Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants

Drought induces moderate, diverse changes in the odour of grassland species

Plants react to drought stress with numerous changes including altered emissions of volatile organic compounds (VOC) from leaves, which provide protection against oxidative tissue damage and mediate numerous biotic interactions. Despite the share of grasslands in the terrestrial biosphere, their importance as carbon sinks and their contribution to global biodiversity, little is known about the influence of drought on VOC profiles of grassland species. Using coupled gas chromatography-mass spectrometry, we analysed the odorants emitted by 22 European grassland species exposed to an eight-week-lasting drought treatment (DT; 30% water holding capacity, WHC). We focused on the odorants emitted during the light phase from whole plant shoots in their vegetative stage. Emission rates were standardised to the dry weight of each shoot. Well-watered (WW) plants (70% WHC) served as control. Drought-induced significant changes included an increase in total emission rates of plant VOC in six and a decrease in three species. Diverging effects on the number of emitted VOC (chemical richness) or on the Shannon diversity of the VOC profiles were detected in 13 species. Biosynthetic pathways-targeted analyses revealed 13 species showing drought-induced higher emission rates of VOC from one, two, three, or four major biosynthetic pathways (lipoxygenase, shikimate, mevalonate and methylerythritol phosphate pathway), while six species exhibited reduced emission rates from one or two of these pathways. Similarity trees of odorant profiles and their drought-induced changes based on a biosynthetically informed distance metric did not match species phylogeny. However, a phylogenetic signal was detected for the amount of terpenoids released by the studied species under WW and DT conditions. A comparative analysis of emission rates of single compounds released by WW and DT plants revealed significant VOC profile dissimilarities in four species only. The moderate drought-induced changes in the odorant emissions of grassland species are discussed with respect to their impact on trophic interactions across the food web. (294 words).

Stomatal improvement for crop stress resistance

The growth and yield of crop plants are threatened by environmental challenges such as water deficit, soil flooding, high salinity, and extreme temperatures, which are becoming increasingly severe under climate change. Stomata contribute greatly to plant adaptation to stressful environments by governing transpirational water loss and photosynthetic gas exchange. Increasing evidence has revealed that stomata formation is shaped by transcription factors, signaling peptides, and protein kinases, which could be exploited to improve crop stress resistance. The past decades have seen unprecedented progress in our understanding of stomata formation, but most of these advances have come from research on model plants. This review highlights recent research in stomata formation in crops and its multifaceted functions in abiotic stress tolerance. Current strategies, limitations, and future directions for harnessing stomatal development to improve crop stress resistance are discussed.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress

Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.

Differential drought tolerance among dichondra (Dichondra repens) genotypes in relation to alterations in chlorophyll metabolism, osmotic adjustment, and accumulation of organic metabolites

Dichondra (Dichondra repens) is an important ground cover plant for landscaping and establishment of green space, but adaptive mechanism of drought tolerance is not well understood in this species. This study was conducted to compare differential response to drought stress among three genotypes (Dr5, Duliujiang, and Dr29) based on integrated physiological, ultrastructural, and metabolic assays. Results showed that drought significantly inhibited photosynthesis, accelerated lipids peroxidation, and also disrupted water balance and cellular metabolism in dichondra plants. Dr5 showed better photochemical efficiency of photosystem II and water homeostasis, less oxidative damage, and more stable chlorophyll metabolism than Duliujinag or Dr29 in response to drought stress. In addition, Dr5 accumulated more amino acids, organic acids, and other metabolites, which was good for maintaining better antioxidant capacity, osmotic homeostasis, and energy metabolism under drought stress. Drought tolerance of Duliujiang was lower than Dr5, but better than Dr29, which could be positively correlated with accumulations of sucrose, maltitol, aconitic acid, isocitric acid, and shikimic acid due to critical roles of these metabolites in osmotic adjustment and metabolic homeostasis. Current findings provide insights into understanding of underlying mechanism of metabolic regulation in dichondra species. Dr5 could be used as an important drought-tolerant resource for cultivation and water-saving breeding.

Drought Stress Responses in Arabica Coffee Genotypes: Physiological and Metabolic Insights

Understanding the impact of drought stress on Arabica coffee physiology and metabolism is essential in the pursuit of developing drought-resistant varieties. In this study, we explored the physiological and metabolite changes in coffee genotypes exhibiting varying degrees of tolerance to drought-namely, the relatively tolerant Ca74110 and Ca74112, and the sensitive Ca754 and CaJ-19 genotypes-under well-watered conditions and during terminal drought stress periods at two time points (0 and 60 days following the onset of stress). The metabolite profiling uncovered significant associations between the growth and the physiological characteristics of coffee genotypes with distinct drought tolerance behaviors. Initially, no marked differences were observed among the genotypes or treatments. However, at the 60-day post-drought onset time point, notably higher shoot growth, biomass, CO2 assimilation, pigments, and various physiological parameters were evident, particularly in the relatively tolerant genotypes. The metabolite profiling revealed elevations in glucose, maltose, amino acids, and organic acids, and decreases in other metabolites. These alterations were more pronounced in the drought-tolerant genotypes, indicating a correlation between enhanced compatible solutes and energy-associated metabolites crucial for drought tolerance mechanisms. This research introduces GC-MS-based metabolome profiling to the study of Ethiopian coffee, shedding light on its intricate responses to drought stress and paving the way for the potential development of drought-resistant coffee seedlings in intensified agro-ecological zones.

