Metabolite Profiles of Maize Leaves in Drought, Heat, and Combined Stress Field Trials Reveal the Relationship between Metabolism and Grain Yield

Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes

The hydrophobic cuticle is the first line of defense between aerial portions of plants and the external environment. On maize (Zea mays L.) silks, the cuticular cutin matrix is infused with cuticular waxes, consisting of a homologous series of very long-chain fatty acids (VLCFAs), aldehydes, and hydrocarbons. Together with VLC fatty-acyl-CoAs (VLCFA-CoAs), these metabolites serve as precursors, intermediates, and end-products of the cuticular wax biosynthetic pathway. To deconvolute the potentially confounding impacts of the change in silk microenvironment and silk development on this pathway, we profiled cuticular waxes on the silks of the inbreds B73 and Mo17, and their reciprocal hybrids. Multivariate interrogation of these metabolite abundance data demonstrates that VLCFA-CoAs and total free VLCFAs are positively correlated with the cuticular wax metabolome, and this metabolome is primarily affected by changes in the silk microenvironment and plant genotype. Moreover, the genotype effect on the pathway explains the increased accumulation of cuticular hydrocarbons with a concomitant reduction in cuticular VLCFA accumulation on B73 silks, suggesting that the conversion of VLCFA-CoAs to hydrocarbons is more effective in B73 than Mo17. Statistical modeling of the ratios between cuticular hydrocarbons and cuticular VLCFAs reveals a significant role of precursor chain length in determining this ratio. This study establishes the complexity of the product-precursor relationships within the silk cuticular wax-producing network by dissecting both the impact of genotype and the allocation of VLCFA-CoA precursors to different biological processes and demonstrates that longer chain VLCFA-CoAs are preferentially utilized for hydrocarbon biosynthesis.

Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple

BACKGROUND

The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses.

RESULTS

Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants.

CONCLUSIONS

The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.

Biochemical characterization and metabolic reprogramming of amino acids in Soybean roots under drought stress

Amino acids play important roles in stress resistance, plant growth, development, and quality, with roots serving as the primary organs for drought response. We conducted biochemical and multi-omics analyses to investigate the metabolic processes of root amino acids in drought-resistant (HN44) and drought-sensitive (HN65) soybean (Glycine max) varieties. Our analysis revealed an increase in total amino acid content in both varieties, with phenylalanine, proline, and methionine accumulating in both. Additionally, several amino acids exhibited significant decreases in HN65 but slight increases in HN44. Multi-omics association analysis identified 13 amino acid-related pathways. We thoroughly examined the changes in genes and metabolites involved in various amino acid metabolism/synthesis and determined core genes and metabolites through correlation networks. The phenylalanine, tyrosine, and tryptophan metabolic pathways and proline, glutamic acid and sulfur-containing amino acid pathways were particularly important for drought resistance. Some candidate genes, such as ProDH and P4HA family genes, and metabolites, such as O-acetyl-L-serine, directly affected up- and downstream metabolism to induce drought resistance. This study provided a basis for soybean drought resistance breeding.

Utilizing transcriptomics and metabolomics to unravel key genes and metabolites of maize seedlings in response to drought stress

BACKGROUND

Drought stress can substantially restrict maize growth and productivity, and global warming and an increasing frequency of extreme weather events are likely to result in more yield losses in the future. Therefore, unraveling the molecular mechanism underlying the response to drought stress is essential for breeding drought-resilient crops.

RESULTS

In this study, we subjected the 3-leaf-period plants of two maize inbred lines, a drought-tolerant line (si287) and a drought-sensitive line (X178), to drought stress for seven days while growing in a chamber. Subsequently, we measured physiological traits and analyzed transcriptomic and metabolic profiles of two inbred lines. Our KEGG analysis of genes and metabolites revealed significant differences in pathways related to glycolysis/gluconeogenesis, flavonoid biosynthesis, starch and sucrose metabolism, and biosynthesis of amino acids. Additionally, our joint analysis identified proline, tryptophan and phenylalanine are crucial amino acids for maize response to drought stress. Furthermore, we concentrated on tryptophan (Trp), which was found to enhance tolerance via IAA-ABA signaling, as well as SA and nicotinamide adenine dinucleotide (NAD) consequent reactive oxygen species (ROS) scavenging. We identified three hub genes in tryptophan biosynthesis, indole-3-acetaldehyde oxidase (ZmAO1, 542,228), catalase 1 (ZmCAT1, 542,369), and flavin-containing monooxygenase 6 (ZmYUC6, 103,629,142), High expression of these genes plays a significant role in regulating drought tolerance. Two metabolites related to tryptophan biosynthesis, quinolinic acid, and kynurenine improved maize tolerance to drought stress by scavenging reactive oxygen species.

CONCLUSIONS

This study illuminates the mechanisms underlying the response of maize seedlings to drought stress. Especially, it identifies novel candidate genes and metabolites, enriching our understanding of the role of tryptophan in drought stress. The identification of distinct resistance mechanisms in maize inbred lines will facilitate the exploration of maize germplasm and the breeding of drought-resilient hybrids.

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.

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Comparison of metabolomic reconfiguration between Columbia and Landsberg ecotypes subjected to the combination of high salinity and increased irradiance

BACKGROUND

Plants growing in the field are subjected to combinations of abiotic stresses. These conditions pose a devastating threat to crops, decreasing their yield and causing a negative economic impact on agricultural production. Metabolic responses play a key role in plant acclimation to stress and natural variation for these metabolic changes could be key for plant adaptation to fluctuating environmental conditions.

RESULTS

Here we studied the metabolomic response of two Arabidopsis ecotypes (Columbia-0 [Col] and Landsberg erecta-0 [Ler]), widely used as genetic background for Arabidopsis mutant collections, subjected to the combination of high salinity and increased irradiance. Our findings demonstrate that this stress combination results in a specific metabolic response, different than that of the individual stresses. Although both ecotypes displayed reduced growth and quantum yield of photosystem II, as well as increased foliar damage and malondialdehyde accumulation, different mechanisms to tolerate the stress combination were observed. These included a relocation of amino acids and sugars to act as potential osmoprotectants, and the accumulation of different stress-protective compounds such as polyamines or secondary metabolites.

