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

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.

Wheat omics: Classical breeding to new breeding technologies

Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.

Widely Targeted Metabolomics Analysis Reveals Key Quality-Related Metabolites in Kernels of Sweet Corn

Sweet corn (Zea mays convar. saccharata var. rugosa) is a major economic vegetable crop. Different sweet corn cultivars vary largely in flavor, texture, and nutrition. The present study performed widely targeted metabolomics analysis based on the HPLC-MS/MS technology to analyze the metabolic profiles in three sweet corn cultivars widely grown in China. A total of 568 metabolites in the three sweet corn cultivars were detected, of which 262 differential metabolites significantly changed among cultivars. Carbohydrates, organic acids, and amino acids were the majority detected primary metabolites. Organic acids were mainly concentrated on shikimate, benzoic acids, and quinic acid with aromatic groups. And the essential amino acids for the human body, methionine and threonine, were highly accumulated in the high-quality cultivar. In addition, phenylpropanoids and alkaloids were the most enriched secondary metabolites while terpenes were low-detected in sweet corn kernels. We found that the flavonoids exist in both free form and glycosylated form in sweet corn kernels. PCA and HCA revealed clear separations among the three sweet corn cultivars, suggesting distinctive metabolome profiles among three cultivars. The differential metabolites were mapped into flavonoid biosynthesis, phenylpropanoid biosynthesis, biosynthesis of amino acids, and other pathways according to the KEGG classification. Furthermore, we identified skimmin, N',N^″-diferuloylspermidine, and 3-hydroxyanthranilic acid as the key quality-related metabolites related to grain quality traits in sweet corn. The results suggested variations of metabolic composition among the three cultivars, providing the reference quality-related metabolites for sweet corn breeding.

Age-dependent increase in α-tocopherol and phytosterols in maize leaves exposed to elevated ozone pollution

Tropospheric ozone is a major air pollutant that significantly damages crop production. Crop metabolic responses to rising chronic ozone stress have not been well studied in the field, especially in C4 crops. In this study, we investigated the metabolomic profile of leaves from two diverse maize (Zea mays) inbred lines and the hybrid cross during exposure to season-long elevated ozone (~100 nl L-1) in the field using free air concentration enrichment (FACE) to identify key biochemical responses of maize to elevated ozone. Senescence, measured by loss of chlorophyll content, was accelerated in the hybrid line, B73 × Mo17, but not in either inbred line (B73 or Mo17). Untargeted metabolomic profiling further revealed that inbred and hybrid lines of maize differed in metabolic responses to ozone. A significant difference in the metabolite profile of hybrid leaves exposed to elevated ozone occurred as leaves aged, but no age-dependent difference in leaf metabolite profiles between ozone conditions was measured in the inbred lines. Phytosterols and α-tocopherol levels increased in B73 × Mo17 leaves as they aged, and to a significantly greater degree in elevated ozone stress. These metabolites are involved in membrane stabilization and chloroplast reactive oxygen species (ROS) quenching. The hybrid line also showed significant yield loss at elevated ozone, which the inbred lines did not. This suggests that the hybrid maize line was more sensitive to ozone exposure than the inbred lines, and up-regulated metabolic pathways to stabilize membranes and quench ROS in response to chronic ozone stress.

Heat Stress Responses and Thermotolerance in Maize

High temperatures causing heat stress disturb cellular homeostasis and impede growth and development in plants. Extensive agricultural losses are attributed to heat stress, often in combination with other stresses. Plants have evolved a variety of responses to heat stress to minimize damage and to protect themselves from further stress. A narrow temperature window separates growth from heat stress, and the range of temperatures conferring optimal growth often overlap with those producing heat stress. Heat stress induces a cytoplasmic heat stress response (HSR) in which heat shock transcription factors (HSFs) activate a constellation of genes encoding heat shock proteins (HSPs). Heat stress also induces the endoplasmic reticulum (ER)-localized unfolded protein response (UPR), which activates transcription factors that upregulate a different family of stress response genes. Heat stress also activates hormone responses and alternative RNA splicing, all of which may contribute to thermotolerance. Heat stress is often studied by subjecting plants to step increases in temperatures; however, more recent studies have demonstrated that heat shock responses occur under simulated field conditions in which temperatures are slowly ramped up to more moderate temperatures. Heat stress responses, assessed at a molecular level, could be used as traits for plant breeders to select for thermotolerance.

Maize Responses Challenged by Drought, Elevated Daytime Temperature and Arthropod Herbivory Stresses: A Physiological, Biochemical and Molecular View

Maize (Zea mays L.) is one of the main cereals grown around the world. It is used for human and animal nutrition and also as biofuel. However, as a direct consequence of global climate change, increased abiotic and biotic stress events have been reported in different regions of the world, which have become a threat to world maize yields. Drought and heat are environmental stresses that influence the growth, development, and yield processes of maize crops. Plants have developed dynamic responses at the physiological, biochemical, and molecular levels that allow them to escape, avoid and/or tolerate unfavorable environmental conditions. Arthropod herbivory can generate resistance or tolerance responses in plants that are associated with inducible and constitutive defenses. Increases in the frequency and severity of abiotic stress events (drought and heat), as a consequence of climate change, can generate critical variations in plant-insect interactions. However, the behavior of herbivorous arthropods under drought scenarios is not well understood, and this kind of stress may have some positive and negative effects on arthropod populations. The simultaneous appearance of different environmental stresses and biotic factors results in very complex plant responses. In this review, recent information is provided on the physiological, biochemical, and molecular responses of plants to the combination of drought, heat stress, and the effect on some arthropod pests of interest in the maize crop.

