detecting key biomolecules involved in plant stress responses, including reactive species, phytohormones, enzymes, and other signaling molecules. By critically evaluating their design principles, practical applications, and distinct advantages over conventional analytical methods, we aim to empower plant scientists in unraveling the spatiotemporal regulation of stress signaling networks. Finally, we propose strategic directions to overcome current technical bottlenecks and maximize the potential of fluorescence-based sensing in advancing sustainable agriculture.

Mechanosensing antagonizes ethylene signaling to promote root gravitropism in rice

Root gravitropism relies on gravity perception by the root cap and requires tightly regulated phytohormone signaling. Here, we isolate a rice mutant that displays root coiling in hydroponics but normal gravitropic growth in soil. We identify COILING ROOT IN WATER 1 (CRW1) encoding an ETHYLENE-INSENSITIVE3 (EIN3)-BINDING F-BOX PROTEIN (OsEBF1) as the causative gene for the mutant phenotype. We show that the OsCRW1-EIN3 LIKE 1 and 2 (OsEIL1/2)-ETHYLENE RESPONSE FACTOR 82 (OsERF82) module controls the production of reactive oxygen species in the root tip, subsequently impacting root cap stability, polar localization of PIN-FORMED 2 (OsPIN2), symmetric distribution of auxin, and ultimately gravitropic growth of roots. The OsEIL1/2-OsERF82 ethylene signaling module is effectively impeded by applying gentle mechanical resistance to root tips, including growing in water-saturated paddy soil. We further show that mechanosensing-induced calcium signaling is required and sufficient for antagonizing the ethylene signaling pathway. This study has revealed previously unanticipated interplay among ethylene, auxin, and mechanosensing in the control of plant gravitropism.

From genes to traits: maximizing phosphorus utilization efficiency in crop plants

Phosphorus (P) is a critical macronutrient for plant growth, but its limited availability requires efficient utilization strategies. The excessive use of P fertilizers leads to low phosphorus utilization efficiency (PUE), causing severe environmental impacts and speeding up the exhaustion of P mineral reserves. Plants respond to inorganic phosphate (Pi) deficiency through complex signaling pathways that trigger changes in gene expression, root architecture, and metabolic pathways to enhance P acquisition and utilization efficiency. By exploring the interplay between genetic regulators and microorganisms, cultivars with superior PUE traits can be developed, which will ensure agricultural resilience and productivity in the face of depleting global P reserves. We highlight the synergistic interaction between genetic regulators and microorganisms to boost PUE as well as recent advancements in unraveling molecular mechanisms governing P homeostasis in plants, emphasizing the urgency to improve plant traits for improved P utilization.

Regulation of starch metabolism in banana fruit: Mechanisms shaping the nutritional quality

Bananas are nutrient-rich fruits that provide starch, essential vitamins, and minerals and play significant importance in the global economy through extensive production, trade, and consumption. Nutrient metabolic processes, such as starch-to-sugar conversion, are fundamental in shaping the quality of banana fruits. Starch accounts for 15%-35% of fresh fruit weight, and its degradation mediated by ethylene signaling components can increase sweetness, soften texture, and increase the palatability of banana fruit. This review summarizes recent advances in the regulatory mechanism underlying starch metabolism in banana fruits, highlights key research questions for future investigation, and proposes promising strategies to manipulate starch levels to develop new banana varieties with enhanced nutritional quality.

Light-driven modulation of plant response to water deficit. A review

The dependence of agriculture on water availability is an important premise justifying attempts to enhance water use efficiency for plant production. Photosynthetic efficiency, directly impacts biomass production, is dependent on both water availability and the quality and quantity of light. Understanding how these factors interact is crucial for improving crop yields. Many overlapping signalling pathways and functions of common bioactive molecules that shape plant responses to both water deficit and light have been identified and discussed in this review. Separate or combined action of these environmental factors include the generation of reactive oxygen species, biosynthesis of abscisic acid, stomatal functioning, chloroplast movement and alterations in the levels of photosynthetic pigments and bioactive molecules. Plant response to water deficit depends on light intensity and its characteristics, with differentiated impacts from UV, blue, and red light bands determining the strength and synergistic or antagonistic nature of interactions. Despite its significance, the combined effects of these environmental factors remain insufficiently explored. The findings highlight the potential for optimising horticultural production through controlled light conditions and regulated deficit irrigation. Future research should assess light and water manipulation strategies to enhance resource efficiency and crop nutritional value.

Comprehensive analysis of morphology, transcriptomics, and metabolomics of banana (Musa spp.) molecular mechanisms related to plant height

Introduction

Plant height is an important agronomic trait that not only affects crop yield but is also related to crop resistance to abiotic and biotic stresses.

Methods

In this study, we analyzed the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) between Brazilian banana and local dwarf banana (Df19) through transcriptomics and metabolomics, and combined morphological differences and endogenous hormone content to analyze and discuss themolecular mechanisms controlling banana height.

Results

Sequencing data showed that a total of 2851 DEGs and 1037 DAMs were detected between Brazilian banana and local dwarf banana (Df19). The main differential biological pathways of DEGs involve plant hormone signaling transduction, Cutin, suberin and wax biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling pathway in plants, amino sugar and nucleotide sugar metabolism, etc. DAMs were mainly enriched in ATP binding cassette (ABC) transporters, amino and nucleotide sugar metabolism, glycerophospholipid metabolism, lysine degradation, and phenylalanine metabolism.

Discussion

Our analysis results indicate that banana plant height is the result of the synergistic effects of hormones such as abscisic acid (ABA), gibberellic acid (GA3), indole-3-acetic acid (IAA), jasmonic acid (JA), brassinosteroids (BR) and other plant hormones related to growth. In addition, transcription factors and ABC transporters may also play important regulatory roles in regulating the height of banana plants.

Effects of the plant growth-promoting rhizobacterium Zobellella sp. DQSA1 on alleviating salt-alkali stress in job's tears seedings and its growth-promoting mechanism

Plant probacteria as a sustainable microbial resource are crucial to plant, which not only promote plant growth but also increase the stress resistance of plants. In this study, whole-genome sequencing of Zobellella sp. DQSA1 was performed, and Zobellella sp. DQSA1 was applied to Job's tears seedings under salt-alkali stress. Whole-genome analysis revealed that Zobellella sp. DQSA1 can produce metabolites such as tryptophan, alpha-linolenic acid and other products through metabolism. In response to the action of Zobellella sp. DQSA1, the contents of jasmonic acid (JA) and indole-3-acetic acid (IAA) in the root system increased by 32.5% and 81.4% respectively, whereas the content of abscisic acid (ABA) decreased by 30.0%, and the contents of other endogenous hormones also significantly differed. Additionally, the physiological and biochemical indices related to growth and salinity demonstrated notable differences. Finally, sequencing analysis revealed that 57 differentially expressed genes (DEGs) were involved in 16 Gene Ontology (GO) pathways. Furthermore, the correlations between the contents of endogenous hormones and 57 DEGs were analyzed, and JA was found to be the most significantly correlated. These results provide a theoretical basis for further exploration of the functions and mechanisms of plant growth-promoting rhizobacteria (PGPR) under salt-alkali stress.