CONCLUSIONS

Our findings reflect an initial identification of metabolic pathways that differentially change under stress combination that could be considered in studies of stress combination of Arabidopsis mutants that include Col or Ler as genetic backgrounds.

Transcriptome and metabolome analysis reveals key genes and secondary metabolites of Casuarina equisetifolia ssp. incana in response to drought stress

Casuarina equisetifolia is drought tolerant, salt tolerant, and able to grow in barren environments. It is often used to reduce wind damage, to prevent sand erosion, and to help establish plant communities in tropical and subtropical coastal zones. To determine the basis for its drought tolerance, we conducted transcriptomic and metabolic analyses of young branchlets under a non-drought treatment (D_0h) and 2-, 12-, and 24-h-long drought treatments (D_2h, D_12h, and D_24h). A total of 5033 and 8159 differentially expressed genes (DEGs) were identified in D_2h/D_0h and D_24h/D_0h. These DEGs were involved in plant hormone signal transduction, jasmonic acid (JA) biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. A total of 148 and 168 differentially accumulated metabolites (DAMs) were identified in D_12h/D_0h and D_24h/D_0h, which were mainly amino acids, phenolic acids, and flavonoids. In conclusion, C. equisetifolia responds to drought by regulating plant hormone signal transduction and the biosynthesis of JA, flavonoid, and phenylpropanoid. These results increase the understanding of drought tolerance in C. equisetifolia at both transcriptional and metabolic levels and provide new insights into coastal vegetation reconstruction and management.

Transcriptional dynamics of maize leaves, pollens and ovules to gain insights into heat stress-related responses

Heat stress (HS) is one of the alarming issues today due to global warming and is the foremost detrimental to crop production. Maize is one of the versatile crops grown over different agro-climatic conditions. However, it is significantly sensitive to heat stress, especially during the reproductive phase. The heat stress tolerance mechanism is yet to be elucidated at the reproductive stage. Thus, the present study focused on identifying transcriptional changes in two inbreds, LM 11 (sensitive to HS) and CML 25 (tolerant to HS), under intense heat stress at 42°C during the reproductive stage from three tissues viz. flag leaf, tassel, and ovule. Samples from each inbred were collected after 5 days of pollinations for RNA isolation. Six cDNA libraries were constructed from three separate tissues of LM 11 and CML 25 and sequenced using an Illumina HiSeq2500 platform. A total of 2,164 (1127 up-regulated and 1037 down-regulated) differentially expressed genes (DEGs) were identified with 1151, 451, and 562 DEGs in comparisons of LM 11 and CML 25, corresponding to a leaf, pollen, and ovule, respectively. Functional annotated DEGs associated with transcription factors (TFs) viz. AP2, MYB, WRKY, PsbP, bZIP, and NAM, heat shock proteins (HSP20, HSP70, and HSP101/ClpB), as well as genes related to photosynthesis (PsaD & PsaN), antioxidation (APX and CAT) and polyamines (Spd and Spm). KEGG pathways analyses showed that the metabolic overview pathway and secondary metabolites biosynthesis pathway, with the involvement of 264 and 146 genes, respectively, were highly enriched in response to heat stress. Notably, the expression changes of the most common HS-responsive genes were typically much more significant in CML 25, which might explain why CML 25 is more heat tolerant. Seven DEGs were common in leaf, pollen, and ovule; and involved in the polyamines biosynthesis pathway. Their exact role in maize heat stress response would warrant further studies. These results enhanced our understanding to heat stress responses in maize.

Ultra-Responses of Asphodelus tenuifolius L. (Wild Onion) and Convolvulus arvensis L. (Field Bindweed) against Shoot Extract of Trianthema portulacastrum L. (Horse Purslane)

Weed infestation is a prime challenge coupled with lowering crop production owing to their competition with crop plants for available resources such as nutrients, water, space, moisture, and sunlight. Among weed control methods, the implementation of synthetic herbicides offers an instant solution for getting rid of weeds; however, they are a direct source of potential hazards for humans and generate resistance against synthetic weedicides, making them less effective. Allelopathy is something that happens in nature that can be used as a weed control method that increases crop yield and decreases dependency on synthetic chemicals. The mode of action of some phytochemicals corresponds to synthetic herbicides. Due to this feature, allelochemicals are used as bio-herbicides in weed management and prove more environmentally friendly than synthetic weedicides. The present investigation aims to assess the ultra-responses of A. tenuifolius and C. arvensis, while growing them in a pot experiment. Various levels of shoot extract (L2, L3, and L4) of T. portulacastrum along with the L1 (distilled water) and L5 (synthetic herbicide) were applied to the weeds. Results indicated that aqueous extracts of shoot of T. portulacastrum significantly (p ≤ 0.05) affect all the measured traits of weeds and their effects were concentration specific. All morphological parameters were suppressed due to biotic stress with an increase in free amino acids and calcium ions along with a decline in metaxylem cell area and cortical thickness in the root, while the vascular bundle area increased. The shoot extract intrusive with metabolisms corresponded with the synthetic herbicide. It is concluded that Trianthema shoot extract has a powerful phytotoxic impact on weeds (A. tenuifolius and C. arvensis) and can be used in bio-herbicide production.

The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress

Global climate change has altered, and will further alter, rainfall patterns and temperatures likely causing more frequent drought and heat waves, which will consequently exacerbate abiotic stresses of plants and significantly decrease the yield and quality of crops. On the one hand, the global demand for food is ever-increasing owing to the rapid increase of the human population. On the other hand, metabolic responses are one of the most important mechanisms by which plants adapt to and survive to abiotic stresses. Here we therefore summarize recent progresses including the plant primary and secondary metabolic responses to abiotic stresses and their function in plant resistance acting as antioxidants, osmoregulatory, and signaling factors, which enrich our knowledge concerning commonalities of plant metabolic responses to abiotic stresses, including their involvement in signaling processes. Finally, we discuss potential methods of metabolic fortification of crops in order to improve their abiotic stress tolerance.