Single and Combined Abiotic Stress in Maize Root Morphology

Plants are continually exposed to multiple stresses, which co-occur in nature, and the net effects are frequently more nonadditive (i.e., synergistic or antagonistic), suggesting "unique" responses with respect to that of the individual stress. Further, plant stress responses are not uniform, showing a high spatial and temporal variability among and along the different organs. In this respect, the present work investigated the morphological responses of different root types (seminal, seminal lateral, primary and primary lateral) of maize plants exposed to single (drought and heat) and combined stress (drought + heat). Data were evaluated by a specific root image analysis system (WinRHIZO) and analyzed by uni- and multivariate statistical analyses. The results indicated that primary roots and their laterals were the types more sensitive to the single and combined stresses, while the seminal laterals specifically responded to the combined only. Further, antagonistic and synergistic effects were observed for the specific traits in the primary and their laterals and in the seminal lateral roots in response to the combined stress. These results suggested that the maize root system modified specific root types and traits to deal with different stressful environmental conditions, highlighting that the adaptation strategy to the combined stress may be different from that of the individual ones. The knowledge of "unique or shared" responses of plants to multiple stress can be utilized to develop varieties with broad-spectrum stress tolerance.

Integrative Analysis of the Metabolome and Transcriptome of Sorghum bicolor Reveals Dynamic Changes in Flavonoids Accumulation under Saline-Alkali Stress

With the perpetuation of soil salinization, it is imperative to improve the salt and alkaline tolerance of crops. Sorghum bicolor, a C4 crop, is often grown in semiarid areas due to its high tolerance of various abiotic stresses. Whether to improve the resistance of the sorghum itself or that of other crops, it is necessary to understand the response of sorghum under saline-alkali stress. An integrative analysis of the metabolome and transcriptome of sorghum under normal conditions and treatments of moderate and severe saline-alkali stress was performed. Among the different accumulated metabolites (DAMs) and differentially expressed genes (DEGs), flavonoid-related DAMs and DEGs were clearly changed. The level of flavonoids was increased under saline-alkali stress, and the change in flavonoids was dynamic as to whether total flavonoids or most flavonoid components accumulated more under moderate saline-alkali stress compared to severe stress. Some flavonoid metabolites were significantly correlated with the expression of flavonoid biosynthesis genes. MYB transcription factors may also contribute to the regulation of flavonoids levels. These findings present the dynamic changes and possible molecular mechanisms of flavonoids under different saline-alkali stresses and provide a foundation for future research and crop improvement.

The Wild Rice Locus CTS-12 Mediates ABA-Dependent Stomatal Opening Modulation to Limit Water Loss Under Severe Chilling Stress

A near-isogenic line (NIL) DC90 which was generated by introgressing a wild rice (Oryza rufipogon Griff.) locus CTS-12 into the 9311(Oryza sativa L. ssp. indica) background confers chilling tolerance phenotype. Here, our pilot trials showed that chilling tolerance was positively correlated with abscisic acid (ABA) biosynthesis. To understand how CTS-12 mediated the ABA-dependent multi-levels of regulation, the integration of transcriptomic and metabolomic profiling using the two-way orthogonal projections to latent structures (O2PLS) and discriminant analysis (OPLS-DA) modeling was performed to investigate the mechanisms underlying chilling tolerance. Our results revealed that metabolic shifts, including the activation of stachyose biosynthesis, amino acid metabolism pathways, phenylpropanoid/flavonoid biosynthesis, ABA biosynthesis, and perturbation of glycolysis, occurred under chilling treatment; in the recovery period, glutamate-related pathways, β-alanine biosynthesis and degradation, and serotonin biosynthesis pathways were differentiated between 9311 and DC90. Particularly, the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs), including galactinol, β-alanine, glutamate, naringenin, serotonin, ABA, and LOC_Os03g44380 (9-cis-epoxycarotenoid dioxygenase 3, OsNCED3), might be involved in the chilling tolerance variation of 9311 and DC90. CRISPR/Cas9-edited OsNCED3 resulted in chilling sensitive of japonica rice ZH11, demonstrating the involvement of ABA pathway in chilling stress response. In addition, chilling tolerance of rice was associated with the balance of water uptake and loss that was modulated by stomatal movement under chilling stress. Therefore, we speculated that the CTS-12-mediated ABA signaling pathway leads to transcriptional regulation of chilling-responsive genes and, in turn, triggers metabolic shifts to coordinately regulate the stomatal movement of guard cells. The results of this study improve our understanding of the multilevel regulation of wild rice in response to chilling stress.