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

The combined application of rutin and silicon alleviates osmotic stress in maize seedlings by triggering accumulation of osmolytes and antioxidants' defense mechanisms

Silicon (Si) has been shown to improve plant defenses against a variety of stresses. However, how rutin (Rut) affects stress factors is yet to be fully explored. Moreover, their combined role in osmotic stress response remains unclear. The current study was performed to determine how the use of Rut and Si, both separately and in combination, improved the physiological resilience of maize seedlings to two levels of osmotic stress (induced by polyethylene glycol (PEG) 6000). We aimed to enhance osmotic stress tolerance with the simultaneous use of Rut and Si. First, we selected the best water status and the lowest membrane damage enhancing concentration of Rut (60 ppm) and Si (1 mM) to research their tolerance and resistance to osmotic stress (moderate: 10% PEG, severe: 15% PEG). The application of Rut and Si separately and together reduced oxidative stress by decreasing the reactive oxygen species and improved the relative water content, osmoprotectants (proline, total soluble sugar, and glycine-betaine), ascorbate level, and some antioxidant defense-related enzyme activities and their gene expression in maize seedlings under osmotic stress. However, these effects were more promising under moderate stress. As a result, findings from the study indicate the synergistic effect of combined Rut and Si on osmotic stress tolerance in maize seedlings. Overall, the combination of Rut and Si was more effective than independent Rut and Si in reducing osmotic stress in maize seedlings. Here, it was clear that Rut played an active role in alleviating stress. This combined application can be useful for developing drought tolerance in crops for the agriculture sector.

Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar

The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue 'omics'-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar (Populus tremula× P. alba) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.

Metabolomics reveal root differential metabolites of different root-type alfalfa under drought stress

Introduction

Alfalfa (Medicago sativa L.) is the favored premium feed ingredient in animal husbandry production which is in serious jeopardy due to soil moisture shortages. It is largely unknown how different root types of alfalfa respond to arid-induced stress in terms of metabolites and phytohormones.

Methods

Therefore, rhizomatous rooted M. sativa 'Qingshui' (or QS), tap-rooted M. sativa 'Longdong' (or LD), and creeping rooted M. varia 'Gannong No. 4' (or GN) were investigated to identify metabolites and phytohormones responses to drought conditions.

Results

We found 164, 270, and 68 significantly upregulated differential metabolites were categorized into 35, 38, and 34 metabolic pathways in QS, LD, and GN within aridity stress, respectively. Amino acids, organic acids, sugars, and alkaloids were the four categories of primary differential metabolites detected, which include 6-gingerol, salicylic acid (SA), indole-3-acetic acid (IAA), gibberellin A4 (GA4), abscisic acid (ABA), trans-cinnamic acid, sucrose, L-phenylalanine, L-tyrosine, succinic acid, and nicotinic acid and so on, turns out these metabolites are essential for the resistance of three root-type alfalfa to aridity coercing.

Discussion

The plant hormone signal transduction (PST) pathway was dramatically enriched after drought stress. IAA and ABA were significantly accumulated in the metabolites, indicating that they play vital roles in the response of three root types of alfalfa to water stress, and QS and LD exhibit stronger tolerance than GN under drought stress.

Metabolomics Reveals Lysinibacillus capsici TT41-Induced Metabolic Shifts Enhancing Drought Stress Tolerance in Kimchi Cabbage (Brassica rapa L. subsp. pekinensis)

Climate change has increased variable weather patterns that affect plants. To address these issues, we developed a microbial biocontrol agent against drought stress in kimchi cabbage (Brassica rapa L. subsp. pekinensis). We selected three bacterial strains (Leifsonia sp. CS9, Bacillus toyonensis TSJ7, and Lysinibacillus capsici TT41) because they showed a survival rate of up to 50% and good growth rate when treated with 30% PEG 6000. The three strains were treated with kimchi cabbage to confirm their enhanced drought stress resistance under non-watering conditions. Among the three strains, the TT41 treated group showed a significant increase in various plant parameters compared with the negative control on the 7th day. We performed extensive profiling of primary and secondary metabolites from kimchi cabbage and the TT41 strain. Multivariate and pathway analyses revealed that only the TT41 group clustered with the well-watered group and showed almost the same metabolome on the 7th day. When treated with TT41, lactic acid was identified as an indicator metabolite that significantly improved drought stress tolerance. Furthermore, lactic acid treatment effectively induced drought stress tolerance in kimchi cabbage, similar to that achieved with the TT41 strain.

Common and specific genetic basis of metabolite-mediated drought responses in rice

Plants orchestrate drought responses at metabolic level but the genetic basis remains elusive in rice. In this study, 233 drought-responsive metabolites (DRMs) were quantified in a large rice population comprised of 510 diverse accessions at the reproductive stage. Large metabolic variations in drought responses were detected, and little correlation of metabolic levels between drought and normal conditions were observed. Interestingly, most of these DRMs could predict drought resistance in high accuracy. Genome-wide association study revealed 2522 significant association signals for 233 DRMs, and 98% (2471/2522) of the signals were co-localized with the association loci for drought-related phenotypic traits in the same population or the linkage-mapped QTLs for drought resistance in other populations. Totally, 10 candidate genes were efficiently identified for nine DRMs, seven of which harbored cis-eQTLs under drought condition. Based on comparative GWAS of common DRMs in rice and maize, representing irrigated and upland crops, we have identified three pairs of homologous genes associated with three DRMs between the two crops. Among the homologous genes, a transferase gene responsible for metabolic variation of N-feruloylputrescine was confirmed to confer enhanced drought resistance in rice. Our study provides not only genetic architecture of metabolic responses to drought stress in rice but also metabolic data resources to reveal the common and specific metabolite-mediated drought responses in different crops.

Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress

Climate change is driving an alarming increase in the frequency and intensity of abiotic and biotic stress factors, negatively impacting plant development and agricultural productivity. To survive, plants respond by inducing changes in below and aboveground metabolism with concomitant alterations in defensive secondary metabolites. While plant responses to the isolated stresses of flooding and insect herbivory have been extensively studied, much less is known about their response in combination. Wild relatives of cultivated plants with robust stress tolerance traits provide an excellent system for comparing how diverse plant species respond to combinatorial stress, and provide insight into potential germplasms for stress-tolerant hybrids. In this study, we compared the below and aboveground changes in the secondary metabolites of maize (Zea mays) and a flood-tolerant wild relative Nicaraguan teosinte (Zea nicaraguensis) in response to flooding, insect herbivory, and their combination. Root tissue was analyzed for changes in belowground metabolism. Leaf total phenolic content and headspace volatile organic compound emission were analyzed for changes in aboveground secondary metabolism. Results revealed significant differences in the root metabolome profiles of teosinte and maize. Notably, the accumulation of the flavonoids apigenin, naringenin, and luteolin during flooding and herbivory differentiated teosinte from maize. Aboveground, terpenes, including trans-α-bergamotene and (E)-4,8-dimethylnona-1,3,7-triene, shaped compositional differences in their volatile profiles between flooding, herbivory, and their combination. Taken together, these results suggest teosinte may be more tolerant than maize due to dynamic metabolic changes during flooding and herbivory that help relieve stress and influence plant-insect interactions.