Heat and drought induced transcriptomic changes in barley varieties with contrasting stress response phenotypes

Drought and heat stress substantially impact plant growth and productivity. When subjected to drought or heat stress, plants exhibit reduction in growth resulting in yield losses. The occurrence of these two stresses together intensifies their negative effects. Unraveling the molecular changes in response to combined abiotic stress is essential to breed climate-resilient crops. In this study, transcriptome profiles were compared between stress-tolerant (Otis), and stress-sensitive (Golden Promise) barley genotypes subjected to drought, heat, and combined heat and drought stress for five days during heading stage. The major differences that emerged from the transcriptome analysis were the overall number of differentially expressed genes was relatively higher in Golden Promise (GP) compared to Otis. The differential expression of more than 900 transcription factors in GP and Otis may aid this transcriptional reprogramming in response to abiotic stress. Secondly, combined heat and water deficit stress results in a unique and massive transcriptomic response that cannot be predicted from individual stress responses. Enrichment analyses of gene ontology terms revealed unique and stress type-specific adjustments of gene expression. Weighted Gene Co-expression Network Analysis identified genes associated with RNA metabolism and Hsp70 chaperone components as hub genes that can be useful for engineering tolerance to multiple abiotic stresses. Comparison of the transcriptomes of unstressed Otis and GP plants identified several genes associated with biosynthesis of antioxidants and osmolytes were higher in the former that maybe providing innate tolerance capabilities to effectively combat hostile conditions. Lines with different repertoire of innate tolerance mechanisms can be effectively leveraged in breeding programs for developing climate-resilient barley varieties with superior end-use traits.

Single and interactive effects of variables associated with climate change on wheat metabolome

One of the key challenges linked with future food and nutritional security is to evaluate the interactive effect of climate variables on plants' growth, fitness, and yield parameters. These interactions may lead to unique shifts in the morphological, physiological, gene expression, or metabolite accumulation patterns, leading to an adaptation response that is specific to future climate scenarios. To understand such changes, we exposed spring wheat to 7 regimes (3 single and 4 combined climate treatments) composed of elevated temperature, the enhanced concentration of CO₂, and progressive drought stress corresponding to the predicted climate of the year 2100. The physiological and metabolic responses were then compared with the current climate represented by the year 2020. We found that the elevated CO₂ (eC) mitigated some of the effects of elevated temperature (eT) on physiological performance and metabolism. The metabolite profiling of leaves revealed 44 key metabolites, including saccharides, amino acids, and phenolics, accumulating contrastingly under individual regimes. These metabolites belong to the central metabolic pathways that are essential for cellular energy, production of biosynthetic pathways precursors, and oxidative balance. The interaction of eC alleviated the negative effect of eT possibly by maintaining the rate of carbon fixation and accumulation of key metabolites and intermediates linked with the Krebs cycle and synthesis of phenolics. Our study for the first time revealed the influence of a specific climate factor on the accumulation of metabolic compounds in wheat. The current work could assist in the understanding and development of climate resilient wheat by utilizing the identified metabolites as breeding targets for food and nutritional security.

Climate Stressors on Growth, Yield, and Functional Biochemistry of two Brassica Species, Kale and Mustard

Due to climate change, the attainment of global food security is facing serious challenges in meeting the growing food demand. Abiotic stresses are the foremost limiting factors for agricultural productivity. However, not much information is available on the effect of multiple abiotic stresses on the morphological and biochemical aspects of kale and mustard. Therefore, an experiment was designed to study the effects of UV-B radiation, CO₂ concentration, and high temperature on the growth, yield, and biochemistry of two Brassica species, namely B. oleracea L. var. acephala Winterbor F1 (hybrid kale) and B. juncea var. Green wave O.G. (mustard greens), which were grown under optimal nutrients and soil moisture conditions in soil-plant-atmosphere-research (SPAR) units. Two levels of UV-B radiation (0 and 10 kJ m^-2 d^-1), two concentrations of CO₂ (420 and 720 ppm), and two different temperature treatments (25/17 °C and 35/27 °C) were imposed 12 days after sowing (DAS). Several morphological and biochemical parameters were measured at harvest (40 DAS) in both species. All the traits declined considerably under individual and multi-stress conditions in both species except under elevated CO₂ levels, which had a positive impact. Marketable fresh weight decreased by 64% and 58% in kale and mustard plants, respectively, growing under UV-B treatment. A slight increase in the chlorophyll content was observed in both species under the UV-B treatment alone and in combination with high temperature and elevated CO₂. Understanding the impacts of high temperature, CO₂, and UV-B radiation treatments on leafy vegetables, such as kale and mustard, can help to improve existing varieties to enhance resilience towards environmental stresses while simultaneously improving yield, morphology, and biochemistry in plants.

Metabolic, physiological and anatomical responses of soybean plants under water deficit and high temperature condition

Water deficit (WD) combined with high temperature (HT) is the major factor limiting agriculture worldwide, and it is predicted to become worse according to the current climate change scenario. It is thus important to understand how current cultivated crops respond to these stress conditions. Here we investigated how four soybean cultivars respond to WD and HT isolated or in combination at metabolic, physiological, and anatomical levels. The WD + HT increased the level of stress in soybean plants when compared to plants under well-watered (WW), WD, or HT conditions. WD + HT exacerbates the increases in ascorbate peroxidase activity, which was associated with the greater photosynthetic rate in two cultivars under WD + HT. The metabolic responses to WD + HT diverge substantially from plants under WW, WD, or HT conditions. Myo-inositol and maltose were identified as WD + HT biomarkers and were connected to subnetworks composed of catalase, amino acids, and both root and leaf osmotic potentials. Correlation-based network analyses highlight that the network heterogeneity increased and a higher integration among metabolic, physiological, and morphological nodes is observed under stress conditions. Beyond unveiling biochemical and metabolic WD + HT biomarkers, our results collectively highlight that the mechanisms behind the acclimation to WD + HT cannot be understood by investigating WD or HT stress separately.