Identification of a genomic region controlling thermotolerance at flowering in maize using a combination of whole genomic re-sequencing and bulked segregant analysis

A novel genomic region controlling thermotolerance at flowering was identified by the combination of whole genomic re-sequencing and bulked segregant analysis in maize. The increasing frequency of extreme high temperature has brought a great threat to the development of maize throughout its life cycle, especially during the flowering phase. However, the genetic basis of thermotolerance at flowering in maize remains poorly understood. Here, we characterized a thermotolerant maize ecotype Abe2 and dissected its genetic basis using a F_2:8 recombinant inbred line (RIL) population generated from a cross between Abe2 and B73. After continuous high temperature stress above 35 °C for 17 days, Abe2 and B73 show distinct leaf scorching phenotype under field conditions. To identify the genomic regions associated with the phenotypic variation, we applied a combination of whole genomic re-sequencing and bulked segregant analysis, and revealed 10,316,744 SNPs and 1,488,302 InDels between the two parental lines, and 2,693,054 SNPs and 313,757 InDels between the two DNA pools generated from the thermos-tolerant and the sensitive individuals of the RIL, of which, 108,655 and 17,853 SNPs may cause nonsynonymous variations. Finally, a 7.41 Mb genomic region on chromosome 1 was identified, and 7 candidate genes were annotated to participate in high temperature-related stress response. A candidate gene Zm00001d033339 encoding a serine/threonine protein kinase was proposed to be the most likely causative gene contributing to the thermotolerance at flowering by involving in stomatal movement (GO: 0010119) via Abscisic acid (ABA) pathway (KO04075). This work could provide an opportunity for gene cloning and pyramiding breeding to improve thermotolerance at flowering in maize.

Leaf Soluble Sugars and Free Amino Acids as Important Components of Abscisic Acid-Mediated Drought Response in Tomato

Water deficit has a global impact on plant growth and crop yield. Climate changes are going to increase the intensity, duration and frequency of severe droughts, particularly in southern and south-eastern Europe, elevating the water scarcity issues. We aimed to assess the contribution of endogenous abscisic acid (ABA) in the protective mechanisms against water deficit, including stomatal conductance, relative water potential and the accumulation of osmoprotectants, as well as on growth parameters. To achieve that, we used a suitable model system, ABA-deficient tomato mutant, flacca and its parental line. Flacca mutant exhibited constitutively higher levels of soluble sugars (e.g., galactose, arabinose, sorbitol) and free amino acids (AAs) compared with the wild type (WT). Water deficit provoked the strong accumulation of proline in both genotypes, and total soluble sugars only in flacca. Upon re-watering, these osmolytes returned to the initial levels in both genotypes. Our results indicate that flacca compensated higher stomatal conductance with a higher constitutive level of free sugars and AAs. Additionally, we suggest that the accumulation of AAs, particularly proline and its precursors and specific branched-chain AAs in both, glucose and sucrose in flacca, and sorbitol in WT, could contribute to maintaining growth rate during water deficit and recovery in both tomato genotypes.

Analysis of melatonin regulation of germination and antioxidant metabolism in different wheat cultivars under polyethylene glycol stress

Melatonin is effective in enhancing various abiotic stress resistances of plants. However, its underlying mechanisms in drought-resistance in winter wheat (Triticum aestivum L.) is not clear. The goal of this work was to investigate the effect of melatonin on seed germination and to evaluate leaf antioxidant physiology for two wheat varieties. Experiments included 20% PEG, melatonin plus 20% PEG and a control using two contrasting wheat varieties (JM22– drought sensitive and HG35– drought resistant). Melatonin levels were 0, 1, 10, 100 and 300 μmol L^-1. Results revealed that 300 μmol L^-1 of melatonin alleviated the negative effect of water stress on germination and increased radicle length, radicle number, and plumule length of the germinated seeds. Principal component analysis showed a significant change in amino acid content during germination and this change was dependent on melatonin concentration and the variety. Lysine (Lys) content in wheat seeds under the PEG plus 300 μmol L^-1 melatonin treatment increased compared with that of the seeds under PEG alone. There was a significant and positive correlation between Lys content and morphological index of germination. During seedling growth, soluble protein was involved in osmotic adjustment and superoxide dismutase (SOD) activity was increased to mitigate the damage in the cytomembrane of JM 22 leaf under 300 μmol L^-1 melatonin plus PEG treatment. The effect of melatonin was dependent on SOD activity increasing significantly for HG35—a drought resistant variety. The results of this work lays a foundation for further studies to determine if melatonin can be economically used to mitigate the impact of dry planting conditions on wheat productivity in North China Plain.

Wheat growth, applied water use efficiency and flag leaf metabolome under continuous and pulsed deficit irrigation

The intensity and frequency of precipitation events are predicted to change over the coming decades. For many areas, longer periods without rainfall are expected. We investigated the importance of irrigation frequency under water deficit conditions for growth, physiology and chemistry of wheat (Triticum aestivum). Drought-stressed plants received 40% of the water provided for control plants and were either watered every other day (continuous drought, cd) or every eight days (pulsed drought, pd). Maximum quantum yield of photosystem II (Fv/Fm), aboveground biomass, applied water use efficiency (WUEapl) and the flag leaf metabolome were assessed twice during development. Fv/Fm was not affected by irrigation. Drought-exposed plants produced less biomass, but had higher WUEapl than control plants. More metabolic features responded to the pd compared to the cd treatment and more features were increased than decreased in pool size in flag leaves. Salicylic acid glucoside was generally decreased under drought. In pd plants, two benzoxazinoid glucosides were enhanced at the first time point and concentrations of several flavonoid glycosides were modulated. This study extends our knowledge about drought effects on wheat; it highlights that the frequency of watering determines how plant growth, physiology and metabolism are affected by drought.

Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance

Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction.

Does the alternative respiratory pathway offer protection against the adverse effects resulting from climate change?

Elevated greenhouse gases (GHGs) induce adverse conditions directly and indirectly, causing decreases in plant productivity. To deal with climate change effects, plants have developed various mechanisms including the fine-tuning of metabolism. Plant respiratory metabolism is highly flexible due to the presence of various alternative pathways. The mitochondrial alternative oxidase (AOX) respiratory pathway is responsive to these changes, and several lines of evidence suggest it plays a role in reducing excesses of reactive oxygen species (ROS) and reactive nitrogen species (RNS) while providing metabolic flexibility under stress. Here we discuss the importance of the AOX pathway in dealing with elevated carbon dioxide (CO2), nitrogen oxides (NOx), ozone (O3), and the main abiotic stresses induced by climate change.

Biomarkers for grain yield stability in rice under drought stress

Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate-glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.

Endogenous Hormones Inhibit Differentiation of Young Ears in Maize (Zea mays L.) Under Heat Stress

Global warming frequently leads to extreme temperatures, which pose a serious threat to the growth, development, and yield formation of crops such as maize. This study aimed to deeply explore the molecular mechanisms of young ear development under heat stress. We selected the heat-tolerant maize variety Zhengdan 958 (T) and heat-sensitive maize variety Xianyu 335 (S), and subjected them to heat stress in the V9 (9th leaf), V12 (12th leaf), and VT (tasseling) growth stages. We combined analysis of the maize phenotype with omics technology and physiological indicators to compare the differences in young ear morphology, total number of florets, floret fertilization rate, grain abortion rate, number of grains, and main metabolic pathways between plants subjected to heat stress and those left to develop normally. The results showed that after heat stress, the length and diameter of young ears, total number of florets, floret fertilization rate, and number of grains all decreased significantly, whereas the length of the undeveloped part at the top of the ear and grain abortion rate increased significantly. In addition, the differentially expressed genes (DEGs) in young ears were significantly enriched in the hormone signaling pathways. The endogenous hormone content in young ears exhibited different changes: zeatin (ZT) and zeatin riboside (ZR) decreased significantly, but gibberellin acid₃ (GA₃), gibberellin acid₄ (GA₄), and abscisic acid (ABA) increased significantly, in ears subjected to heat stress. In the heat-tolerant maize variety, the salicylic acid (SA), and jasmonic acid (JA) content in the vegetative growth stage also increased in ears subjected to heat stress, whereas the opposite effect was observed for the heat-sensitive variety. The changes in endogenous hormone content of young ears that were subjected to heat stress significantly affected ear development, resulting in a reduction in the number of differentiated florets, fertilized florets and grains, which ultimately reduced the maize yield.

Metabolomics: A Way Forward for Crop Improvement

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice

Metabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions.

Improvement of the breeding efficiencies of heterotic crops adaptive to different conditions can mitigate the food shortage crisis due to overpopulation and climate change. To date, diverse molecular markers have been used to guide field phenotypic selection, whereas accurate predictions of complex heterotic traits are rarely reported. Here, we present a practical metabolome-based strategy for predicting yield heterosis in rice. The dissection of population structure based on untargeted metabolite profiles as the initial critical step in multivariate modeling performed better than the screening of predictive variables. Then the assessment of each predictive variable’s contribution to predictive models according to all latent factors was more precise than the conventional first one. Metabolites belonging to specific pathways were closely associated with yield heterosis, and the up-regulation of galactose metabolism promoted robust yield heterosis in hybrids under different growth conditions. Our study demonstrates that metabolome-based predictive models with correctly dissected population structure and screened predictive variables can facilitate accurate predictions of yield heterosis and have great potential for establishing molecular marker–based precision breeding programs.

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Heat stress is a major limiting factor for crop productivity. Tomato is highly sensitive to heat stress, which can result in a total yield loss. To adapt to current and future heat stress, there is a dire need to develop heat tolerant cultivars. Here, we review recent attempts to improve screening for heat tolerance and to exploit genetic and genomic resources in tomatoes. We provide key factors related to phenotyping environments and traits (morphological, physiological, and metabolic) to be considered to identify and breed thermo-tolerant genotypes. There is significant variability in tomato germplasm that can be harnessed to breed for thermo-tolerance. Based on our review, we propose that the use of advanced backcross populations and chromosome segments substitution lines is the best means to exploit variability for heat tolerance in non-cultivated tomato species. We applied a meta quantitative trait loci (MQTL) analysis on data from four mapping experiments to co-localize QTL associated with heat tolerance traits (e.g., pollen viability, number of pollen, number of flowers, style protrusion, style length). The analysis revealed 13 MQTL of which 11 were composed of a cluster of QTL. Overall, there was a reduction of about 1.5-fold in the confidence interval (CI) of the MQTL (31.82 cM) compared to the average CI of individual QTL (47.4 cM). This confidence interval is still large and additional mapping resolution approaches such as association mapping and multi-parent linkage mapping are needed. Further investigations are required to decipher the genetic architecture of heat tolerance surrogate traits in tomatoes. Genomic selection and new breeding techniques including genome editing and speed breeding hold promise to fast-track development of improved heat tolerance and other farmer- and consumer-preferred traits in tomatoes.