Genome-Wide Identification and Expression Analysis of the Stearoyl-Acyl Carrier Protein Δ9 Desaturase Gene Family under Abiotic Stress in Barley

Stearoyl-acyl carrier protein (ACP) Δ9 desaturase (SAD) is a critical fatty acid dehydrogenase in plants, playing a prominent role in regulating the synthesis of unsaturated fatty acids (UFAs) and having a significant impact on plant growth and development. In this study, we conducted a comprehensive genomic analysis of the SAD family in barley (Hordeum vulgare L.), identifying 14 HvSADs with the FA_desaturase_2 domain, which were divided into four subgroups based on sequence composition and phylogenetic analysis, with members of the same subgroup possessing similar genes and motif structures. Gene replication analysis suggested that tandem and segmental duplication may be the major reasons for the expansion of the SAD family in barley. The promoters of HvSADs contained various cis-regulatory elements (CREs) related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). In addition, expression analysis indicated that HvSADs exhibit multiple tissue expression patterns in barley as well as different response characteristics under three abiotic stresses: salt, drought, and cold. Briefly, this evolutionary and expression analysis of HvSADs provides insight into the biological functions of barley, supporting a comprehensive analysis of the regulatory mechanisms of oil biosynthesis and metabolism in plants under abiotic stress.

Plant response to heavy metal stress toxicity: the role of metabolomics and other omics tools

Metabolomic investigations offers a significant foundation for improved comprehension of the adaptability of plants to reconfigure the key metabolic pathways and their response to changing climatic conditions. Their application to ecophysiology and ecotoxicology help to assess potential risks caused by the contaminants, their modes of action and the elucidation of metabolic pathways associated with stress responses. Heavy metal stress is one of the most significant environmental hazards affecting the physiological and biochemical processes in plants. Metabolomic tools have been widely utilised in the massive characterisation of the molecular structure of plants at various stages for understanding the diverse aspects of the cellular functioning underlying heavy metal stress-responsive mechanisms. This review emphasises on the recent progressions in metabolomics in plants subjected to heavy metal stresses. Also, it discusses the possibility of facilitating effective management strategies concerning metabolites for mitigating the negative impacts of heavy metal contaminants on the growth and productivity of plants.

Assessment of the changes in seed yield and nutritional quality of quinoa grown under rainfed Mediterranean environments

Climate change is considered a serious threat to agriculture and food security. It is linked to rising temperatures and water shortages, conditions that are expected to worsen in the coming decades. Consequently, the introduction of more drought-tolerant crops is required. Quinoa (Chenopodium quinoa Willd.) has received great attention worldwide due to the nutritional properties of its seeds and its tolerance to abiotic stress. In this work, the agronomic performance and seed nutritional quality of three quinoa varieties were studied during two consecutive years (2019-2020) under three water environmental conditions of Southwestern Europe (irrigated conditions, fresh rainfed, and hard rainfed) with the goal of determining the impact of rainfed conditions on this crop performance. High precipitations were recorded during the 2020 growing season resulting in similar grain yield under irrigation and fresh rainfed conditions. However, in 2019, significant yield differences with penalties under water-limiting conditions were found among the evaluated environmental conditions. Furthermore, nutritional and metabolomic differences were observed among seeds harvested from different water environments including the progressive accumulation of glycine betaine accompanied by an increase in saponin and a decrease in iron with water limitation. Generally, water-limiting environments were associated with increased protein contents and decreased yields preserving a high nutritional quality despite particular changes. Overall, this work contributes to gaining further knowledge about how water availability affects quinoa field performance, as it might impact both seed yield and quality. It also can help reevaluate rainfed agriculture, as water deficit can positively impact the nutritional quality of seeds.

Physiological and metabolomic responses of the ethylene insensitive squash mutant etr2b to drought

The squash gain-of-function mutant etr2b disrupts the ethylene-binding domain of ethylene receptor CpETR2B, conferring partial ethylene insensitivity, changes in flower and fruit development, and enhanced salt tolerance. In this paper, we found that etr2b also confers a growth advantage as well as a physiological and metabolomic response that make the mutant better adapted to drought. Mutant plants had a higher root and leaf biomass than WT under both well-watered and drought conditions, but the reduction in growth parameters in response to drought was similar in WT and etr2b. Water deficit reduced all gas-exchange parameters in both WT and etr2b, but under moderate drought the mutant increased photosynthesis rate in comparison with control conditions, and showed a higher leaf CO2 concentration, transpiration rate, and stomata conductance than WT. The response of etr2b to drought indicates that ethylene is a negative regulator of plant growth under both control and drought. Since etr2b increased ABA content in well-watered plant, but prevented the induction of ABA production in response to drought, it is likely that the etr2b response under drought is not mediated by ABA. A 1H NMR metabolomic analysis revealed that etr2b enhances the accumulation of osmolytes (soluble sugars and trigonelline), unsaturated and polyunsaturated fatty acids, and phenolic compounds under drought, concomitantly with a reduction of malic- and fumaric-acid. The role of CpETR2B and ethylene in the regulation of these drought-protective metabolites is discussed.