Light regulates seed dormancy through FHY3-mediated activation of ACC OXIDASE 1 in Arabidopsis

Seed dormancy enables plants to delay germination until conditions are favorable for the survival of the next generation. Seed dormancy and germination are controlled by a combination of external and internal signals, in which light and ethylene act as critical regulators. However, how light and ethylene are interlinked to control these two processes remains to be investigated. Here, we show that ethylene and its precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), promote seed germination under light. Light facilitates the conversion of ACC to ethylene, in which phytochrome B (phyB) and FAR-RED ELONGATED HYPOCOTYL3 (FHY3) are functionally required. ACC oxidases (ACOs) catalyze the conversion of ACC to ethylene, among which ACO1 is specifically and predominantly expressed in imbibed seeds. Ethylene induces FHY3 protein accumulation in imbibed seeds, whereby FHY3 directly binds to ACO1 promoter and specifically mediates light-promoted ACO1 expression. Light promotes ACO1 protein accumulation. Overexpression of ACO1 significantly promotes seed germination, and almost completely restores the dormant defect of fhy3 loss-of-function mutants. In summary, this study reveals an ethylene-responsive regulatory cascade of phyB-FHY3-ACO1 that integrates external light input with internal factors to regulate seed dormancy and germination.

GABA and Proline Application Induce Drought Resistance in Oilseed Rape

This study investigates the effects of γ-aminobutyric acid (GABA) and proline, both individually and in combination, on the growth of oilseed rape under drought stress and following the resumption of irrigation. The goal was to determine whether the exogenous application of these compounds enhances the plants response to prolonged water deficit and, if so, to identify the biochemical processes involved in the plant tissue. The experiment was conducted under controlled laboratory conditions. After 21 days of plant cultivation, at the 3-4 leaf stage, seedlings were sprayed with aqueous solutions of GABA (0.1 mM) and proline (0.1 mM). The plants were then subjected to 8 days of severe drought stress, after which irrigation was resumed, and recovery was assessed over 4 days. The results showed that both amino acids alleviated the drought-induced stress as indicated by higher relative water content (RWC), increased levels of endogenous proline and photosynthetic pigments in leaves, and enhanced survival and growth recovery after drought. GABA-treated plants maintained membrane integrity and preserved plasma membrane (PM) ATPase activity during prolonged drought stress while reducing ethylene, H2O2, and MDA levels. Proline also influenced these biochemical responses, though to a lesser extent. The combination of GABA and proline facilitated better recovery of oilseed rape compared to the drought control group following rewatering. Notably, GABA treatment resulted in a significant increase in gene expression compared to the untreated control. Molecular analysis of drought-responsive genes revealed that the gene expression in plants treated with both proline and GABA was typically intermediate between those treated with proline alone and those treated with GABA alone. Based on these findings, we propose that GABA application could serve as an alternative to proline for improving oilseed rape's drought tolerance, potentially increasing both crop yield and quality.

Rice grain size: current regulatory mechanisms and future perspectives

Rice is a staple food for over half of the world's population. To feed the growing population, molecular breeders aim to increase grain yield. Grain size is an important factor for crop productivity, and it has been extensively studied. However, molecular breeders face a major challenge in further improving crop productivity in terms of grain yield and quality. Grain size is a complex trait controlled by multiple genes. Over the past few decades, genetic studies have identified various gene families involved in grain size development. The list of molecular mechanisms, and key regulators involved in grain size development is constantly expanding, making it difficult to understand the main regulators that play crucial roles in grain development. In this review, we focus on the major regulators of grain size, including G-protein signaling, the mitogen-activated protein kinase (MAPK) pathway, transcriptional regulation, the ubiquitin-proteasome degradation (UPD) pathway, and phytohormone signaling. These molecular mechanisms directly or indirectly regulate grain size. We provided a comprehensive understanding of the genes involved in these mechanisms and cross discussions about how these mechanisms are interlinked. This review serves as a valuable resource for understanding the molecular mechanisms that govern grain development and can aid in the development of molecular breeding strategies.

Potential Residual Pesticide Consumption: A Stratified Analysis of Brazilian Families

Food safety is essential to ensure that food is safe for human consumption, particularly in light of the growing global and environmental changes, including population growth and climate variations. Meeting the increasing demand for food requires enhancing and protecting agricultural systems. A common strategy is the use of pesticides, which serve to protect cultivated plants from pests, diseases, and weeds. However, improper and excessive use of these products can lead to negative impacts, spanning economic, environmental, and human health aspects. Concerns about pesticide residues in food are global, as their effects on human health vary depending on exposure and quantity. The main objective of this study was to estimate the potential residual consumption (PRC) of pesticides present in food consumed by Brazilian households. Using a specific methodology, it was identified that pineapple had the highest average PRC (121.01 mg), primarily due to the high residue of the active ingredient ethephon. On the other hand, Dithiocarbamates showed the highest residual quantity. Tebuconazole was the most repeated in the samples. It was observed that the insecticide class was responsible for the highest average PRC in households, estimated at 142.45 mg annually, while higher-income families and those located in rural areas showed a greater propensity for potential residual pesticide consumption due to the higher consumption of fruits and vegetables. Additionally, it was found that households where the head of the family is male, highly educated, and older than 40 years present a higher risk of potential residual pesticide consumption. These results highlight the need for public policies focused on sanitary inspection, the training of professionals in the field, the rational use of pesticides by producers, and proper hygiene practices by consumers to mitigate health risks.

ACS2 and ACS6, especially ACS2 is involved in MPK6 evoked production of ethylene under Cd stress, which exacerbated Cd toxicity in Arabidopsis thaliana

As one of the heavy metal pollutants with strong biological toxicity, cadmium (Cd) is easily absorbed by plant roots, which seriously restricts the growth of plants, causes the quality of agricultural products to decline and threatens human health. Many complex signal transduction pathways are involved in the process of plant response to Cd stress. Among them, plant hormone ethylene is an important signal molecule for plant response to various environmental stresses, and its regulatory mechanism and signal transduction pathway in Cd stress response need to be further clarified. Here, we discovered that Cd stress induced a significant increment in ethylene production in Arabidopsis roots, and the amount of ethylene produced was positively correlated with the inhibition of Arabidopsis root growth and Cd accumulation. Simultaneously, Cd stress stimulated the detoxification mechanism within cells and promoted the expression of METAL TOLERANCE PROTEIN 3 (MTP3), IRON-REGULATED TRANSPORTER2 (IRT2), IRON REGULATED GENE 2 (IREG2) genes implicated in Cd vacuolar compartmentation. However, whether this is associated with ethylene signal transduction remains to be further explored. Further studies have revealed that the Cd induced ethylene burst is attributed to the up-regulation of the expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes that mediated by MITONGEN-ACTIVATED PROTEIN KINASE 6 (MAPK6) in Arabidopsis roots, and among them, ACS2 and ACS6, especially ACS2, are involved in MAPK6-induced ethylene production under Cd stress. The results of this study provide new ideas for understanding the signal transduction pathway of plant response to Cd stress.

Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems

Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.

Genome-wide characterization and expression profiling of the TGA gene family in sweet orange (Citrus sinensis) reveal CsTGA7 responses to multiple phytohormones and abiotic stresses

Citrus is widely recognized as one of the most economically important fruit crops worldwide. However, citrus growth is frequently hindered by external environmental stresses, which severely limit its development and yield. The TGA (TGACG motif-binding factor) transcription factors (TFs) are members of the bZIP family and play essential roles in plant defense responses and organ development. Nevertheless, the systematic identification and functional analysis of the TGA family in citrus remains unreported. In this study, genome-wide analysis identified a total of seven CsTGA TFs in Citrus sinensis, which were classified into five subgroups. Phylogenetic and syntenic analysis revealed that the CsTGA genes are highly conserved, with no tandem or segmental duplication events among family members. Promoter sequence analysis identified numerous cis-acting elements associated with transcriptional regulation, phytohormone response, and environmental adaptation in the promoters of CsTGA genes. The expression patterns under five phytohormones and three abiotic stresses demonstrated significant responses of multiple CsTGA genes under various forms of adversity. Among all tested treatments, CsTGA7 showed the most robust response to multiple stresses. Tissue-specific expression pattern analysis revealed potential functional biases among CsTGA genes. In-depth analysis showed that CsTGA7 localized in the nucleus and possessed transcriptional activation activity, consistent with the typical characteristic of transcriptional regulators. In summary, our research systematically investigated the genomic signature of the TGA family in C. sinensis and unearthed CsTGA7 with potential functions in phytohormone signaling transduction and abiotic stress responses. Our study establishes a basis for further exploration of the function of CsTGA genes under abiotic stress.

Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants

Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood. Through comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress-related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis. To genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience. Our work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine-tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution.

Mitigating drought stress by application of drought-tolerant Bacillus spp. enhanced root architecture, growth, antioxidant and photosynthetic genes expression in sugarcane

Plant growth-promoting rhizobacteria (PGPR) are promising candidates that enhance plant growth under stressful conditions. In this study, 10 bacterial isolates were screened for their IAA production, among them JTB1 and MT22 isolates were selected which produced high IAA levels under 10% PEG and 2% NaCl stress. The isolates showed a high capacity for phosphate solubilization and ACC deaminase activity. Phytogenic analysis showed that the isolate belonged to Bacillus megaterium species JTB1 and MT22. Application of JTB1, MT22, and their consortia as PGPR significantly promoted root development and sugarcane growth under moderate and severe drought stress. Sugarcane growth promotion resulted from the retardation of reactive oxygen species (ROS) synthesis, malondialdehyde (MDA), electrolyte leakage, and cell damage by increasing antioxidant scavenging systems, such as catalase (CAT) and ascorbate peroxidase (APX), owing to PGPR inoculation under drought stress. Inoculation with PGPR resulted in increased auxin transporter expression, which modulated the increase in photosynthetic gene expression of RBC-L, PEPC, SPS in sugarcane under drought stress. The application of JTB1, MT22, or their consortia seemed to have similar effects on all observed parameters. Collectively, these results indicated that inoculation with PGPR enhanced root development and increased the antioxidant system and photosynthetic activity, which promoted sugarcane growth under drought stress.

Qualitative and Quantitative Analyses of 1-Aminocyclopropane-1-carboxylic Acid Concentrations in Plants Organs Using Phenyl Isothiocyanate Derivatization

1-Aminocyclopropane-1-carboxylic acid (ACC) is a direct precursor of phytohormone ethylene. We used a phenyl isothiocyanate (PITC) derivatization modification method combined with spectrographic analysis to isolate and identify three products of the derivatization reactions of ACC and PITC. The MRM+ mode of UPLC-MS/MS was used to establish the analysis of 6-phenyl-5-thioxo-4,6-diazaspiro[2.4]heptan-7-one (PTH-ACC). Three fragment ions detected at the precursor ion (m/z 219.10) were selected for qualitative analysis (m/z 98.10, 77.15, and 72.10), and the most abundant product ion (m/z 98.10) was selected for quantitative analysis. The conditions for the derivatization reaction for the main product PTH-ACC were analyzed and optimized using response surface methodology, resulting in the optimal derivatization conditions being a reaction temperature of 90 °C, a reaction time of 1.5 h, and a formic acid (FA) concentration of 40%. ACC concentrations in 25-200 mg rice samples was successfully determined. Moreover, the ACC concentrations in the shoots, seeds, and roots of rice, maize, and cotton seedlings were all analyzed. The ACC concentrations were found to exhibit tissue specificity. Interestingly, during the ripening process in tomato and mango fruits, the concentrations of ACC in the fruits showed an initial increase, followed by a decrease. In black nightshade fruits, ACC content was the highest in the immature stage, decreased with fruit ripening, and remained stable from the semimature to mature stages. These results provide a reliable analysis technology foundation for the study of ethylene.

Transcriptomics highlights dose-dependent response of poplar to a phenanthrene contamination

Polycyclic aromatic hydrocarbon (PAH) contamination in industrial soils poses significant environmental challenges, necessitating cost-effective bioremediation approaches like tree-based phytoremediation. However, the defence mechanisms and adaptability of trees to PAH exposure remain poorly understood, while the identification of molecular markers could help in the detection of toxicity symptoms. This study explores the molecular response of Populus canadensis to a phenanthrene (PHE) contamination gradient (from 100 to 2000 mg kg-1) using RNA-seq analysis of roots and leaves after 4 weeks of exposure. Both differentially expressed genes (DEGs) and DRomics, a dose-response tool, identified transcriptomic changes, with about 50% of deregulated genes responding significantly at a benchmark dose (i.e. minimal dose that produces a significant effect) below 400 mg PHE kg-1. The highest number of DEGs was found both at a low concentration (200 and 700 mg kg-1) and at the highest concentrations (1500-2000 mg kg-1) for both roots and leaves. Ethylene signalling genes were activated via ABA-independent pathways at low concentrations and ABA-dependent pathways at high concentrations. Across the gradient, responses to oxidative stress were triggered, including reactive oxygen species scavenging and phenylpropanoid biosynthesis, specifically at 1500-2000 mg kg-1. Additionally, PHE disrupted pathways related to plant responses to biotic stress. These findings revealed unexpected dose-dependent transcriptomic shifts, demonstrating poplar's adaptive defence mechanisms against PHE toxicity.

Integrated analysis of the transcriptome and hormone metabolome elucidates the regulatory mechanisms governing walnut bud germination

The walnut (Juglans regia) is an important oilseed tree species characterized by its extensive distribution, high oil yield, and nutrient-dense kernels, which provide substantial economic benefits. However, the rising incidence of late-spring frosts, exacerbated by global climate change, has adversely affected walnut yields. A comprehensive understanding of the regulatory mechanisms involved in bud dormancy, germination, and development is essential for developing strategies to mitigate the effects of late-spring frosts and for breeding frost-resistant cultivars. This study focused on W13, a protogynous walnut variety with early germination of dormant buds in spring, employing a combination of transcriptomic and hormone metabolomic analyses. Our results emphasized four key biological processes-cellular response to ethylene stimulus, phenylpropanoid metabolic process, ethylene-activated signaling pathway, and monooxygenase activity-along with several relevant pathways, including plant hormone signal transduction, flavone and flavonol biosynthesis, biosynthesis of secondary metabolites, and MAPK signaling pathway, all crucial for walnut bud germination. Additionally, bud germination is closely associated with alterations in various hormone signaling pathways, including abscisic acid, auxin, cytokinin, ethylene, gibberellins, jasmonic acid, and salicylic acid. By assessing hormone levels and gene expression at different developmental stages, we pinpointed potential regulatory genes and critical hormones associated with bud germination. Furthermore, through weighted correlation network analysis, we constructed a co-expression network, identifying gene modules specifically expressed during dormancy, germination, budding, and leafing phases. The hub genes within these modules are likely pivotal in regulating walnut bud germination. Our analysis also revealed that genes from various transcription factor families are central within the co-expression network, indicating their significant roles in the bud germination process. Correlation network analysis of hormone and gene further illuminated the mechanisms through which genes and hormones jointly influence walnut bud germination. These findings establish a crucial molecular basis for a more comprehensive understanding of the mechanisms governing germination and development in dormant walnut buds.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development. Hormonal signaling and the maintenance of ROS homeostasis are interconnected, playing indispensable roles in growth, development, and stress responses and orchestrating diverse molecular responses during environmental adversities. Nine principal classes of phytohormones have been categorized: auxins, brassinosteroids, cytokinins, and gibberellins primarily oversee developmental growth regulation, while abscisic acid, ethylene, jasmonic acid, salicylic acid, and strigolactones are the main orchestrators of environmental stress responses. Coordination between phytohormones and transcriptional regulation is crucial for effective plant responses, especially in drought stress. Understanding the interplay of ROS and phytohormones is pivotal for elucidating the molecular mechanisms involved in plant stress responses. This review provides an overview of the intricate relationship between ROS, redox metabolism, and the nine different phytohormones signaling in plants, shedding light on potential strategies for enhancing drought tolerance for sustainable crop production.