Transcriptome and metabolome profiling of interspecific CSSLs reveals general and specific mechanisms of drought resistance in cotton

In order to understand the molecular mechanism of cotton's response to drought during the flowering and boll stage, transcriptomics and metabolomics were carried out for two introgression lines (drought-tolerant line: T307; drought-sensitive line: S48) which were screened from Gossypium hirsutum cv. 'Emian22' with some gene fragments imported from Gossypium barbadense acc. 3-79, under drought stress by withdrawing water at flowering and boll stage. Results showed that the basic drought response in cotton included a series of broad-spectrum responses, such as amino acid synthesis, hormone (abscisic acid, ABA) signal transduction, and mitogen-activated protein kinases signal transduction pathway, which activated in both drought-tolerant and drought-sensitive lines. However, the difference of their imported fragments and diminished sequences triggers endoplasmic reticulum (ER) protein processing, photosynthetic-related pathways (in leaves), and membrane solute transport (in roots) in drought-tolerant line T307, while these are missed or not activated in drought-sensitive line S48, reflecting the different drought tolerance of the two genotypes. Virus-induced gene silencing assay of drought-tolerant differentially expressed heat shock protein (HSP) genes (mainly in leaf) and ATP-binding cassette (ABC) transporter genes (mainly in roots) indicated that those genes play important role in cotton drought tolerant. Combined analysis of transcriptomics and metabolomics highlighted the important roles of ER-stress-related HSP genes and root-specific ABC transporter genes in plants drought tolerance. These results provide new insights into the molecular mechanisms underlying the drought stress adaptation in cotton.

Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize (Zea mays L.)

High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.

Mass Spectrometry-Based Nontargeted and Targeted Analytical Approaches in Fingerprinting and Metabolomics of Food and Agricultural Research

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatography-tandem MS metabolomics, direct analysis using ambient mass spectrometry, as well as development in MS data deconvolution software packages and databases for metabolomic studies. Various nontargeted and targeted approaches are employed in marker compounds identification, material adulteration detection, and the analysis of specific classes of secondary metabolites. In the newly emerged applications, the recent advances in computer tools for the fast deconvolution of MS data in targeted secondary metabolite analysis are highlighted.

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel

BACKGROUND

Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited.

RESULTS

Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions.

CONCLUSION

Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.

Dynamic changes in metabolic and lipidomic profiles of tea plants during drought stress and re-watering

Tea (Camellia sinensis L.), as an evergreen plant, needs a humid environment. Water deficit would diminish tea yield and quality. We analyzed the dynamic changes in the metabolite and lipid profiling of tea leaves under various drought conditions and re-watering to determine the metabolic changes in tea leaves responding to drought challenges. In all, 119 metabolites showed substantial alterations in drought-stressed tea plants, including sugars and sugar alcohols, amino acids, and tricarboxylic acid cycle intermediates and lipids. We detected 29 lipids and they were classified into phosphatidylglycerol (PG), phosphatidic acid (PA), sulfoquinovosyl-diacylglycerol (SQDG), phosphatidylcholine (PC), lyso-phosphatidylcholine (LysoPC), and phosphatidylinositol (PI). The levels of sugar, sugar alcohol, and sugar precursors may change as a response to drought stress. Compared with these metabolites, the membrane lipids showed more dynamic changes in tea under drought stresses. Furthermore, metabolic recovery was only partial, with the majority of the examined metabolites exhibiting significantly different levels between samples from re-watered and well-watered tea plants. The findings also showed that comprehensive metabolomic and lipidomic approaches were efficient in elucidating the impacts of drought stress on tea plant metabolism. Our findings are valuable for understanding the mechanisms behind drought tolerance in tea plants from the metabolism perspective and utilizing the compounds to improve the drought tolerance of tea plants.

All Are in a Drought, but Some Stand Out: Multivariate Analysis in the Selection of Agronomic Efficient Popcorn Genotypes

The search for productive germplasm adapted to adverse conditions is an important action to mitigate the harmful effects of climate change. The aim was to identify the yield potential of 50 popcorn inbred lines grown in field conditions, in two crop seasons (CS), and under contrasting water conditions (WC). Morphoagronomic, physiological, and root system traits were evaluated. Joint and individual analyses of variance were performed, in addition to the multivariate GT bip-lot analysis. Expressive reductions between WC were observed in 100-grain weight (100 GW), popping expansion (PE), grain yield (GY), expanded popcorn volume per ha (EPV), row number per ear (RNE), plant height (PH), relative chlorophyll content (SPAD), and nitrogen balance index (NBI). It was found that the SPAD, 100 GW, GY, PE, and grain number per ear (GNE) traits had the most significant impact on the selection of genotypes. Regardless of WC and CS, the ideal lines were L294 and L688 for PE; L691 and L480 for GY; and L291 and L292 for both traits. SPAD, 100 GW, and GNE can contribute to the indirect selection. Our work contributes to understanding the damage caused by drought and the integration of traits for the indirect selection of drought-tolerant popcorn genotypes.

Adjusting sowing date improves the photosynthetic capacity and grain yield by optimizing temperature condition around flowering of summer maize in the North China Plain

Adjusting the sowing date to optimize temperature conditions is a helpful strategy for mitigating the adverse impact of high temperature on summer maize growth in the North China Plain (NCP). However, the physiological processes of variation in summer maize yield with sowing date-associated changes in temperature conditions around flowering remain to be poorly understood. In this study, field experiments with two maize varieties and three sowing dates (early sowing date, SD1, 21 May; conventional sowing date, SD2, 10 June; delay sowing date, SD3, 30 June) were conducted at Xinxiang of Henan Province in 2019 and 2020. Early sowing markedly decreased the daily mean temperature (T _mean), maximum temperature (T _max), and minimum temperature (T _min) during pre-silking, while delay sowing markedly decreased those temperatures during post-silking. Under these temperature conditions, both varieties under SD1 at 12-leaf stage (V12) and silking stage (R1) while under SD3 at R1 and milking stage (R3) possessed significantly lower malondialdehyde (MDA) content in leaf due to higher activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) compared to SD2. Therefore, SD1 at V12 and R1 stages and SD3 at R1 and R3 stages for both varieties showed significantly higher photosynthetic capacity, including higher SPAD, F _v /F _m, P _n, T _r, and G _s, which promoted greater pre-silking dry matter (DM) accumulation for SD1 to increase the kernel number, and promoted greater post-silking DM accumulation for SD3 to increase the kernel weight, eventually increased the grain yield of SD1 and SD3 compared to SD2. Results of regression analysis demonstrated that T _mean, T _max, and T _min values from V12 to R1 stages lower than 26.6, 32.5, and 20.3°C are necessary for improving the kernel number, while T _mean, T _max, T _min, and accumulated temperature (AT) values from R1 to R3 stages lower than 23.2, 28.9, 17.3, and 288.6°C are necessary for improving the kernel weight. Overall, optimal temperature conditions around flowering can be obtained by early (21 May) or delay (30 June) sowing to improve the kernel number or kernel weight due to improved photosynthetic capacity, eventually increasing the grain yield of summer maize in the NCP.