Morphological Structure and Physiological and Biochemical Responses to Drought Stress of Iris japonica

Drought is among the most important abiotic stresses on plants, so research on the physiological regulation mechanisms of plants under drought stress can critically increase the economic and ecological value of plants in arid regions. In this study, the effects of drought stress on the growth status and biochemical indicators of Iris japonica were explored. Under drought stress, the root system, leaves, rhizomes, and terrestrial stems of plants were sequentially affected; the root system was sparse and slender; and the leaves lost their luster and gradually wilted. Among the physiological changes, the increase in the proline and soluble protein content of Iris japonica enhanced the cellular osmotic pressure and reduced the water loss. In anatomical structures, I. japonica chloroplasts were deformed after drought treatment, whereas the anatomical structures of roots did not substantially change. Plant antioxidant systems play an important role in maintaining cellular homeostasis; but, as drought stress intensified, the soluble sugar content of terrestrial stems was reduced by 55%, and the ascorbate peroxidase, glutathione reductase, and monodehydroascorbate reductase (MDHAR) activities of leaves and the MDHAR activity of roots were reduced by 29%, 40%, 22%, and 77%, respectively. Overall, I. japonica was resistant to 63 days of severe drought stress and resisted drought through various physiological responses. These findings provide a basis for the application of I. japonica in water-scarce areas.

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

BACKGROUND

Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR.

RESULTS

We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress.

CONCLUSIONS

The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.

Phytochemical Analysis and Antioxidant Evaluation of the Ethanolic Extract of the Leaves of Abutilon indicum

BACKGROUND

In Indian traditional medicine, the Abutilon indicum plant, colloquially known as "Country mallow" or "Thuthi", has been vouched for its efficacy in treating conditions such as bronchitis and diabetes. The study aimed to explore the chemical constituents and antioxidant strength of the ethanolic extracts derived from the leaves of this plant (ELEAI).

OBJECTIVES

To qualitatively pinpoint the phytochemicals in the ethanolic extract of abutilon indicum leaves (ELEAI), utilize high-performance thin layer chromatography (HPTLC) to quantitatively analyze the identified compounds within the ELEAI, and gauge its antioxidant capability through the DPPH method, benchmarking the outcomes against the recognized standard, ascorbic acid.

METHODS

Abutilon indicum leaves, originating from Telangana, were authenticated by taxonomists at Osmania University. After cleaning and drying, the leaves were powdered. A mixture of ethanol and water (70:30 ratio) was then used to extract the compounds in a Soxhlet extractor for a duration of 72 hours at a temperature of 60°C. The liquid extract was subsequently evaporated to form a light-brown powder, which was stored at 20°C under shade for later use.

RESULTS

Preliminary analyses indicated that ELEAI was rich in both primary and secondary metabolites. Luteolin, a known phytochemical, was quantitatively confirmed in the extract using HPTLC. Impressively, the DPPH assay highlighted ELEAI's remarkable antioxidant capabilities.

CONCLUSION

Abutilon indicum showcases notable therapeutic potential with its rich phytochemical content and strong antioxidant activity, making it a promising candidate for further pharmacological research and natural drug formulation.

Rhizobacteria-enhanced drought tolerance and post-drought recovery of creeping bentgrass involving differential modulation of leaf and root metabolism

Rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCd) that inhibits ethylene production may mitigate stress damages. The objectives of this study were to examine whether a novel strain of ACCd-producing bacteria, Paraburkholderia aspalathi "WSF23," promotes plant tolerance to drought stress and post-stress recovery and determine changes in metabolic profiles in leaves and roots associated with the positive ACCd-bacteria effects in cool-season perennial grass species. Creeping bentgrass (Agrostis Stolonifera L. cv. "Penncross") plants were inoculated with P. aspalathi "WSF23" and exposed to drought by withholding irrigation for 35 days, followed by re-watering for 15 days in growth chambers. Inoculated plants demonstrated increased turf quality, canopy density, and root growth during drought stress and more rapid re-growth upon re-watering. Metabolomic analysis demonstrated that inoculation with P. aspalathi "WSF 23" increased the content of metabolites in the metabolic pathways related to stress defense, including osmoregulation, cell wall stability, and antioxidant protection in both leaves and roots, as well as nitrogen metabolism in roots of creeping bentgrass exposed to drought stress. The promotion of post-stress recovery by P. aspalathi "WSF 23" was mainly associated with enhanced carbohydrate and pyrimidine metabolism and zeatin biosynthesis pathways in leaves and increased carbohydrates, biosynthesis of DNA and proteins, cellular metabolism, and TCA cycle activity in roots. These results provide insights into the metabolic pathways regulated by "WSF23," with the PGPR conferring improvements in drought stress tolerance and post-drought recovery in a perennial grass species.

Comprehensive Transcriptome and Metabolome Analyses Reveal Primary Molecular Regulation Pathways Involved in Peanut under Water and Nitrogen Co-Limitation

The yield and quality of peanut (Arachis hypogaea L.), an oil crop planted worldwide, are often limited by drought stress (DS) and nitrogen (N) deficiency. To investigate the molecular mechanism by which peanut counteracts DS and N deficiency, we conducted comprehensive transcriptomic and metabolomic analyses of peanut leaves. Herein, 829 known differentially accumulated metabolites, 324 differentially expressed transcription factors, and 5294 differentially expressed genes (DEGs) were identified under different water and N conditions. The transcriptome analysis demonstrated that drought-related DEGs were predominantly expressed in "glycolysis/gluconeogenesis" and "glycerolipid metabolism", while N-deficiency-related DEGs were mainly expressed in starch and sucrose metabolism, as well as in the biosynthesis of amino acid pathways. The biosynthesis, transport, and catabolism of secondary metabolites accounted for a large proportion of the 1317 DEGs present in water and N co-limitation. Metabolomic analysis showed that the metabolic accumulation of these pathways was significantly dependent on the stress conditions. Additionally, the roles of metabolites and genes in these pathways, such as the biosynthesis of amino acids and phenylpropanoid biosynthesis under different stress conditions, were discussed. The results demonstrated that different genes, metabolic pathways, and metabolites were related to DS and N deficiency. Thus, this study elucidates the metabolic pathways and functional genes that can be used for the improvement of peanut resistance to abiotic stress.

Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response

Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.

Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth

Studying intraspecific variation in multistress responses is central for predicting and managing the population dynamics of wild plant species under rapid global change. Yet, it remains a challenging goal in this field to integrate knowledge on the complex biochemical underpinnings for the targeted 'non-model' species. Here, we studied divergence in combined drought and heat responses among Northern and Southern European populations of the dune plant Cakile maritima, by combining comprehensive plant phenotyping with metabolic profiling via FT-ICR-MS and UPLC-TQ-MS/MS. We observed pronounced constitutive divergence in growth phenology, leaf functional traits, and defence chemistry (glucosinolates and alkaloids) among population origins. Most importantly, the magnitude of growth reduction under drought was partly weaker in southern plants and associated with divergence in plastic growth responses (leaf abscission) and the modulation of primary and specialized metabolites with known central functions not only in plant abiotic but also in biotic stress responses. Our study indicates that divergent selection has shaped the constitutive and drought-/heat-induced expression of numerous morphological and biochemical functional traits to mediate higher abiotic stress resistance in southern Cakile populations, and highlights that metabolomics can be a powerful tool to explore the underlying mechanisms of local adaptation in 'non-model' species.

Evaluation of Differentially Expressed Genes in Leaves vs. Roots Subjected to Drought Stress in Flax (Linum usitatissimum L.)

Drought stress is a common environmental challenge that plants face, severely constraining plant growth and reducing crop yield and quality. Several studies have highlighted distinct responses between monocotyledonous and dicotyledonous plants. However, the mechanisms underlying flax tolerance to abiotic stress, such as drought, remain unclear. In this study, we investigated the morphological, physiological, and biochemical characteristics and the genome-wide gene expression of oil flax and fiber flax in response to drought stress. The results revealed that drought stress caused significant wilting of flax leaves. Within the first 24 h of stress, various physiological and biochemical characteristics exhibited rapid responses. These included fresh weight, relative water content (RWC), proline, soluble protein, soluble sugar, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in the leaves or roots of flax. Additionally, drought stress led to a significant rise in lignin content in fiber flax. In addition, the transcriptome analysis demonstrated genome-wide variations in gene expression induced by drought stress. Specifically, genes associated with photosynthesis, proline biosynthesis, and phytohormone metabolism exhibited significant differences in expression levels under stress conditions in flax. These findings highlight the rapid response of flax to drought stress within a short-term period. Our experiment also revealed that, although there were variations in the levels of small compound content or gene expression between Longya10 and Fany under drought stress, most stress-resistance responses were similar. Furthermore, the results provide additional evidence supporting the existence of mechanisms underlying the response to drought stress in plants.

The Metabolic Profile of Young, Watered Chickpea Plants Can Be Used as a Biomarker to Predict Seed Number under Terminal Drought

Chickpea is the second-most-cultivated legume globally, with India and Australia being the two largest producers. In both of these locations, the crop is sown on residual summer soil moisture and left to grow on progressively depleting water content, finally maturing under terminal drought conditions. The metabolic profile of plants is commonly, correlatively associated with performance or stress responses, e.g., the accumulation of osmoprotective metabolites during cold stress. In animals and humans, metabolites are also prognostically used to predict the likelihood of an event (usually a disease) before it occurs, e.g., blood cholesterol and heart disease. We sought to discover metabolic biomarkers in chickpea that could be used to predict grain yield traits under terminal drought, from the leaf tissue of young, watered, healthy plants. The metabolic profile (GC-MS and enzyme assays) of field-grown chickpea leaves was analysed over two growing seasons, and then predictive modelling was applied to associate the most strongly correlated metabolites with the final seed number plant^-1. Pinitol (negatively), sucrose (negatively) and GABA (positively) were significantly correlated with seed number in both years of study. The feature selection algorithm of the model selected a larger range of metabolites including carbohydrates, sugar alcohols and GABA. The correlation between the predicted seed number and actual seed number was R² adj = 0.62, demonstrating that the metabolic profile could be used to predict a complex trait with a high degree of accuracy. A previously unknown association between D-pinitol and hundred-kernel weight was also discovered and may provide a single metabolic marker with which to predict large seeded chickpea varieties from new crosses. The use of metabolic biomarkers could be used by breeders to identify superior-performing genotypes before maturity is reached.

Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.

Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways

Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.

Cheap, cost-effective, and quick stress biomarkers for drought stress detection and monitoring in plants

The detection and monitoring of drought stress in plants growing in their natural habitat are essential for the study of plant stress physiology. However, with the advent of plant phenotyping and new -omics technologies, the application of simple, cheap, cost-effective, quick, and practical methods to assess drought stress in plants seems more challenging than ever, particularly in low-income countries. Here, currently available methods that do not require specialized equipment, but reliably detect and monitor drought stress in plants at low cost will be discussed. This will not only boost research on plant stress physiology in low-income countries but will also help several laboratories with very limited resources around the globe to perform high-quality research.

Radon adsorption and air purification by Spanish moss (Tillandsia usneoides) and its metabolic response to radon exposure

The capacity of Spanish moss (Tillandsia usneoides), an aerial plant, to adsorb radon (Rn) and absorb CO₂ was assessed to analyze its capacity to remove pollutants from indoor air and to determine its radon (Rn) tolerance mechanism. Transcriptomics and metabolomics techniques were used to analyze the response of the plant to Rn exposure. Spanish moss absorbed indoor CO₂ at night using the type of photosynthesis termed crassulacean acid metabolism. The CO₂ absorption efficiency of the plant was mainly affected by the light duration and diurnal temperature differences. The highest purification efficiency was 48.25%, and the scales on the Spanish moss leaf surface were the key sites for Rn adsorption. Metabolome analysis showed that Rn exposure induced differential metabolites significantly enriched in the metabolism of lipids, amino acids, nucleotides, and carbohydrates. Transcriptome analysis showed significantly upregulated expression levels of functional genes in Rn-exposed leaves. Rn had significant effects on respiratory metabolism, as indicated by upregulated expression of metabolites and functional genes related to the glycolysis pathway, pyruvate oxidation, tricarboxylic acid cycle, and oxidative phosphorylation pathway. These responses indicated that the internal mechanism by which Spanish moss alleviates Rn stress involves an enhancement of cellular energy supplies and regulation of respiratory metabolic pathways to allow adaptation to Rn pollution.