Transcription factor PagERF110 inhibits leaf development by direct regulating PagHB16 in poplar

Ethylene-responsive factor (ERF) family genes are crucial for plant growth and development. This study analyzed the functional role of the PagERF110 gene in leaf development of Populus alba×P. glandulosa. PagERF110 contains the AP2 conserved domain and exhibits transcriptional activation activity at its C-terminus. Overexpression of PagERF110 in transgenic poplar trees resulted in reduced leaf size, leaf area, and vein xylem thickness. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiments confirmed that PagERF110 interacts with PagACD32.1. Transcriptome sequencing revealed that PagERF110 regulates the expression of key genes involved in leaf development. Furthermore, yeast one-hybrid (Y1H) assays, GUS staining, and ChIP experiments collectively confirmed that PagERF110 targets the expression of PagHB16. In summation, our findings demonstrate that PagERF110 functions as a negative regulator in poplar leaf development.

ETHYLENE RESPONSE FACTOR6, A Central Regulator of Plant Growth in Response to Stress

ETHYLENE RESPONSE FACTOR6 (ERF6) has emerged as a central player in stress-induced plant growth inhibition. It orchestrates complex pathways that enable plants to acclimate and thrive in challenging environments. In response to various abiotic and biotic stresses, ERF6 is promptly activated through both ethylene-dependent and -independent pathways, and contributes to enhanced stress tolerance mechanisms by activating a broad spectrum of genes at various developmental stages. Despite the crucial role of ERF6, there is currently a lack of published comprehensive insights into its function in plant growth and stress response. In this respect, based on the tight connection between ethylene and ERF6, we review the latest research findings on how ethylene regulates stress responses and the mechanisms involved. In addition, we summarize the trends and advances in ERF6-mediated plant performance under optimal and stressful conditions. Finally, we also highlight key questions and suggest potential paths to unravel the ERF6 regulon in future research.

Shifts in plant architecture drive species-specific responses to drought in a Sorghum recombinant inbred line population

Drought stress severely impedes plant growth, development, and yield. Therefore, it is critical to uncover the genetic mechanisms underlying drought resistance to ensure future food security. To identify the genetic controls of these responses in Sorghum, an agriculturally and economically important grain crop, an interspecific recombinant inbred line (RIL) population was established by crossing a domesticated inbred line of Sorghum bicolor (TX7000) with its wild relative, Sorghum propinquum. This RIL population was evaluated under drought conditions, allowing for the identification of quantitative trait loci (QTL) that contribute to drought resistance. We detected eight QTL in the drought population that explain a significant portion of the observed variation for four traits (height, aboveground biomass, relative water content, and leaf temperature/transpiration). The allelic effects of, and the candidate genes within, these QTL emphasize: (1) the influence of domestication on drought-responsive phenotypes, such as height and aboveground biomass, and (2) how control of water uptake and/or loss can be driven by species-specific plant architecture. Our findings shed light on the interconnected roles of shoot and root responses in drought resistance as it relates to regulation of water uptake and/or loss, while the detected allelic effects demonstrate how maintenance of grain production and yield under drought is a likely result of domestication-derived drought tolerance.

From Division to Death: Metabolomic Analysis of Nicotiana tabacum BY-2 Cells Reveals the Complexity of Life in Batch Culture

Tobacco BY-2 cell culture is one of the most widely used models in plant biology. The main advantage of BY-2 suspension cultures is the synchronization of cell development and the appearance of polar elongation. In batch culture, BY-2 cells passed through the lag, proliferation, elongation, and stationary phases. During this process, the composition of the growth medium changed dramatically. Sucrose was rapidly eliminated; hexose first accumulated and then depleted. The medium's pH initially decreased and then rose with aging. As a result of the crosstalk between the internal and external stimuli, cells pass through complicated systemic rearrangements, which cause metabolomic alterations. The early stages were characterized by high levels of amino acids and sterols, which could be interpreted as the result of synthetic activity. The most intense rearrangements occurred between the proliferation and active elongation stages, including repression of amino acid accumulation and up-regulation of sugar metabolism. Later stages were distinguished by higher levels of secondary metabolites, which may be a non-specific response to deteriorating conditions. Senescence was followed by some increase in fatty acids and sterols as well as amino acids, and probably led to self-destructive processes. A correlation analysis revealed relationships between metabolites' covariation, their biochemical ratio, and the growth phase.

Imaging the spatial distribution of structurally diverse plant hormones

Plant hormones are essential and structurally diverse molecules that regulate various aspects of plant growth, development, and stress responses. However, the precise analysis of plant hormones in complex biological samples poses a challenge due to their low concentrations, dynamic levels, and intricate spatial distribution. Moreover, the complexity and interconnectedness of hormone signaling networks make it difficult to simultaneously trace multiple hormone spatial distributions. In this review, we provide an overview of currently recognized small-molecule plant hormones, signal peptide hormones, and plant growth regulators, along with the analytical methods employed for their analysis. We delve into the latest advancements in mass spectrometry imaging and in situ fluorescence techniques, which enable the examination of the spatial distribution of plant hormones. The advantages and disadvantages of these imaging techniques are further discussed. Finally, we propose potential avenues in imaging techniques to further enhance our understanding of plant hormone biology.

Genome-wide identification of the EIN3/EIL gene family in Ginkgo biloba and functional study of a GbEIL in the ethylene signaling pathway

ETHYLENE-INSENSITIVE3 (EIN3) or EIN3-Like (EIL) proteins, play critical roles in integrating ethylene signaling and physiological regulation in plants by modulating the expression of various downstream genes, such as ethylene-response factors (ERFs). However, little is known about the characteristics of EIN3/EILs in the gymnosperm Ginkgo biloba. In the present study, a genome-wide comparative analysis of Ginkgo EIN3/EIL gene family was performed with those from an array of species, including bryophytes (Physcomitrella patens), gymnosperms (Cycas panzhihuaensis), and angiosperms (Arabidopsis thaliana, Gossypium raimondii, Gossypium hirsutum, Oryza sativa, and Brachypodium distachyon). Within the constructed phylogenetic tree for the 53 EIN3/EILs identified, 5 GbEILs from G. biloba, 2 PpEILs from P. patens, and 3 CpEILs from C. panzhihuaensis were assigned to one cluster, suggesting that their derivation occurred after the split of their ancestors and angiosperms. Although considerable divergence accumulated in amino acid sequences along with the evolutionary process, the specific EIN3_DNA-binding domains were evolutionarily conserved among the 53 EIN3/EILs. Collinearity analysis indicated that whole-genome or segmental duplication and subsequent purifying selection might have prompted the generation and evolution of EIN3/EIL multigene families. Based on the expression patterns of five GbEILs at the four developmental stages of Ginkgo ovules, one GbEIL gene (Gb_03292) was further investigated for its role in mediating ethylene signaling. The functional activity of Gb_03292 was closely related to ethylene signaling, as it complemented the triple response via ectopic expression in ein3eil1 double mutant Arabidopsis. Additionally, GbEIL likely modulates the expression of a Ginkgo ERF (Gb_15517) by directly binding to its promoter. These results demonstrated that the GbEIL gene could have participated in mediating ethylene signal transduction during ovule development in G. biloba. The present study also provides insights into the conservation of ethylene signaling across the gymnosperm G. biloba and angiosperm species.