Impact of Combined Heat and Drought Stress on the Potential Growth Responses of the Desert Grass Artemisia sieberi alba: Relation to Biochemical and Molecular Adaptation

Artemisia sieberi alba is one of the important plants frequently encountered by the combined effect of drought and heat stress. In the present study, we investigated the individual and combined effect of drought and heat stress on growth, photosynthesis, oxidative damage, and gene expression in A. sieberi alba. Drought and heat stress triggered oxidative damage by increasing the accumulation of hydrogen peroxide, and therefore electrolyte leakage. The accumulation of secondary metabolites, such as phenol and flavonoids, and proline, mannitol, inositol, and sorbitol, was increased due to drought and heat stress exposure. Photosynthetic attributes including chlorophyll synthesis, stomatal conductance, transpiration rate, photosynthetic efficiency, and chlorophyll fluorescence parameters were drastically reduced due to drought and heat stress exposure. Relative water content declined significantly in stressed plants, which was evident by the reduced leaf water potential and the water use efficiency, therefore, affecting the overall growth performance. Relative expression of aquaporin (AQP), dehydrin (DHN1), late embryogenesis abundant (LEA), osmotin (OSM-34), and heat shock proteins (HSP70) were significantly higher in stressed plants. Drought triggered the expression of AQP, DHN1, LEA, and OSM-34 more than heat, which improved the HSP70 transcript levels. A. sieberi alba responded to drought and heat stress by initiating key physio-biochemical and molecular responses, which were distinct in plants exposed to a combination of drought and heat stress.

Different ways to die in a changing world: Consequences of climate change for tree species performance and survival through an ecophysiological perspective

Anthropogenic activities such as uncontrolled deforestation and increasing greenhouse gas emissions are responsible for triggering a series of environmental imbalances that affect the Earth's complex climate dynamics. As a consequence of these changes, several climate models forecast an intensification of extreme weather events over the upcoming decades, including heat waves and increasingly severe drought and flood episodes. The occurrence of such extreme weather will prompt profound changes in several plant communities, resulting in massive forest dieback events that can trigger a massive loss of biodiversity in several biomes worldwide. Despite the gravity of the situation, our knowledge regarding how extreme weather events can undermine the performance, survival, and distribution of forest species remains very fragmented. Therefore, the present review aimed to provide a broad and integrated perspective of the main biochemical, physiological, and morpho-anatomical disorders that may compromise the performance and survival of forest species exposed to climate change factors, particularly drought, flooding, and global warming. In addition, we also discuss the controversial effects of high CO2 concentrations in enhancing plant growth and reducing the deleterious effects of some extreme climatic events. We conclude with a discussion about the possible effects that the factors associated with the climate change might have on species distribution and forest composition.

Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought

Water limits crop productivity, so selecting for a minimal yield gap in drier environments is critical to mitigate against climate change and land-use pressure. We investigated the responses of relative water content (RWC), stomatal conductance, chlorophyll content, and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and in field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites, and yield gap-based drought tolerance (YDT; the ratio of yield in water-limited versus well-watered conditions) across 18 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2=0.85, P<8E-6) and RWC under field drought (r2=0.77, P<0.05). Moreover, multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: serine, asparagine, methionine, and lysine (R2=0.98; P<0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for selection of wheat cultivars with high field-derived YDT.

Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

BACKGROUND

Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes.

RESULTS

Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame.

CONCLUSION

The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.

A metabolome-based core hybridisation strategy for the prediction of rice grain weight across environments

Marker-based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilised two independent F1 hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method. A stable predictive model for TGW was built based on hybrids from the population in 2012 (r = 0.75) but failed to properly predict TGW for hybrids from the population in 2015 (r = 0.27). After integrating hybrids from both populations into the training set, the TGW of hybrids could be predicted but was largely dependent on population structures. Then, core hybrids from each population were determined by principal component analysis and the TGW of hybrids in both environments were successfully predicted (r > 0.60). Moreover, adjusting the population structures and numbers of predictive analytes increased TGW predictability for hybrids in 2015 (r = 0.72). Our study demonstrates that the TGW of F1 hybrids across environments can be accurately predicted based on parental untargeted metabolite profiles with a core hybridisation strategy in rice. Metabolic biomarkers identified from early developmental stage tissues, which are grown under experimental conditions, may represent a workable approach towards the robust prediction of major agronomic traits for climate-adaptive varieties.

Metabolic responses of rice cultivars with different tolerance to combined drought and heat stress under field conditions

BACKGROUND

Rice is susceptible to both drought and heat stress, in particular during flowering and grain filling, when both grain yield and quality may be severely compromised. However, under field conditions, these 2 stresses rarely occur separately. Under well-watered conditions, plants avoid heat stress by transpirational cooling, while this is not possible under drought conditions. Although investigating combined drought and heat stress is clearly more agronomically relevant than analyzing the effects of the single stresses, only a few studies of this stress combination, in particular under field conditions, have been published.

RESULTS

Three rice cultivars differing in drought and heat tolerance were grown in the field under control and drought conditions in 3 consecutive years. Drought was applied either during flowering or during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Analysis by gas chromatography-mass spectrometry showed distinct metabolic profiles for the 3 investigated organs (flag leaves, flowering spikelets, developing seeds). The metabolic stress responses of the plants also strongly differed between cultivars and organs. Correlation analysis identified potential metabolic markers for grain yield and quality under combined drought and heat stress from both stress-regulated metabolites and from metabolites with constitutive differences between the cultivars.