How Central Carbon Metabolites of Mexican Mint (Plectranthus amboinicus) Plants Are Impacted under Different Watering Regimes

Plants are sessile, and their ability to reprogram their metabolism to adapt to fluctuations in soil water level is crucial but not clearly understood. A study was performed to determine alterations in intermediate metabolites involved in central carbon metabolism (CCM) following exposure of Mexican mint (Plectranthus amboinicus) to varying watering regimes. The water treatments were regular watering (RW), drought (DR), flooding (FL), and resumption of regular watering after flooding (DHFL) or after drought (RH). Leaf cluster formation and leaf greening were swift following the resumption of regular watering. A total of 68 key metabolites from the CCM routes were found to be significantly (p < 0.01) impacted by water stress. Calvin cycle metabolites in FL plants, glycolytic metabolites in DR plants, total tricarboxylic acid (TCA) cycle metabolites in DR and DHFL plants, and nucleotide biosynthetic molecules in FL and RH plants were significantly (p < 0.05) increased. Pentose phosphate pathway (PPP) metabolites were equally high in all the plants except DR plants. Total Calvin cycle metabolites had a significantly (p < 0.001) strong positive association with TCA cycle (r = 0.81) and PPP (r = 0.75) metabolites. Total PPP metabolites had a moderately positive association with total TCA cycle metabolites (r = 0.68; p < 0.01) and a negative correlation with total glycolytic metabolites (r = -0.70; p < 0.005). In conclusion, the metabolic alterations of Mexican mint plants under different watering regimes were revealed. Future studies will use transcriptomic and proteomic approaches to identify genes and proteins that regulate the CCM route.

Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice

Background

The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown.

Results

This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways.

Conclusion

Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

The impact of boron nutrient supply in mulberry (Morus alba) response to metabolomics, enzyme activities, and physiological parameters

Boron (B) is essential for normal and healthy plant growth. Therefore, Boron stress is a common abiotic stress that limits plant growth and productivity. However, how mulberry copes with boron stress remains unclear. In this study, seedlings of the Morus alba cultivar, Yu-711, were treated with five different concentrations of boric acid (H₃BO₃), including deficient (0 and 0.02 mM), sufficient (0.1 mM) and toxic (0.5 and 1 mM) levels. Physiological parameters, enzymatic activities and non-targeted liquid chromatography-mass spectrometry (LC-MS) technique were employed to evaluate the effects of boron stress on the net photosynthetic rate (Pn), chlorophyll content, stomatal conductance (Gs), transpiration rate (Tr), intercellular CO₂ concentration (Ci) and metabolome signatures. Physiological analysis revealed that Boron deficiency and toxicity induced a decline in P_n, C_i, G_s, T_r, and chlorophyll content. Also, enzymatic activities, including catalase (CAT) and superoxide dismutase (SOD), decreased, while POD activity increased in response to Boron stress. Osmotic substances such as soluble sugars, soluble proteins, and proline (PRO) presented elevated levels under all Boron concentrations. Metabolome analysis indicated that differential metabolites, including amino acids, secondary metabolites, carbohydrates, and lipids, played a key role in Yu-711's response to Boron stress. These metabolites were mainly involved in amino acid metabolism, biosynthesis of other secondary metabolites, lipid metabolism, metabolism of cofactors and vitamins, and metabolism of other amino acids pathways. Our findings reveal the various metabolites pathways in mulberry response to boron nutrient supply and may serve as fundamental knowledge in breeding resistance mulberry plants, so that it can cope with climate changes.

Integrated transcriptome and metabonomic analysis of key metabolic pathways in response to cadmium stress in novel buckwheat and cultivated species

INTRODUCTION

Buckwheat (Fagopyrum tataricum), an important food crop, also has medicinal uses. It is widely planted in Southwest China, overlapping with planting areas remarkably polluted by cadmium (Cd). Therefore, it is of great significance to study the response mechanism of buckwheat under Cd stress and further develop varieties with excellent Cd tolerance.

METHODS

In this study, two critical periods of Cd stress treatment (days 7 and 14 after Cd treatment) of cultivated buckwheat (Pinku-1, named K33) and perennial species (F. tatari-cymosum Q.F. Chen) (duoku, named DK19) were analyzed using transcriptome and metabolomics.

RESULTS

The results showed that Cd stress led to changes in reactive oxygen species (ROS) and the chlorophyll system. Moreover, Cd-response genes related to stress response, amino acid metabolism, and ROS scavenging were enriched or activated in DK19. Transcriptome and metabolomic analyses highlighted the important role of galactose, lipid (glycerophosphatide metabolism and glycerophosphatide metabolism), and glutathione metabolism in response to Cd stress in buckwheat, which are significantly enriched at the gene and metabolic levels in DK19.

DISCUSSION

The results of the present study provide valuable information for a better understanding of the molecular mechanisms underlying Cd tolerance in buckwheat and useful clues for the genetic improvement of drought tolerance in buckwheat.

Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress

Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.

Morphological and Physio-Chemical Responses to PEG-Induced Water Stress in Vanilla planifolia and V. pompona Hybrids

Vanilla planifolia is an orchid of cultural and economic value. However, its cultivation in many tropical countries is threatened by water stress. In contrast, V. pompona is a species that is tolerant of prolonged periods of drought. Due to the need for plants' resistant to water stress, the use of hybrids of these two species is considered. Therefore, the objective of this study was to evaluate the morphological and physio-chemical responses of in vitro vanilla seedlings of the parental genotype V. planifolia, and the hybrids V. planifolia × V. pompona and V. pompona × V. planifolia, which were then exposed over five weeks to polyethylene glycol-induced water stress (-0.49 mPa). Stem and root length, relative growth rate, number of leaves and roots, stomatal conductance, specific leaf area, and leaf water content were determined. Metabolites potentially associated with the response to water stress were identified in leaves, through untargeted and targeted metabolomics. Both hybrids exhibited a smaller decrease in the morphophysiological responses compared to V. planifolia and exhibited an enrichment of metabolites such as carbohydrates, amino acids, purines, phenols, and organic acids. Hybrids of these two species are considered as a potential alternative to the traditional cultivation of vanilla to face drought in a global warming scenario.