Structure-Activity of Plant Growth Bioregulators and Their Effects on Mammals

In this review, we emphasize structure-activity and the effects on mammals of plant growth bioregulators. plant growth bioregulators can be referred to as "biochemical effectors" since they are substances having biological activity. It is possible to distinguish between "bioregulators" and "regulators" due to the significance of the compounds mentioned above in biochemistry and agrobiology. Thus, "plant growth bioregulators" (PGBRs) are the names given to naturally occurring chemical substances produced by biosynthetic processes. PGBRs affect both plant reign and animal reign. A plethora of plant growth bioregulators were described in the literature, so the structure, activity in plants, and their effects on mammals are presented.

Constitutive expression of cucumber CsACS2 in Arabidopsis Thaliana disrupts anther dehiscence through ethylene signaling and DNA methylation pathways

KEY MESSAGE

Constitutive expression of cucumber CsACS2 in Arabidopsis disrupts anther dehiscence and male fertility via ethylene signaling and DNA methylation, revealing new avenues for enhancing crop reproductive traits. The cucumber gene CsACS2, encoding ACC (1-aminocyclopropane-1-carboxylic acid) synthase, plays a pivotal role in ethylene biosynthesis and sex determination. This study investigates the effects of constitutive CsACS2 expression in Arabidopsis thaliana on anther development and male fertility. Transgenic Arabidopsis plants overexpressing CsACS2 exhibited male sterility due to inhibited anther dehiscence, which was linked to suppressed secondary cell wall thickening. RNA-Seq analysis revealed upregulation of ethylene signaling pathway genes and downregulation of secondary cell wall biosynthesis genes, with gene set enrichment analysis indicating the involvement of DNA methylation. Rescue experiments demonstrated that silver nitrate (AgNO₃) effectively restored fertility, while 5-azacytidine (5-az) partially restored it, highlighting the roles of ethylene signaling and DNA methylation in this process. Constitutive CsACS2 expression in Arabidopsis disrupts anther development through ethylene signaling and DNA methylation pathways, providing new insights into the role of ethylene in plant reproductive development and potential applications in crop improvement.

The Effects of Anthropogenic Stressors on Above- and Belowground Phytochemical Diversity of the Wetland Grass, Phragmites australis

Coastal wetlands face threats from climate change-induced flooding and biological invasions. Plants respond to these stressors through changes in their phytochemical metabolome, but it is unclear whether stressors affecting one tissue compartment (e.g., leaves) create vulnerabilities in others (e.g., roots) or elicit similar responses across tissues. Additionally, responses to multiple simultaneous stressors remain poorly understood due to the focus on individual metabolites in past studies. This study aims to elucidate how the phytochemical metabolome of three Phragmites australis (Cav.) lineages, common in the Mississippi River Delta, responds to flooding and infestation by the non-native scale insect Nipponaclerda biwakoensis (Kuwana). Among these lineages, one is non-native and poses a threat to North American wetlands. Results indicate that metabolomic responses are highly specific, varying with lineage, tissue type, stressor type, and the presence of multiple stressors. Notably, the non-native lineage displayed high chemical evenness, while the other two showed stressor-dependent responses. The 10 most informative features identified by a machine learning model showed less than 1% overlap with known metabolites linked to water and herbivory stress, underscoring gaps in our understanding of plant responses to environmental stressors. Our metabolomic approach offers a valuable tool for identifying candidate plant genotypes for wetland restoration.

Diverse functional interactions between ABA and ethylene in plant development and responses to stress

Abscisic acid (ABA) and ethylene are two essential hormones that play crucial roles throughout the entire plant life cycle and in their tolerance to abiotic or biotic stress. In recent decades, increasing research has revealed that, in addition to their individual roles, these two hormones are more likely to function through their interactions, forming a complex regulatory network. More importantly, their functions change and their interactions vary from synergistic to antagonistic depending on the specific plant organ and development stage, which is less focused, compared and systematically summarized. In this review, we first introduce the general synthesis and action signaling pathways of these two plant hormones individually and their interactions in relation to seed dormancy and germination, primary root growth, shoot development, fruit ripening, leaf senescence and abscission, and stomatal movement regulation under both normal and stress conditions. A better understanding of the complex interactions between ABA and ethylene will enhance our knowledge of how plant hormones regulate development and respond to stress and may facilitate the development of crops with higher yields and greater tolerance to stressful environments through tissue-specific genetic modifications in the future.

Photoperiod and temperature as dominant environmental drivers triggering chemical compositions of garlic bulb during growth

Photoperiod and temperature are crucial for plant growth and development, but the accumulation patterns and regulatory mechanisms of garlic in response to these factors remain unclear. Compared to normal conditions (12/12 h light/dark; 22/15 °C day/night), increasing the photoperiod by 1 h each month with normal temperature (13/11, 14/10, 15/9, 16/8 h; light/dark; 22/15 °C day/night) or increasing photoperiod by 1 h with a 1.5 °C increase in temperature (13/11, 14/10, 15/9, 16/8 h light/dark; 23.5/16, 25/17, 26.5/18, 28/19 °C day/night) at monthly intervals substantially affects garlic growth in early G204, mid-G666, and late G390 harvest cultivars. For both increased photoperiod and temperature, the environment most favorable for bulb growth is characterized by the maximum accumulation of hormones (IAA, JA, and ZT) during bulb formation, while higher levels of ACC, phenolic acids, and organosulfur compounds are observed during the harvesting stage. Furthermore, the accumulation patterns of alliin and allicin in garlic bulbs for G204, G666, and G390 cultivars significantly increased, with fold changes of (2.0, 1.8, and 1.9) and (1.8, 1.7, and 1.5), respectively, in response to increased photoperiod and temperature conditions. Additionally, the accumulation pattern in G204, and G666 was similar but notably distinct from late harvest G390 during growth. In this study, metabolomics models were constructed to assess chemical composition variations and predict the differences among three garlic varieties during the growth stages. These models revealed functional component variations and provided reliable predictions, offering valuable insights for estimating garlic chemical compositions and identifying optimal environmental conditions for growth.

Transcriptome analysis reveals regulatory mechanism of postharvest softening in kiwiberry

BACKGROUND

Kiwiberry is an emerging edible fruit with market potential owing to its advantages of small size, thin and hairless skin, and sweet taste. However, kiwiberry is highly susceptible to softening after harvest, which poses a challenge for storage and transport. To reveal the underlying cause of kiwiberry softening, it is essential to investigate the characteristics of postharvest fruit and the molecular mechanisms that affect changes in fruit firmness.

RESULTS

Morphological observations and analysis of physical parameters showed that the skin of kiwiberry did not change markedly from the 1st to the 7th day after harvest, while the colour of the inner pericarp gradually turned yellow. By the 9th day of room temperature storage, the kiwiberries began to rot. The hardness decreased rapidly from the 1st to the 5th day postharvest, reaching the low level on the 5th day. The starch and pectin contents of kiwiberry showed a downward trend with increasing storage time. Transcriptome sequencing and weighted gene co-expression network analysis identified 29 key genes associated with the changes in the hardness of kiwiberry after harvest. Gene Ontology enrichment analysis indicated that these 29 genes are mainly involved in pectin metabolism, starch synthesis, starch decomposition, and starch metabolism. In addition, three transcription factors, AGL31, HAT14, and ALC, were identified to be strongly positively correlated with the 29 genes that affect the hardness changes of kiwiberry after harvest, and 28 of the 29 key genes were predicted to be regulated by HAT14.