CONCLUSIONS

Gas chromatography-mass spectrometry resolved metabolic responses to combined drought and heat stress in different organs of field-grown rice. The metabolite profiles can be used to identify potential marker metabolites for yield stability and grain quality that are expected to improve breeding efforts towards developing rice cultivars that are resilient to climate change.

Transcriptomic and Metabolomic Analysis of the Heat-Stress Response of Populus tomentosa Carr

Plants have evolved mechanisms of stress tolerance responses to heat stress. However, little is known about metabolic responses to heat stress in trees. In this study, we exposed Populus tomentosa Carr. to control (25 °C) and heat stress (45 °C) treatments and analyzed the metabolic and transcriptomic effects. Heat stress increased the cellular concentration of H2O2 and the activities of antioxidant enzymes. The levels of proline, raffinose, and melibiose were increased by heat stress, whereas those of pyruvate, fumarate, and myo-inositol were decreased. The expression levels of most genes (PSB27, PSB28, LHCA5, PETB, and PETC) related to the light-harvesting complexes and photosynthetic electron transport system were downregulated by heat stress. Association analysis between key genes and altered metabolites indicated that glycolysis was enhanced, whereas the tricarboxylic acid (TCA) cycle was suppressed. The inositol phosphate; galactose; valine, leucine, and isoleucine; and arginine and proline metabolic pathways were significantly affected by heat stress. In addition, several transcription factors, including HSFA2, HSFA3, HSFA9, HSF4, MYB27, MYB4R1, and bZIP60 were upregulated, whereas WRKY13 and WRKY50 were downregulated by heat stress. Interestingly, under heat stress, the expression of DREB1, DREB2, DREB2E, and DREB5 was dramatically upregulated at 12 h. Our results suggest that proline, raffinose, melibiose, and several genes (e.g., PSB27, LHCA5, and PETB) and transcription factors (e.g., HSFAs and DREBs) are involved in the response to heat stress in P. tomentosa.

Physiological and Metabolic Responses of Rice to Reduced Soil Moisture: Relationship of Water Stress Tolerance and Grain Production

Access to adequate irrigation resources is critical for sustained agricultural production, and rice, a staple cereal grain for half of the world population, is one of the biggest users of irrigation. To reduce water use, several water saving irrigation systems have been developed for rice production, but a reliable system to evaluate cultivars for water stress tolerance is still lacking. Here, seven rice cultivars that have diverse yield potential under water stress were evaluated in a field study using four continuous irrigation regimes varying from saturation to wilting point. To understand the relationship between water stress and yield potential, the physiological and leaf metabolic responses were investigated at the critical transition between vegetative and reproductive growth stages. Twenty-nine metabolite markers including carbohydrates, amino acids and organic acids were found to significantly differ among the seven cultivars in response to increasing water stress levels with amino acids increasing but organic acids and carbohydrates showing mixed responses. Overall, our data suggest that, in response to increasing water stress, rice cultivars that do not show a significant yield loss accumulate carbohydrates (fructose, glucose, and myo-inositol), and this is associated with a moderate reduction in stomatal conductance (g_s), particularly under milder stress conditions. In contrast, cultivars that had significant yield loss due to water stress had the greatest reduction in g_s, relatively lower accumulation of carbohydrates, and relatively high increases in relative chlorophyll content (SPAD) and leaf temperature (Tm). These data demonstrate the existence of genetic variation in yield under different water stress levels which results from a suite of physiological and biochemical responses to water stress. Our study, therefore, suggests that in rice there are different physiological and metabolic strategies that result in tolerance to water stress that should be considered in developing new cultivars for deficit irrigation production systems that use less water.

Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO2] and temperature

INTRODUCTION

By mid-century, global atmospheric carbon dioxide concentration ([CO₂]) is predicted to reach 600 μmol mol^-1 with global temperatures rising by 2 °C. Rising [CO₂] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions.

OBJECTIVES

This experiment aimed to understand the effects of elevated [CO₂] (600 μmol mol^-1) and warming (+ 2 °C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles.

METHODS

We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO₂] and temperature, and statistical analyses were used to integrate the data.

RESULTS

Elevated temperature altered the content of amino acids and secondary metabolites. The transcriptome of Guinea grass shows a clear time point separations, with the changes in the elevated temperature and [CO₂] combination plots.

CONCLUSION

Field transcriptomics and metabolomics revealed that elevated temperature and [CO₂] result in alterations in transcript and metabolite profiles associated with environmental response, secondary metabolism and stomatal function. These metabolic responses are consistent with greater growth and leaf area production under elevated temperature and [CO₂]. These results show that tropical C₄ grasslands may have unpredicted responses to global climate change, and that warming during a cool growing season enhances growth and alleviates stress.