FLS2-RBOHD module regulates changes in the metabolome of Arabidopsis in response to abiotic stress

Through crosstalk, FLAGELLIN SENSITIVE 2 (FLS2) and RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) are involved in regulating the homeostasis of cellular reactive oxygen species (ROS) and are linked to the metabolic response of plants toward both biotic and abiotic stress. In the present study, we examined the metabolome of Arabidopsis seedlings under drought and salt conditions to better understand the potential role of FLS2 and RBOHD-dependent signaling in the regulation of abiotic stress response. We identified common metabolites and genes that are regulated by FLS2 and RBOHD, and are involved in the response to drought and salt stress. Under drought conditions, D-aspartic acid and the expression of associated genes, such as ASPARAGINE SYNTHASE 2 (ASN2), increased in both fls2 and robed/f double mutants. The accumulation of amino acids, carbohydrates, and hormones, such as L-proline, D-ribose, and indoleacetaldehyde increased in both fls2 and rbohd/f double mutants under salt conditions, as did the expression of related genes, such as PROLINE IMINOPEPTIDASE, PHOSPHORIBOSYL PYROPHOSPHATE SYNTHASE 5, and NITRILASE 3. Collectively, these results indicate that the FLS2-RBOHD module regulates plant response to drought and salt stress through ROS signaling by adjusting the accumulation of metabolites and expression of genes related to metabolite synthesis.

Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco

Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

Responses of differential metabolites and pathways to high temperature in cucumber anther

Cucumber is one of the most important vegetable crops, which is widely planted all over the world. Cucumber always suffers from high-temperature stress in South China in summer. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis was used to study the differential metabolites of cucumber anther between high-temperature (HT) stress and normal condition (CK). After HT, the pollen fertility was significantly reduced, and abnormal anther structures were observed by the paraffin section. In addition, the metabolomics analysis results showed that a total of 125 differential metabolites were identified after HT, consisting of 99 significantly upregulated and 26 significantly downregulated metabolites. Among these differential metabolites, a total of 26 related metabolic pathways were found, and four pathways showed significant differences, namely, porphyrin and chlorophyll metabolism; plant hormone signal transduction; amino sugar and nucleotide sugar metabolism; and glycine, serine, and threonine metabolism. In addition, pollen fertility was decreased by altering the metabolites of plant hormone signal transduction and amino acid and sugar metabolism pathway under HT. These results provide a comprehensive understanding of the metabolic changes in cucumber anther under HT.

Mitochondrial alternative oxidase enhanced ABA-mediated drought tolerance in Solanum lycopersicum

The phytohormone abscisic acid (ABA) plays essential roles in modulating drought stress responses. Mitochondrial alternative oxidase (AOX) is critical for reactive oxygen species (ROS) scavenging in drought stress responses. However, whether ABA signal in concert with AOX to moderate drought stress response remains largely unclear. In our study, we uncover the positive role of AOX in ABA-mediated drought tolerance in tomato (Solanum lycopersicum). Here, we report that ABA participates in the regulation of alternative respiration, and the increased AOX was found to improve drought tolerance by reducing total ROS accumulation. We also found that transcription factor ABA response element-binding factor 1 (SlAREB1) can directly bind to the promoter of AOX1a to activate its transcription. Virus-induced gene silencing (VIGS) of SlAREB1 compromised the ABA-induced alternative respiratory pathway, disrupted redox homeostasis and decreased plant resistance to drought stress, while overexpression of AOX1a in TRV2-SlAREB1 plants partially rescued the severe drought phenotype. Taken together, our results indicated that AOX1a plays an essential role in ABA-mediated drought tolerance partially in a SlAREB1-dependent manner, providing new insights into how ABA modulates ROS levels to cope with drought stress by AOX.

Grape Berry Responses to Sequential Flooding and Heatwave Events: A Physiological, Transcriptional, and Metabolic Overview

Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenarios.

Identification of Competing Endogenous RNAs (ceRNAs) Network Associated with Drought Tolerance in Medicago truncatula with Rhizobium Symbiosis

Drought, bringing the risks of agricultural production losses, is becoming a globally environmental stress. Previous results suggested that legumes with nodules exhibited superior drought tolerance compared with the non-nodule group. To investigate the molecular mechanism of rhizobium symbiosis impacting drought tolerance, transcriptome and sRNAome sequencing were performed to identify the potential mRNA-miRNA-ncRNA dynamic network. Our results revealed that seedlings with active nodules exhibited enhanced drought tolerance by reserving energy, synthesizing N-glycans, and medicating systemic acquired resistance due to the early effects of symbiotic nitrogen fixation (SNF) triggered in contrast to the drought susceptible with inactive nodules. The improved drought tolerance might be involved in the decreased expression levels of miRNA such as mtr_miR169l-5p, mtr_miR398b, and mtr_miR398c and its target genes in seedlings with active nodules. Based on the negative expression pattern between miRNA and its target genes, we constructed an mRNA-miR169l-ncRNA ceRNA network. During severe drought stress, the lncRNA alternative splicings TCONS_00049507 and TCONS_00049510 competitively interacted with mtr_miR169l-5p, which upregulated the expression of NUCLEAR FACTOR-Y (NF-Y) transcription factor subfamily NF-YA genes MtNF-YA2 and MtNF-YA3 to regulate their downstream drought-response genes. Our results emphasized the importance of SNF plants affecting drought tolerance. In conclusion, our work provides insight into ceRNA involvement in rhizobium symbiosis contributing to drought tolerance and provides molecular evidence for future study.