CONCLUSIONS

These results reveal the changes in morphological characteristics and physiological indicators during the postharvest ripening and softening of kiwiberry stored under room temperature conditions. Transcriptome analysis identified 29 key genes and three transcription factors that affect the firmness changes of postharvest kiwiberry. The results of this study thus provide insight into the transcriptional regulatory mechanism of kiwiberry softening during storage to improve the postharvest quality.

Transcriptome profiling of two rice varieties reveals their molecular responses under high night-time temperature

High night-time temperatures (HNT) pose a threat to the sustainability of crop production, including rice. HNT can affect crop productivity and quality by influencing plant physiology, morphology, and phenology. The ethylene perception inhibitor, 1-methylcyclopropene (1-MCP), can minimize HNT-induced damage to plant membranes, thereby preventing decrease in rice yield. In this study, we employed a transcriptome approach to investigate the effects of HNT, 1-MCP, and their interaction on two Texas rice varieties, Antonio and Colorado. The plants were exposed to temperatures of 25°C (ambient night-time temperature, ANT) and 30°C (HNT) using an infrared heating system from the booting stage until harvest, while 1-MCP was applied at the booting stage of rice development. Several physiological and agronomical traits were evaluated under each condition to assess plant responses. Leaf tissues were collected from the plants grown in the ANT and HNT conditions after the heat stress and 1-MCP treatments. Based on agronomic performance, Colorado was less negatively affected than Antonio under HNT, showing a slight reduction in spikelet fertility and leaf photosynthetic rate but no significant reduction in yield. The application of 1-MCP significantly mitigated the adverse effects of HNT in Antonio. However, no significant differences were observed in yield and leaf photosynthetic rate in Colorado. Furthermore, transcriptomic data revealed distinct responsive mechanisms in Antonio and Colorado in response to both HNT and 1-MCP. Several ethylene and senescence-related transcription factors (TFs) were identified only in Antonio, suggesting that 1-MCP affected the ethylene signaling pathway in Antonio but not in Colorado. These findings contribute to our understanding of the physiological differences between varieties exhibiting susceptible and tolerant responses to high night-time temperatures, as well as their response to 1-MCP and ethylene regulation under 1-MCP.

The RNA helicase LOS4 regulates pre-mRNA splicing of key genes (EIN2, ERS2, CTR1) in the ethylene signaling pathway

KEY MESSAGE

The Arabidopsis RNA helicase LOS4 plays a key role in regulating pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. The plant hormone ethylene plays diverse roles in plant growth, development, and responses to stress. Ethylene is perceived by the membrane-bound ethylene receptors complex, and then triggers downstream components, such as EIN2, to initiate signal transduction into the nucleus, leading to the activation of ethylene-responsive genes. Over the past decades, substantial information has been accumulated regarding gene cloning, protein-protein interactions, and downstream gene expressions in the ethylene pathway. However, our understanding of mRNA post-transcriptional processing and modification of key genes in the ethylene signaling pathway remains limited. This study aims to provide evidence demonstrating the involvement of the Arabidopsis RNA helicase LOS4 in pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. Various genetic approaches including RNAi gene silencing, CRISPR-Cas9 gene editing, and amino acid mutations were employed in this study. When LOS4 was silenced or knocked down, the ethylene sensitivity of etiolated seedlings was significantly enhanced. Further investigation revealed errors in the EIN2 pre-mRNA splicing when LOS4 was knocked down. In addition, aberrant pre-mRNA splicing was observed in the ERS2 and CTR1 genes in the pathway. Biochemical assays indicated that the los4-2 (E94K) mutant protein exhibited increased ATP binding and enhanced ATP hydrolytic activity. Conversely, the los4-1 (G364R) mutant had reduced substrate RNA binding and lower ATP binding activities. These findings significantly advanced our comprehension of the regulatory functions and molecular mechanisms of RNA helicase in ethylene signaling.

Small chemical molecules regulating the phytohormone signalling alter the plant's physiological processes to improve stress adaptation, growth and productivity

Small chemical molecules are attractive agents for improving the plant processes associated with plant growth and stress tolerance. Recent advances in chemical biology and structure-assisted drug discovery approaches have opened up new avenues in plant biology to discover new drug-like molecules to improve plant processes for sustained food production. Several compounds targeting phytohormone biosynthesis or signalling cascades were designed to alter plant physiological mechanisms. Altering Abscisic acid synthesis and its signalling process can improve drought tolerance, and the processes targeted are reversible. Molecules targeting cytokinin, Auxin, and gibberellic acid regulate plant physiological processes and can potentially improve plant growth, biomass and productivity. The potential of molecules may be exploited as agrochemicals to enhance agricultural productivity. The discovery of small molecules provides new avenues to improve crop production in changing climatic conditions and the nutritional quality of foods. We present the rational combinations of small molecules with inhibitory and co-stimulatory effects and discuss future opportunities in this field.

The case for sporadic cyanogenic glycoside evolution in plants

Cyanogenic glycosides are α-hydroxynitrile glucosides present in approximately 3000 different plant species. Upon tissue disruption, cyanogenic glycosides are hydrolyzed to release toxic hydrogen cyanide as a means of chemical defense. Over 100 different cyanogenic glycosides have been reported, with structural diversity dependent on the precursor amino acid, and subsequent modifications. Cyanogenic glycosides represent a prime example of sporadic metabolite evolution, with the metabolic trait arising multiple times throughout the plant lineage as evidenced by recruitment of different enzyme families for biosynthesis. Here, we review the latest developments within cyanogenic glycoside biosynthesis, and argue possible factors driving sporadic evolution including shared intermediates and crossovers with other metabolic pathways crossovers, and metabolite multifunctionality beyond chemical defense.

Ethylene in fruits: beyond ripening control

Fruits are a rich source of nutrients, minerals, and dietary fibers for both humans and animals. While the gaseous phytohormone ethylene is well-known for its role in controlling fruit ripening, there is growing evidence that ethylene also plays crucial roles in regulating other developmental processes of fruits, such as sex determination, fruit set, and fruit growth. In this review, we aim to revisit these findings from various species like cucumber, melon, tomato, rice, maize, and more. These studies not only enhance our understanding of ethylene's function in fruits but also highlight the potential for manipulating ethylene to improve crops. Furthermore, we discuss recent studies that show the ethylene precursor ACC (1-AMINOCYCLOPROPANE-1-CARBOXYLATE), and the ethylene signaling components EIN2 (ETHYLENE INSENSITIVE2) and EIN3 (ETHYLENE INSENSITIVE3) have ethylene-independent function in specific conditions. This phenomenon, combined with findings of dosage-dependent ethylene functions in certain conditions, highlights the importance of analyzing mutants with completely blocked ethylene pathways in different species at specific developmental stages and tissue types. Overall, this review offers a timely and essential summary of ethylene's role in sex determination, fruit formation, and fruit growth, which could be beneficial for horticulture crop breeding.