Comparative metabolomic profiling in the roots and leaves in contrasting genotypes reveals complex mechanisms involved in post-anthesis drought tolerance in wheat

Understanding the contrasting biochemical changes in different plant parts in response to drought can help to formulate smart strategies to develop drought tolerant genotypes. The current study used metabolomics and physiological approaches to understand the differential biochemical changes coupled with physiological adjustments in leaves and roots to cope with drought stress in two wheat genotypes, LA754 (drought tolerant) and AGS2038 (drought sensitive). The gas chromatography-mass spectrometry (GC-MS) analysis and physiological trait estimation were performed in the roots and leaves after drought imposition. Drought induced reduction was observed in all physiological and yield related traits. In LA754, higher numbers of metabolites were altered in leaves (45) compared to roots (20) which indicates that plants allocated more resources to leaves in tolerant genotype. In addition, the metabolic components of the root were less affected by the stress which supports the idea that the roots are more drought tolerant than the leaf or shoot. In AGS2038, thirty and twenty eight metabolites were altered in the leaves and roots, respectively. This indicates that the sensitive genotype compromised resource allocation to leaves, rather allocated more towards roots. Tryptophan, valine, citric acid, fumaric acid, and malic acid showed higher accumulation in leaf in LA754, but decreased in the root, while glyceric acid was highly accumulated in the root, but not in the leaf. The results demonstrated that the roots and shoots have a different metabolic composition, and shoot metabolome is more variable than the root metabolome. Though the present study demonstrated that the metabolic response of shoots to drought contrasts with that of roots, some growth metabolites (protein, sugar, etc) showed a mirror increase in both parts. Protein synthesis and energy cycle was active in both organs, and the organs were metabolically activated to enhance water uptake and maintain growth to mitigate the effect of drought.

Metabolite profiling and genome-wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling

Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low-Pi-sensitive lines and six low-Pi-tolerant lines under Pi-sufficient and Pi-deficient conditions to identify pathways and genes associated with the low-Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi-deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low- and normal-Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi-sensitive and Pi-resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low-Pi-responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome-wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose-6-phosphate-1-epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi-deficient responses and give multiple insights into improving the efficiency of Pi use in maize.

Metabolic response to drought in six winter wheat genotypes

Wheat is one of the most important cereals, whose growth and development is strongly limited by drought. This study investigated the physiological and metabolic response of six winter wheat cultivars to drought with the emphasis on the induction of dominant metabolites affected by the treatment and genotypes or both. The plants were exposed to a moderate (non-lethal) drought stress, which was induced by withholding watering for six days under controlled greenhouse conditions. A decline in CO2 assimilation (Pn) and transpiration rate, stomata closure, a decrease in relative water content (RWC) and increase of malondialdehyde content were observed in drought-treated plants of all cultivars. These changes were most pronounced in Ellvis, while Soissons was able to retain the higher RWC and Pn. Among the studied metabolites, sugars (sucrose, glucose, fructose, several disaccharides), organic acids (malic acid, oxalic acids), amino acids (proline, threonine, gamma-aminobutyric acid (GABA), glutamine) and sugar alcohols such as myo-inositol accumulated to higher levels in the plants exposed to drought stress in comparison with the control. The accumulation of several metabolites in response to drought differed between the genotypes. Drought induced the production of sucrose, malic acid and oxalic acid, unknown organic acid 1, unknown disaccharide 1, 2 and 3, GABA, L-threonine, glutamic acid in four (Soissons, Žitarka, Antonija or Toborzó) out of six genotypes. In addition, Soissons, which was the most drought tolerant genotype, accumulated the highest amount of unknown disaccharide 5, galactonic and phosphoric acids. The two most drought sensitive cultivars, Srpanjka and Ellvis, demonstrated different metabolic adjustment in response to the stress treatment. Srpanjka responded to drought by increasing the amount of glucose and fructose originated from hydrolyses of sucrose and accumulating unidentified sugar alcohols 1 and 2. In Ellvis, drought caused inhibition of photosynthetic carbon metabolism, as evidence by the decreased Pn, gs, RWC and accumulation levels of sugar metabolites (sucrose, glucose and fructose). The results revealed the differences in metabolic response to drought among the genotypes, which drew attention on metabolites related with general response and on those metabolites which are part of specific response that may play an important role in drought tolerance.

Comparative Physiological and Metabolic Analysis Reveals a Complex Mechanism Involved in Drought Tolerance in Chickpea (Cicer arietinum L.) Induced by PGPR and PGRs

The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGRs) can be applied to improve the growth and productivity of plants, with potential to be used for genetic improvement of drought tolerance. However, for genetic improvement to be achieved, a solid understanding of the physiological and biochemical changes in plants induced by PGPR and PGR is required. The present study was carried out to investigate the role of PGPR and PGRs on the physiology and biochemical changes in chickpea grown under drought stress conditions and their association with drought tolerance. The PGPR, isolated from the rhizosphere of chickpea, were characterized on the basis of colony morphology and biochemical characters. They were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH₃), and exopolysaccharides (EPS) production. The isolated PGPR strains, named P1, P2, and P3, were identified by 16S-rRNA gene sequencing as Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium, respectively. The seeds of two chickpea varieties, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerant) were soaked for 2-3 h prior to sowing in 24 h old cultures of isolates. The salicylic acid (SA) and putrescine (Put) were sprayed (150 mg/L) on 25 day old chickpea seedlings. The results showed that chickpea plants treated with a consortium of PGPR and PGRs significantly enhanced the chlorophyll, protein, and sugar contents compared to irrigated and drought conditions. Leaf proline content, lipid peroxidation, and activities of antioxidant enzymes (CAT, APOX, POD, and SOD) all increased in response to drought stress but decreased due to the PGPR and PGRs treatment. An ultrahigh performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis was carried out for metabolic profiling of chickpea leaves planted under controlled (well-irrigated), drought, and consortium (drought plus PGPR and PGRs) conditions. Proline, L-arginine, L-histidine, L-isoleucine, and tryptophan were accumulated in the leaves of chickpea exposed to drought stress. Consortium of PGPR and PGRs induced significant accumulation of riboflavin, L-asparagine, aspartate, glycerol, nicotinamide, and 3-hydroxy-3-methyglutarate in the leaves of chickpea. The drought sensitive chickpea variety showed significant accumulation of nicotinamide and 4-hydroxy-methylglycine in PGPR and PGR treated plants at both time points (44 and 60 days) as compared to non-inoculated drought plants. Additionally, arginine accumulation was also enhanced in the leaves of the sensitive variety under drought conditions. Metabolic changes as a result of drought and consortium conditions highlighted pools of metabolites that affect the metabolic and physiological adjustments in chickpea that reduce drought impacts.