Effects of Storage Temperature on Indica-Japonica Hybrid Rice Metabolites, Analyzed Using Liquid Chromatography and Mass Spectrometry

The Yongyou series of indica-japonica hybrid rice has excellent production potential and storage performance. However, little is known about the underlying mechanism of its storage resistance. In this study, Yongyou 1540 rice (Oryza sativa cv. yongyou 1540) was stored at different temperatures, and the storability was validated though measuring nutritional components and apparent change. In addition, a broad-targeted metabolomic approach coupled with liquid chromatography-mass spectrometry was applied to analyze the metabolite changes. The study found that under high temperature storage conditions (35 °C), Yongyou 1540 was not significantly worse in terms of fatty acid value, whiteness value, and changes in electron microscope profile. A total of 19 key differential metabolites were screened, and lipid metabolites related to palmitoleic acid were found to affect the aging of rice. At the same time, two substances, guanosine 3′,5′-cyclophosphate and pipecolic acid, were beneficial to enhance the resistance of rice under harsh storage conditions, thereby delaying the deterioration of its quality and maintaining its quality. Significant regulation of galactose metabolism, alanine, aspartate and glutamate metabolism, butyrate metabolism, and arginine and proline metabolism pathways were probably responsible for the good storage capacity of Yongyou 1540.

Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops

Climate change is a major threat to crop productivity that negatively affects food security worldwide. Increase in global temperatures are usually accompanied by drought, flooding and changes in soil nutrients composition that dramatically reduced crop yields. Against the backdrop of climate change, human population increase and subsequent rise in food demand, finding new solutions for crop adaptation to environmental stresses is essential. The effects of single abiotic stress on crops have been widely studied, but in the field abiotic stresses tend to occur in combination rather than individually. Physiological, metabolic and molecular responses of crops to combined abiotic stresses seem to be significantly different to individual stresses. Although in recent years an increasing number of studies have addressed the effects of abiotic stress combinations, the information related to the root system response is still scarce. Roots are the underground organs that directly contact with the soil and sense many of these abiotic stresses. Understanding the effects of abiotic stress combinations in the root system would help to find new breeding tools to develop more resilient crops. This review will summarize the current knowledge regarding the effects of combined abiotic stress in the root system in crops. First, we will provide a general overview of root responses to particular abiotic stresses. Then, we will describe how these root responses are integrated when crops are challenged to the combination of different abiotic stress. We will focus on the main changes on root system architecture (RSA) and physiology influencing crop productivity and yield and convey the latest information on the key molecular, hormonal and genetic regulatory pathways underlying root responses to these combinatorial stresses. Finally, we will discuss possible directions for future research and the main challenges needed to be tackled to translate this knowledge into useful tools to enhance crop tolerance.

Interplay between abiotic (drought) and biotic (virus) stresses in tomato plants

With climate warming, drought becomes a vital challenge for agriculture. Extended drought periods affect plant-pathogen interactions. We demonstrate an interplay in tomato between drought and infection with tomato yellow leaf curl virus (TYLCV). Infected plants became more tolerant to drought, showing plant readiness to water scarcity by reducing metabolic activity in leaves and increasing it in roots. Reallocation of osmolytes, such as carbohydrates and amino acids, from shoots to roots suggested a role of roots in protecting infected tomatoes against drought. To avoid an acute response possibly lethal for the host organism, TYLCV down-regulated the drought-induced activation of stress response proteins and metabolites. Simultaneously, TYLCV promoted the stabilization of osmoprotectants' patterns and water balance parameters, resulting in the development of buffering conditions in infected plants subjected to prolonged stress. Drought-dependent decline of TYLCV amounts was correlated with HSFA1-controlled activation of autophagy, mostly in the roots. The tomato response to combined drought and TYLCV infection points to a mutual interaction between the plant host and its viral pathogen.

γ-Aminobutyric acid plays a key role in plant acclimation to a combination of high light and heat stress

Plants are frequently subjected to different combinations of abiotic stresses, such as high light (HL) intensity, and elevated temperatures. These environmental conditions pose a threat to agriculture production, affecting photosynthesis, and decreasing yield. Metabolic responses of plants, such as alterations in carbohydrates and amino acid fluxes, play a key role in the successful acclimation of plants to different abiotic stresses, directing resources toward stress responses, and suppressing growth. Here we show that the primary metabolic response of Arabidopsis (Arabidopsis thaliana) plants to HL or heat stress (HS) is different from that of plants subjected to a combination of HL and HS (HL+HS). We further demonstrate that the combined stress results in a unique metabolic response that includes increased accumulation of sugars and amino acids coupled with decreased levels of metabolites participating in the tricarboxylic acid cycle. Among the amino acids exclusively accumulated during HL+HS, we identified the nonproteinogenic amino acid γ-aminobutyric acid (GABA). Analysis of different mutants deficient in GABA biosynthesis (GLUTAMATE DESCARBOXYLASE 3 [gad3]) as well as mutants impaired in autophagy (autophagy-related proteins 5 and 9 [atg5 and atg9]), revealed that GABA plays a key role in the acclimation of plants to HL+HS, potentially by promoting autophagy. Taken together, our findings identify a role for GABA in regulating plant responses to combined stress.