Soybean ethylene response factors GmENS1 and GmENS2 promote nodule senescence

The final phase in root nodule development is nodule senescence. The mechanism underlying the initiation of nodule senescence requires further elucidation. In this study, we investigate the intrinsic signals governing soybean (Glycine max L. Merr.) nodule senescence, uncovering ethylene as a key signal in this intricate mechanism. Two AP2/ethylene response factor (ERF) transcription factor (TF) genes, GmENS1 and GmENS2 (Ethylene-responsive transcription factors required for Nodule Senescence), exhibit heightened expression levels in both aged nodules and nodules treated with ethylene. An overexpression of either GmENS1 or GmENS2 accelerates senescence in soybean nodules, whereas the knockout or knockdown of both genes delays senescence and enhances nitrogenase activity. Furthermore, our findings indicate that GmENS1 and GmENS2 directly bind to the promoters of GmNAC039, GmNAC018, and GmNAC030, encoding 3 NAC (NAM, ATAF1/2, and CUC2) TFs essential for activating soybean nodule senescence. Notably, the nodule senescence process mediated by GmENS1 or GmENS2 overexpression is suppressed in the soybean nac039/018/030 triple mutant compared with the wild-type control. These data indicate GmENS1 and GmENS2 as pivotal TFs mediating ethylene-induced nodule senescence through the direct activation of GmNAC039/GmNAC018/GmNAC030 expression in soybean.

Ethylene, a Signaling Compound Involved in Seed Germination and Dormancy

The present review is focused on current findings on the involvement of ethylene in seed biology. The responsiveness of seeds to ethylene depends on the species and the dormancy status, improving concentrations ranging from 0.1 to 200 μL L-1. The signaling pathway of ethylene starts with its binding to five membrane-anchored receptors, which results in the deactivation of Constitutive Triple Response 1 (CTR1, a protein kinase) that does not exert its inhibitory effect on Ethylene Insensitive 2 (EIN2) by phosphorylating its cytosolic C-terminal domain. An analysis of germination in the presence of inhibitors of ethylene synthesis or action, and using seeds from mutant lines altered in terms of the genes involved in ethylene synthesis (acs) and the signaling pathway (etr1, ein2, ein4, ctr1 and erf1), demonstrates the involvement of ethylene in the regulation of seed dormancy. The promoting effect of ethylene is also regulated through crosstalk with abscisic acid (ABA) and gibberellins (GAs), essential hormones involved in seed germination and dormancy, and Reactive Oxygen Species (ROS). Using a mutant of the proteolytic N-degron pathway, Proteolysis (PRT6), the Ethylene Response Factors (ERFs) from group VII (HRE1, HRE2, RAP 2.2, RAP2.3 and RAP 2.12) have also been identified as being involved in seed insensitivity to ethylene. This review highlights the key roles of EIN2 and EIN3 in the ethylene signaling pathway and in interactions with different hormones and discusses the responsiveness of seeds to ethylene, depending on the species and the dormancy status.

LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response, but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to a warm ambient temperature. Together, our findings illustrate a mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response by activating specific bivalent genes in Arabidopsis.

Comparative Analysis of Phytohormone Biosynthesis Genes Responses to Long-Term High Light in Tolerant and Sensitive Wheat Cultivars

Phytohormones are vital for developmental processes, from organ initiation to senescence, and are key regulators of growth, development, and photosynthesis. In natural environments, plants often experience high light (HL) intensities coupled with elevated temperatures, which pose significant threats to agricultural production. However, the response of phytohormone-related genes to long-term HL exposure remains unclear. Here, we examined the expression levels of genes involved in the biosynthesis of ten phytohormones, including gibberellins, cytokinins, salicylic acid, jasmonic acid, abscisic acid, brassinosteroids, indole-3-acetic acid, strigolactones, nitric oxide, and ethylene, in two winter wheat cultivars, Xiaoyan 54 (XY54, HL tolerant) and Jing 411 (J411, HL sensitive), when transferred from low light to HL for 2-8 days. Under HL, most genes were markedly inhibited, while a few, such as TaGA2ox, TaAAO3, TaLOG1, and TaPAL2, were induced in both varieties. Interestingly, TaGA2ox2 and TaAAO3 expression positively correlated with sugar content but negatively with chlorophyll content and TaAGP expression. In addition, we observed that both varieties experienced a sharp decline in chlorophyll content and photosynthesis performance after prolonged HL exposure, with J411 showing significantly more sensitivity than XY54. Hierarchical clustering analysis classified the phytohormone genes into the following three groups: Group 1 included six genes highly expressed in J411; Group 2 contained 25 genes drastically suppressed by HL in both varieties; and Group 3 contained three genes highly expressed in XY54. Notably, abscisic acid (ABA), and jasmonic acid (JA) biosynthesis genes and their content were significantly higher, while gibberellins (GA) content was lower in XY54 than J411. Together, these results suggest that the differential expression and content of GA, ABA, and JA play crucial roles in the contrasting responses of tolerant and sensitive wheat cultivars to leaf senescence induced by long-term HL. This study enhances our understanding of the mechanisms underlying HL tolerance in wheat and can guide the development of more resilient wheat varieties.

Exploring ethylene-related genes in Cannabis sativa: implications for sexual plasticity

KEY MESSAGE

Presented here are model Yang cycle, ethylene biosynthesis and signaling pathways in Cannabis sativa. C. sativa floral transcriptomes were used to predict putative ethylene-related genes involved in sexual plasticity in the species. Sexual plasticity is a phenomenon, wherein organisms possess the ability to alter their phenotypic sex in response to environmental and physiological stimuli, without modifying their sex chromosomes. Cannabis sativa L., a medically valuable plant species, exhibits sexual plasticity when subjected to specific chemicals that influence ethylene biosynthesis and signaling. Nevertheless, the precise contribution of ethylene-related genes (ERGs) to sexual plasticity in cannabis remains unexplored. The current study employed Arabidopsis thaliana L. as a model organism to conduct gene orthology analysis and reconstruct the Yang Cycle, ethylene biosynthesis, and ethylene signaling pathways in C. sativa. Additionally, two transcriptomic datasets comprising male, female, and chemically induced male flowers were examined to identify expression patterns in ERGs associated with sexual determination and sexual plasticity. These ERGs involved in sexual plasticity were categorized into two distinct expression patterns: floral organ concordant (FOC) and unique (uERG). Furthermore, a third expression pattern, termed karyotype concordant (KC) expression, was proposed, which plays a role in sex determination. The study revealed that CsERGs associated with sexual plasticity are dispersed throughout the genome and are not limited to the sex chromosomes, indicating a widespread regulation of sexual plasticity in C. sativa.

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana

Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 h post inoculation [hpi]) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi. These DEGs were predominantly associated with defense response, ethylene, and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly upregulated after inoculation, and more of them were enriched near genes in Colfax than other soybean lines. Notably, we identified a long non-coding RNA (lncRNA) within the mapped region of the resistance gene that exhibited exclusive upregulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH (where H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.)

KEY MESSAGE

Multi-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle. Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length-width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9-13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.

Application of multiomics analysis to plant flooding response

Flooding, as a natural disaster, plays a pivotal role in constraining the growth and development of plants. Flooding stress, including submergence and waterlogging, not only induces oxygen, light, and nutrient deprivation, but also alters soil properties through prolonged inundation, further impeding plant growth and development. However, hypoxia (or anoxia) is the most serious and direct damage to plants caused by flooding. Moreover, flooding disrupts the structural integrity of plant cell walls and compromises endoplasmic reticulum functionality, while hindering nutrient absorption and shifting metabolic processes from normal aerobic respiration to anaerobic respiration. It can be asserted that flooding exerts comprehensive effects on plants encompassing phenotypic changes, transcriptional alterations, protein dynamics, and metabolic shifts. To adapt to flooding environments, plants employ corresponding adaptive mechanisms at the phenotypic level while modulating transcriptomic profiles, proteomic characteristics, and metabolite levels. Hence, this study provides a comprehensive analysis of transcriptomic, proteomic, and metabolomics investigations conducted on flooding stress on model plants and major crops, elucidating their response mechanisms from diverse omics perspectives.