Molecular Breeding and Drought Tolerance in Chickpea

Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).

Mechanisms involved in drought stress tolerance triggered by rhizobia strains in wheat

Rhizobium spp. is a well-known microbial plant biostimulant in non-legume crops, but little is known about the mechanisms by which rhizobia enhance crop productivity under drought stress. This work analyzed the mechanisms involved in drought stress alleviation exerted by Rhizobium leguminosarum strains in wheat plants under water shortage conditions. Two (LBM1210 and LET4910) of the four R. leguminosarum strains significantly improved the growth parameters (fresh and dry aerial weight, FW and DW, respectively), chlorophyll content, and relative water content (RWC) compared to a non-inoculated control under water stress, providing values similar to or even higher for FW (+4%) and RWC (+2.3%) than the non-inoculated and non-stressed control. Some other biochemical parameters and gene expression explain the observed drought stress alleviation, namely the reduction of MDA, H₂O₂ (stronger when inoculating with LET4910), and ABA content (stronger when inoculating with LBM1210). In agreement with these results, inoculation with LET4910 downregulated DREB2 and CAT1 genes in plants under water deficiency and upregulated the CYP707A1 gene, while inoculation with LBM1210 strongly upregulated the CYP707A1 gene, which encodes an ABA catabolic enzyme. Conversely, from our results, ethylene metabolism did not seem to be involved in the alleviation of drought stress exerted by the two strains, as the expression of the CTR1 gene was very similar in all treatments and controls. The obtained results regarding the effect of the analyzed strains in alleviating drought stress are very relevant in the present situation of climate change, which negatively influences agricultural production.

Identification and differential analysis of noncoding RNAs in response to drought in Phyllostachys aureosulcata f. spectabilis

The role of noncoding RNAs (ncRNAs) in plant resistance to abiotic stresses is increasingly being discovered. Drought stress is one of the most common stresses that affecting plant growth, and high intensity drought has a significant impact on the normal growth of plants. In this study, a high-throughput sequencing was performed on plant tissue samples of Phyllostachys aureosulcata f. spectabilis C. D. Chu et C. S. Chao by drought treatment for 0, 2, 4 and 6 days. The sequencing results were analysed bioinformatically. We detected 336,946 RNAs among all 12 samples, including 192,098 message RNAs (mRNAs), 142,761 long noncoding RNAs (lncRNAs), 1,670 circular RNAs (circRNAs), and 417 microRNAs (miRNAs). We detected 2,419 differentially expressed (DE) ncRNAs, including 213 DE circRNAs, 2,088 DE lncRNAs and 118 DE miRNAs. Then, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to functionally predict DE ncRNAs. The results showed that most DE ncRNAs are involved in the response to drought stress, mainly in biochemical reactions involved in some metabolites, as well as in organelle activities. In addition, we validated two random circRNAs and demonstrated their circularity. We also found a stable internal reference gene available for Phyllostachys aureosulcata f. spectabilis and validated the accuracy of this experiment by quantitative real-time polymerase chain reaction (qRT-PCR).

Transcriptome Profiling to the Effects of Drought Stress on Different Propagation Modes of Tea Plant (Camellia sinensis)

Tea plant (Camellia sinensis) is an important economic beverage crop. Drought stress seriously affects the growth and development of tea plant and the accumulation of metabolites, as well as the production, processing, yield and quality of tea. Therefore, it is necessary to understand the reaction mechanism of tea plant under drought conditions and find efficient control methods. Based on transcriptome sequencing technology, this study studied the difference of metabolic level between sexual and asexual tea plants under drought stress. In this study, there were multiple levels of up-regulation and down-regulation of differential genes related to cell composition, molecular function and biological processes. Transcriptomic data show that the metabolism of tea plants with different propagation modes of QC and ZZ is different under drought conditions. In the expression difference statistics, it can be seen that the differential genes of QC are significantly more than ZZ; GO enrichment analysis also found that although differential genes in biological process are mainly enriched in the three pathways of metabolic, single organism process and cellular process, cellular component is mainly enriched in cell, cell part, membrane, and molecular function, and binding, catalytic activity, and transporter activity; the enrichment order of differential genes in these pathways is different in QC and ZZ. This difference is caused by the way of reproduction. The further study of these differential genes will lay a foundation for the cultivation methods and biotechnology breeding to improve the quality of tea.

Carex rigescens caffeic acid O-methyltransferase gene CrCOMT confer melatonin-mediated drought tolerance in transgenic tobacco

Melatonin is an important, multifunctional protective agent against a variety of abiotic and biotic stressors in plants. Caffeic acid O-methyltransferase (COMT) catalyzes the last step of melatonin synthesis in plants and reportedly participates in the regulation of stress response and tolerance. However, few studies have reported its function in melatonin-mediated drought resistance. In this study, CrCOMT was identified and was strongly induced by drought stress in Carex rigescens. CrCOMT overexpression in transgenic tobacco increased tolerance to drought stress with high levels of seed germination, relative water content, and survival rates. CrCOMT overexpression in tobacco improved membrane stability, and plants exhibited lower relative electrolytic leakage and malondialdehyde content, as well as higher photochemical efficiency than the wildtype (WT) under drought stress. The transgenic plants also had higher levels of proline accumulation and antioxidant enzyme activity, which decreased oxidative stress damage due to reactive oxygen species (ROS) hyperaccumulation under drought stress. The transcription of drought stress response and ROS scavenging genes was significantly higher in the CrCOMT overexpression plants than in the WT plants. In addition, CrCOMT transgenic tobacco plants exhibited higher melatonin content under drought stress conditions. Exogenous melatonin was applied to C. rigescens under drought stress to confirm the function of melatonin in mediating drought tolerance; the relative water content and proline content were higher, and the relative electrolytic leakage was lower in melatonin-treated C. rigescens than in the untreated plants. In summary, these results show that CrCOMT plays a positive role in plant drought stress tolerance by regulating endogenous melatonin content.

Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.