Uncovering the Gene Regulatory Network of Maize Hybrid ZD309 under Heat Stress by Transcriptomic and Metabolomic Analysis

Maize is an important cereal crop but is sensitive to heat stress, which significantly restricts its grain yield. To explore the molecular mechanism of maize heat tolerance, a heat-tolerant hybrid ZD309 and its parental lines (H39_1 and M189) were subjected to heat stress, followed by transcriptomic and metabolomic analyses. After six-day-heat treatment, the growth of ZD309 and its parental lines were suppressed, showing dwarf stature and rolled leaf compared with the control plants. ZD309 exhibited vigorous growth; however, M189 displayed superior heat tolerance. By transcriptomic and metabolomic analysis, hundreds to thousands of differentially expressed genes (DEGs) and metabolites (DEMs) were identified. Notably, the female parent H39 shares more DEGs and DEMs with the hybrid ZD309, indicating more genetic gain derived from the female instead of the male. A total of 299 heat shock genes detected among three genotypes were greatly aggregated in sugar transmembrane transporter activity, plasma membrane, photosynthesis, protein processing in the endoplasmic reticulum, cysteine, and methionine metabolism. A total of 150 heat-responsive metabolites detected among three genotypes were highly accumulated, including jasmonic acid, amino acids, sugar, flavonoids, coumarin, and organic acids. Integrating transcriptomic and metabolomic assays revealed that plant hormone signal transduction, cysteine, and methionine metabolism, and α-linolenic acid metabolism play crucial roles in heat tolerance in maize. Our research will be facilitated to identify essential heat tolerance genes in maize, thereby contributing to breeding heat resistance maize varieties.

'Omics' approaches in developing combined drought and heat tolerance in food crops

Global climate change will significantly increase the intensity and frequency of hot, dry days. The simultaneous occurrence of drought and heat stress is also likely to increase, influencing various agronomic characteristics, such as biomass and other growth traits, phenology, and yield-contributing traits, of various crops. At the same time, vital physiological traits will be seriously disrupted, including leaf water content, canopy temperature depression, membrane stability, photosynthesis, and related attributes such as chlorophyll content, stomatal conductance, and chlorophyll fluorescence. Several metabolic processes contributing to general growth and development will be restricted, along with the production of reactive oxygen species (ROS) that negatively affect cellular homeostasis. Plants have adaptive defense strategies, such as ROS-scavenging mechanisms, osmolyte production, secondary metabolite modulation, and different phytohormones, which can help distinguish tolerant crop genotypes. Understanding plant responses to combined drought/heat stress at various organizational levels is vital for developing stress-resilient crops. Elucidating the genomic, proteomic, and metabolic responses of various crops, particularly tolerant genotypes, to identify tolerance mechanisms will markedly enhance the continuing efforts to introduce combined drought/heat stress tolerance. Besides agronomic management, genetic engineering and molecular breeding approaches have great potential in this direction.

Changes in Metabolic Profiles of Pea (Pisum sativum L.) as a Result of Repeated Short-Term Soil Drought and Subsequent Re-Watering

The metabolic re-arrangements of peas (Pisum sativum L.) under soil drought and re-watering are still not fully explained. The search for metabolic markers of the stress response is important in breeding programs, to allow for the selection drought-resistant cultivars. During the present study, changes in the polar metabolite content in pea plant shoots were measured under repeated short-term soil drought and subsequent re-watering. A gas chromatograph, equipped with a mass spectrometer (GC-MS), was used for the metabolite profiling of pea plants during their middle stage of vegetation (14-34 days after sowing, DAS). The major changes occurred in the concentration of amino acids and some soluble carbohydrates. Among them, proline, γ-aminobutyric acid (GABA), branched-chain amino acids, hydroxyproline, serine, myo-inositol, and raffinose were accumulated under each soil drought and decreased after re-watering. Besides, the obtained results show that the first drought/re-watering cycle increased the ability of pea plants to restore a metabolic profile similar to the control after the second similar stress. The accumulation of proline seems to be an important part of drought memory in pea plants. However, confirmation of this suggestion requires metabolite profiling studies on a broader spectrum of pea cultivars.

Alpha-Linolenic Acid Mediates Diverse Drought Responses in Maize (Zea mays L.) at Seedling and Flowering Stages

Water shortage caused by long-term drought is one of the most serious abiotic stress factors in maize. Different drought conditions lead to differences in growth, development, and metabolism of maize. In previous studies, proteomics and genomics methods have been widely used to explain the response mechanism of maize to long-term drought, but there are only a few articles related to metabolomics. In this study, we used transcriptome and metabolomics analysis to characterize the differential effects of drought stress imposed at seedling or flowering stages on maize. Through the association analysis of genes and metabolites, we found that maize leaves had 61 and 54 enriched pathways under seedling drought and flowering drought, respectively, of which 13 and 11 were significant key pathways, mostly related to the biosynthesis of flavonoids and phenylpropanes, glutathione metabolism and purine metabolism. Interestingly, we found that the α-linolenic acid metabolic pathway differed significantly between the two treatments, and a total of 10 differentially expressed genes and five differentially abundant metabolites have been identified in this pathway. Some differential accumulation of metabolites (DAMs) was related to synthesis of jasmonic acid, which may be one of the key pathways underpinning maize response to different types of long-term drought. In general, metabolomics provides a new method for the study of water stress in maize and lays a theoretical foundation for drought-resistant cultivation of silage maize.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

Recent Advances for Drought Stress Tolerance in Maize (Zea mays L.): Present Status and Future Prospects

Drought stress has severely hampered maize production, affecting the livelihood and economics of millions of people worldwide. In the future, as a result of climate change, unpredictable weather events will become more frequent hence the implementation of adaptive strategies will be inevitable. Through utilizing different genetic and breeding approaches, efforts are in progress to develop the drought tolerance in maize. The recent approaches of genomics-assisted breeding, transcriptomics, proteomics, transgenics, and genome editing have fast-tracked enhancement for drought stress tolerance under laboratory and field conditions. Drought stress tolerance in maize could be considerably improved by combining omics technologies with novel breeding methods and high-throughput phenotyping (HTP). This review focuses on maize responses against drought, as well as novel breeding and system biology approaches applied to better understand drought tolerance mechanisms and the development of drought-tolerant maize cultivars. Researchers must disentangle the molecular and physiological bases of drought tolerance features in order to increase maize yield. Therefore, the integrated investments in field-based HTP, system biology, and sophisticated breeding methodologies are expected to help increase and stabilize maize production in the face of climate change.

Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes

Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.