Genome-wide identification and analysis of the EIN3/EIL gene family in broomcorn millet (Panicum miliaceum L.)

The EIN3/EIL gene family holds a pivotal role as it encodes a crucial transcription factor in plants. During the process of polyploidization in broomcorn millet (Panicum miliaceum L.), there is an intriguing above-average amplification observed within the EIN3/EIL gene family. Nonetheless, our current knowledge of this gene family in broomcorn millet remains limited. Hence, in this study, we conducted a comprehensive analysis of the EIN3/EIL gene family in broomcorn millet, aiming to provide a deeper understanding of the potential evolutionary changes. Additionally, we analyzed the EIN3/EIL gene family of Panicum hallii L., a close relative of broomcorn millet, to enhance our characterization efforts. Within this study, we identified a total of 15 EIN3/EIL genes specific to broomcorn millet. Through covariance analysis, it was revealed that all PmEIL genes, except PmEIL1 and PmEIL15, had duplicate copies generated through genome-wide duplication events. Importantly, the Ka/Ks values of all duplicated genes were found to be less than 1, indicating strong purifying selection. Phylogenetic analysis showed that these genes could be categorized into four distinct evolutionary branches, showcasing similar characteristics among members within the same branch. However, there appeared to be an uneven distribution of cis-acting elements amid the EIN3/EIL genes. Further examination of transcriptomic data shed light on the diverse spatiotemporal and stress-related expression patterns exhibited by the EIN3/EIL genes in broomcorn millet. Notably, under cold stress, the expression of PmEIL3/4/8/14 was significantly up-regulated, while under drought stress, PmEIL4/5/6 displayed significant up-regulation. Intriguingly, the expression pattern of PmEIL15 showed an opposite pattern in resistant and sensitive cultivars. The findings of this study augment our understanding of the EIN3/EIL gene family in broomcorn millet and offer a valuable reference for future investigations into polyploid studies. Moreover, this study establishes a theoretical foundation for further exploration of the ethylene signaling pathway in broomcorn millet.

Phytohormonal regulation determines the organization pattern of shoot aerenchyma in greater duckweed (Spirodela polyrhiza)

Airspace or aerenchyma is crucial for plant development and acclimation to stresses such as hypoxia, drought, and nutritional deficiency. Although ethylene-mediated signaling cascades are known to regulate aerenchyma formation in stems and roots under hypoxic conditions, the precise mechanisms remain unclear. Moreover, the cellular dynamics underlying airspace formation in shoots are poorly understood. We investigated the stage-dependent structural dynamics of shoot aerenchyma in greater duckweed (Spirodela polyrhiza), a fast-growing aquatic herb with well-developed aerenchyma in its floating fronds. Using X-ray micro-computed tomography and histological analysis, we showed that the spatial framework of aerenchyma is established before frond volume increases, driven by cell division and expansion. The substomatal cavity connecting aerenchyma to stomata formed via programmed cell death (PCD) and was closely associated with guard cell development. Additionally, transcriptome analysis and pharmacological studies revealed that the organization of aerenchyma in greater duckweed is determined by the interplay between PCD and proliferation. This balance is governed by spatiotemporal regulation of phytohormone signaling involving ethylene, abscisic acid, and salicylic acid. Overall, our study reveals the structural dynamics and phytohormonal regulation underlying aerenchyma development in duckweed, improving our understanding of how plants establish distinct architectural arrangements. These insights hold the potential for wide-ranging application, not only in comprehending aerenchyma formation across various plant species but also in understanding how airspaces are formed within the leaves of terrestrial plants.

Photosynthetic Activities, Phytohormones, and Secondary Metabolites Induction in Plants by Prevailing Compost Residue

Compost residue enriches soil health with the potential to enhance plant metabolism and hormonal balance, but has not yet been studied. A study was performed to determine how prevailing compost residue induces tomato (Solanum lycopersicum 'Scotia') plant morpho-physiology, phytohormones, and secondary metabolites. Plants were grown in soils with a previous history of annual (AN) and biennial (BI) compost amendments. The controls were soil without compost (C) amendment and municipal solid waste compost (MSWC) alone. The MSWC- and AN-plants had similar and significantly (p < 0.05) highest growth and photosynthetic activities compared to the BI- or C-plants. Total phenolics and lipid peroxidase activity were significantly (p < 0.001) high in BI-plants, while hydrogen peroxide and antioxidant capacity were significantly (p < 0.001) high in AN-plants. MSWC-plants recorded the highest cis-abscisic acid, followed by AN-, and then BI- and C-plants. Cis-zeatin, trans-zeatin, and isopentenyladenine ribosides were detected in the MSWC- and AN-plants but not in the BI- or C-plants. Furthermore, gibberellins GA53, GA19, and GA8 were high in the MSWC-plants, but only GA8 was detected in the AN plants and none in the others. Besides, MSWC plants exhibited the highest content of 1-aminocyclopropane-1-carboxylic acid. Conjugated salicylic acid was highest in the BI-plants, while jasmonic acid-isoleucine was highest in MSWC-plants and C plants. In conclusion, prevailing compost chemical residues upregulate plant growth, phytohormones, and metabolic compounds that can potentially increase plant growth and abiotic stress defense. Future work should investigate the flow of these compounds in plants under abiotic stress.

High expression of ethylene response factor BcERF98 delays the flowering time of non-heading Chinese cabbage

MAIN CONCLUSION

BcERF98 is induced by ethylene signaling and inhibits the expression of BcFT by interacting with BcNF-YA2 and BcEIP9, thereby inhibiting plant flowering. Several stresses trigger the accumulation of ethylene, which then transmits the signal to ethylene response factors (ERFs) to participate in the regulation of plant development to adapt to the environment. This study clarifies the function of BcERF98, a homolog of AtERF98, in the regulation of plant flowering time mediated by high concentrations of ethylene. Results indicate that BcERF98 is a nuclear and the cell membrane-localized transcription factor and highly responsive to ethylene signaling. BcERF98 inhibits the expression of BcFT by interacting with BcEIP9 and BcNF-YA2, which are related to flowering time regulation, thereby participating in ethylene-mediated plant late flowering regulation. The results have enriched the theoretical knowledge of flowering regulation in non-heading Chinese cabbage (NHCC), providing the scientific basis and gene reserves for cultivating new varieties of NHCC with different flowering times.

A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms

Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions; however, its drought-tolerance mechanisms remain poorly understood. Here, we report the assembly of a reference-grade genome for A. mongolicus, describe its evolutionary history within the legume family, and examine its drought-tolerance mechanisms. The assembled genome is 843.07 Mb in length, with 98.7% of the sequences successfully anchored to the nine chromosomes of A. mongolicus. The genome is predicted to contain 47 611 protein-coding genes, and 70.71% of the genome is composed of repetitive sequences; these are dominated by transposable elements, particularly long-terminal-repeat retrotransposons. Evolutionary analyses revealed two whole-genome duplication (WGD) events at 130 and 58 million years ago (mya) that are shared by the genus Ammopiptanthus and other legumes, but no species-specific WGDs were found within this genus. Ancestral genome reconstruction revealed that the A. mongolicus genome has undergone fewer rearrangements than other genomes in the legume family, confirming its status as a "relict plant". Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed, both under normal conditions and in response to polyethylene glycol-induced dehydration. Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress, suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Ectopic expression of AmERF2, an ethylene response factor unique to A. mongolicus, can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants, demonstrating the potential for application of A. mongolicus genes in crop improvement.