Ovary Abortion Induced by Combined Waterlogging and Shading Stress at the Flowering Stage Involves Amino Acids and Flavonoid Metabolism in Maize

Maize (Zea mays L.) crops on the North China Plain are often subject to continuous overcast rain at the flowering stage. This causes waterlogging and shading stresses simultaneously and leads to huge yield losses, but the causes of these yield losses remain largely unknown. To explore the factors contributing to yield loss caused by combined waterlogging and shading stress at the flowering stage, we performed phenotypic, physiological, and quasi-targeted metabolomics analyses of maize plants subjected to waterlogging, shading, and combined waterlogging and shading (WS) treatments. Analyses of phenotypic and physiological indexes showed that, compared with waterlogging or shading alone, WS resulted in lower source strength, more severe inhibition of ovary and silk growth at the ear tip, a reduced number of emerged silks, and a higher rate of ovary abortion. Changes in carbon content and enzyme activity could not explain the ovary abortion in our study. Metabolomic analyses showed that the events occurred in ovaries and silks were closely related to abortion, WS forced the ovary to allocate more resources to the synthesis of amino acids involved in the stress response, inhibited the energy metabolism, glutathione metabolism and methionine salvage pathway, and overaccumulation of H₂O₂. In silks, WS led to lower accumulation levels of specific flavonoid metabolites with antioxidant capacity, and to over accumulation of H₂O₂. Thus, compared with each single stress, WS more seriously disrupted the normal metabolic process, and resulted more serious oxidative stress in ovaries and silks. Amino acids involved in the stress response in ovaries and specific flavonoid metabolites with antioxidant capacity in silks play important roles during ovary abortion. These results identify novel traits for selection in breeding programs and targets for genome editing to increase maize yield under WS stress.

Genetic Approaches to Enhance Multiple Stress Tolerance in Maize

The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.

Tomato Yellow Leaf Curl Virus (TYLCV) Promotes Plant Tolerance to Drought

A growing body of research points to a positive interplay between viruses and plants. Tomato yellow curl virus (TYLCV) is able to protect tomato host plants against extreme drought. To envisage the use of virus protective capacity in agriculture, TYLCV-resistant tomato lines have to be infected first with the virus before planting. Such virus-resistant tomato plants contain virus amounts that do not cause disease symptoms, growth inhibition, or yield loss, but are sufficient to modify the metabolism of the plant, resulting in improved tolerance to drought. This phenomenon is based on the TYLCV-dependent stabilization of amounts of key osmoprotectants induced by drought (soluble sugars, amino acids, and proteins). Although in infected TYLCV-susceptible tomatoes, stress markers also show an enhanced stability, in infected TYLCV-resistant plants, water balance and osmolyte homeostasis reach particularly high levels. These tomato plants survive long periods of time during water withholding. However, after recovery to normal irrigation, they produce fruits which are not exposed to drought, similarly to the control plants. Using these features, it might be possible to cultivate TYLCV-resistant plants during seasons characterized by water scarcity.

Assessing Drought and Heat Stress-Induced Changes in the Cotton Leaf Metabolome and Their Relationship With Hyperspectral Reflectance

The study of phenotypes that reveal mechanisms of adaptation to drought and heat stress is crucial for the development of climate resilient crops in the face of climate uncertainty. The leaf metabolome effectively summarizes stress-driven perturbations of the plant physiological status and represents an intermediate phenotype that bridges the plant genome and phenome. The objective of this study was to analyze the effect of water deficit and heat stress on the leaf metabolome of 22 genetically diverse accessions of upland cotton grown in the Arizona low desert over two consecutive years. Results revealed that membrane lipid remodeling was the main leaf mechanism of adaptation to drought. The magnitude of metabolic adaptations to drought, which had an impact on fiber traits, was found to be quantitatively and qualitatively associated with different stress severity levels during the two years of the field trial. Leaf-level hyperspectral reflectance data were also used to predict the leaf metabolite profiles of the cotton accessions. Multivariate statistical models using hyperspectral data accurately estimated (R ² > 0.7 in ∼34% of the metabolites) and predicted (Q ² > 0.5 in 15-25% of the metabolites) many leaf metabolites. Predicted values of metabolites could efficiently discriminate stressed and non-stressed samples and reveal which regions of the reflectance spectrum were the most informative for predictions. Combined together, these findings suggest that hyperspectral sensors can be used for the rapid, non-destructive estimation of leaf metabolites, which can summarize the plant physiological status.

The metabolomic landscape of rice heterosis highlights pathway biomarkers for predicting complex phenotypes

Understanding the molecular mechanisms underlying complex phenotypes requires systematic analyses of complicated metabolic networks and contributes to improvements in the breeding efficiency of staple cereal crops and diagnostic accuracy for human diseases. Here, we selected rice (Oryza sativa) heterosis as a complex phenotype and investigated the mechanisms of both vegetative and reproductive traits using an untargeted metabolomics strategy. Heterosis-associated analytes were identified, and the overlapping analytes were shown to underlie the association patterns for six agronomic traits. The heterosis-associated analytes of four yield components and plant height collectively contributed to yield heterosis, and the degree of contribution differed among the five traits. We performed dysregulated network analyses of the high- and low-better parent heterosis hybrids and found multiple types of metabolic pathways involved in heterosis. The metabolite levels of the significantly enriched pathways (especially those from amino acid and carbohydrate metabolism) were predictive of yield heterosis (area under the curve = 0.907 with 10 features), and the predictability of these pathway biomarkers was validated with hybrids across environments and populations. Our findings elucidate the metabolomic landscape of rice heterosis and highlight the potential application of pathway biomarkers in achieving accurate predictions of complex phenotypes.

Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement

"Omics" techniques (including genomics, transcriptomics, metabolomics, proteomics, and metagenomics) have been employed with huge success in the improvement of agricultural crops. As marine aquaculture of macroalgae expands globally, biologists are working to domesticate species of macroalgae by applying these techniques tested in agriculture to wild macroalgae species. Metabolomics has revealed metabolites and pathways that influence agriculturally relevant traits in crops, allowing for informed crop crossing schemes and genomic improvement strategies that would be pivotal to inform selection on macroalgae for domestication. Advances in metagenomics have improved understanding of host-symbiont interactions and the potential for microbial organisms to improve crop outcomes. There is much room in the field of macroalgal biology for further research toward improvement of macroalgae cultivars in aquaculture using metabolomic and metagenomic analyses. To this end, this review discusses the application and necessary expansion of the omics tool kit for macroalgae domestication as we move to enhance seaweed farming worldwide.

Genomic basis underlying the metabolome-mediated drought adaptation of maize

Background

Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive.

Results

Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance.

Conclusion

Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02481-1.

Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change?

Actinorhizal plants have been regarded as promising species in the current climate change context due to their high tolerance to a multitude of abiotic stresses. While combined salt-heat stress effects have been studied in crop species, their impact on the model actinorhizal plant, Casuarina glauca, has not yet been fully addressed. The effect of single salt (400 mM NaCl) and heat (control at 26/22 °C, supra optimal temperatures at 35/22 °C and 45/22 °C day/night) conditions on C. glauca branchlets was characterised at the physiological level, and stress-induced metabolite changes were characterised by mass spectrometry-based metabolomics. C. glauca could withstand single salt and heat conditions. However, the harshest stress condition (400 mM NaCl, 45 °C) revealed photosynthetic impairments due to mesophyll and membrane permeability limitations as well as major stress-specific differential responses in C and N metabolism. The increased activity of enzymatic ROS scavengers was, however, revealed to be sufficient to control the plant oxidative status. Although C. glauca could tolerate single salt and heat stresses, their negative interaction enhanced the effects of salt stress. Results demonstrated that C. glauca responses to combined salt-heat stress could be explained as a sum of the responses from each single applied stress.

A Metabolomics Approach and Chemometric Tools for Differentiation of Barley Cultivars and Biomarker Discovery

One of the ultimate goals of plant breeding is the development of new crop cultivars capable of withstanding increasing environmental stresses, to sustain the constantly growing population and economic demands. Investigating the chemical composition of the above and underground tissues of cultivars is crucial for the understanding of common and specific traits thereof. Using an untargeted metabolomics approach together with appropriate chemometrics tools, the differential metabolite profiles of leaf and root extracts from five cultivars of barley (‘Erica’, ‘Elim’, ‘Hessekwa’, ‘S16’ and ‘Agulhas’) were explored and potential signatory biomarkers were revealed. The study was conducted on seedlings grown for 21 days under identical controlled conditions. An ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) was employed to analyse hydromethanolic leaf and root extracts of barley cultivars. Furthermore, unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint cultivar-specific metabolites. Among all the classes of metabolites annotated, phenolic acids and derivatives formed the largest group and also represented the most discriminatory metabolites. In roots, saponarin, an important allelochemical differentially distributed across cultivars, was the only flavonoid annotated. The application of an untargeted metabolomics approach in phenotyping grain crops such as barley was demonstrated, and the metabolites responsible for differentiating between the selected cultivars were revealed. The study provides insights into the chemical architecture of barley, an agro-economically relevant cereal crop; and reiterates the importance of metabolomics tools in plant breeding practices for crop improvement.

Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants

Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a significant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular responses to drought tolerance in plants and discuss possible strategies to help plants to counteract unfavorable drought periods.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

Using precision phenotyping to inform de novo domestication

An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.

Assessing Protein Synthesis and Degradation Rates in Arabidopsis thaliana Using Amino Acid Analysis

Plants continually synthesize and degrade proteins, for example, to adjust protein content during development or during adaptation to new environments. In order to estimate global protein synthesis and degradation rates in plants, we developed a relatively simple and inexpensive method using a combination of ¹³ CO₂ labeling and mass spectrometry-based analyses. Arabidopsis thaliana plants are subjected to a 24-hr ¹³ CO₂ pulse followed by a 4-day ¹² CO₂ chase. Soluble alanine and serine from total protein and glucose from cell wall material are analyzed by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and their ¹³ C enrichment (%) is estimated. The rate of protein synthesis during the ¹³ CO₂ pulse experiment is defined as the rate of incorporation of labeled amino acids into proteins normalized by a correction factor for incomplete enrichment in free amino acid pools. The rate of protein degradation is estimated as the difference between the rate of protein synthesis and the relative growth rate calculated using the ¹³ C enrichment of glucose from cell wall material. Degradation rates are also estimated from the ¹² CO₂ pulse experiment. The following method description includes setting up and performing labeling experiments, preparation and measurement of samples, and calculation steps. In addition, an R script is provided for the calculations. 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Setting up the ¹³ CO₂ labeling system and stable isotope labeling of Arabidopsis thaliana rosette leaves Basic Protocol 2: Extraction of soluble amino acids for GC-TOF-MS analysis Basic Protocol 3: Preparation of amino acids from total protein for GC-TOF-MS analysis Basic Protocol 4: Preparation of sugars from cell wall material for GC-TOF-MS analysis Basis Protocol 5: GC-TOF-MS analysis of ¹³ C-labeled samples and estimation of ¹³ C enrichment (%) Basis Protocol 6: Estimation of protein synthesis and degradation rates.

Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses

In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.

Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses

In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.

Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress

Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high temperatures and high salinity, and metabolomics has the potential for elucidating the response-to-stress mechanisms and develop resistance strategies in affected cultivars. This review describes the characteristics of each of the stages of metabolomic studies in plants and the role of metabolomics in the characterization of the response of various plant species to abiotic stresses.

Metabolic Profile Discriminates and Predicts Arabidopsis Susceptibility to Virus under Field Conditions

As obligatory parasites, plant viruses alter host cellular metabolism. There is a lack of information on the variability of virus-induced metabolic responses among genetically diverse plants in a natural context with daily changing conditions. To decipher the metabolic landscape of plant-virus interactions in a natural setting, twenty-six and ten accessions of Arabidopsis thaliana were inoculated with Turnip mosaic virus (TuMV), in two field experiments over 2 years. The accessions were measured for viral accumulation, above-ground biomass, targeted and untargeted metabolic profiles. The phenotypes of the accessions ranged from susceptibility to resistance. Susceptible and resistant accessions were shown to have different metabolic routes after inoculation. Susceptible genotypes accumulate primary and secondary metabolites upon infection, at the cost of hindered growth. Twenty-one metabolic signatures significantly accumulated in resistant accessions whereas they maintained their growth as mock-inoculated plants without biomass penalty. Metabolic content was demonstrated to discriminate and be highly predictive of the susceptibility of inoculated Arabidopsis. This study is the first to describe the metabolic landscape of plant-virus interactions in a natural setting and its predictive link to susceptibility. It provides new insights on plant-virus interactions. In this undomesticated species and in ecologically realistic conditions, growth and resistance are in a permanent conversation.