UPLC-HRMS-based untargeted metabolic profiling reveals changes in chickpea (Cicer arietinum) metabolome following long-term drought stress

Genetic improvement for drought tolerance in chickpea requires a solid understanding of biochemical processes involved with different physiological mechanisms. The objective of this study is to demonstrate genetic variations in altered metabolic levels in chickpea varieties (tolerant and sensitive) grown under contrasting water regimes through ultrahigh-performance liquid chromatography/high-resolution mass spectrometry-based untargeted metabolomic profiling. Chickpea plants were exposed to drought stress at the 3-leaf stage for 25 days, and the leaves were harvested at 14 and 25 days after the imposition of drought stress. Stress produced significant reduction in chlorophyll content, F_v /F_m , relative water content, and shoot and root dry weight. Twenty known metabolites were identified as most important by 2 different methods including significant analysis of metabolites and partial least squares discriminant analysis. The most pronounced increase in accumulation due to drought stress was demonstrated for allantoin, l-proline, l-arginine, l-histidine, l-isoleucine, and tryptophan. Metabolites that showed a decreased level of accumulation under drought conditions were choline, phenylalanine, gamma-aminobutyric acid, alanine, phenylalanine, tyrosine, glucosamine, guanine, and aspartic acid. Aminoacyl-tRNA and plant secondary metabolite biosynthesis and amino acid metabolism or synthesis pathways were involved in producing genetic variation under drought conditions. Metabolic changes in light of drought conditions highlighted pools of metabolites that affect the metabolic and physiological adjustment in chickpea that reduced drought impacts.

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance

The heat shock response is crucial for organism survival in natural environments. RNA structure is known to influence numerous processes related to gene expression, but there have been few studies on the global RNA structurome as it prevails in vivo. Moreover, how heat shock rapidly affects RNA structure genome-wide in living systems remains unknown. We report here in vivo heat-regulated RNA structuromes. We applied Structure-seq chemical [dimethyl sulfate (DMS)] structure probing to rice (Oryza sativa L.) seedlings with and without 10 min of 42 °C heat shock and obtained structural data on >14,000 mRNAs. We show that RNA secondary structure broadly regulates gene expression in response to heat shock in this essential crop species. Our results indicate significant heat-induced elevation of DMS reactivity in the global transcriptome, revealing RNA unfolding over this biological temperature range. Our parallel Ribo-seq analysis provides no evidence for a correlation between RNA unfolding and heat-induced changes in translation, in contrast to the paradigm established in prokaryotes, wherein melting of RNA thermometers promotes translation. Instead, we find that heat-induced DMS reactivity increases correlate with significant decreases in transcript abundance, as quantified from an RNA-seq time course, indicating that mRNA unfolding promotes transcript degradation. The mechanistic basis for this outcome appears to be mRNA unfolding at both 5' and 3'-UTRs that facilitates access to the RNA degradation machinery. Our results thus reveal unexpected paradigms governing RNA structural changes and the eukaryotic RNA life cycle.

Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction

BACKGROUND

Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Gene transcripts and metabolites are important regulatory intermediates that link genetic variations to higher-order complex traits such as wood development and drought response. A few prior studies have associated intermediate phenotypes including mRNA expression and metabolite levels with a limited number of molecular markers, but the identification of genetic variations that regulate intermediate phenotypes needs further investigation.

RESULTS

We identified 1841 single nucleotide polymorphisms (SNPs) associated with 191 gene expression mRNA phenotypes and 524 SNPs associated with 53 metabolite level phenotypes using 2.8 million exome-derived SNPs. The identified SNPs reside in genes with a wide variety of functions. We further integrated the identified SNPs and the associated expressed genes and metabolites into networks. We described the SNP-SNP interactions that significantly impacted the gene transcript abundance and metabolite level in the networks. Key loci and genes in the wood development and drought response networks were identified and analyzed.

CONCLUSIONS

This work provides new candidate genes for research on the genetic basis of gene expression and metabolism linked to wood development and drought response in loblolly pine and highlights the efficiency of using association-mapping-based networks to discover candidate genes with important roles in complex biological processes.

Crop metabolomics: from diagnostics to assisted breeding

BACKGROUND

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

AIM OF REVIEW

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Translational metabolomics applied to crop breeding programs.

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding

INTRODUCTION

In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context.

OBJECTIVES

Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass.

METHODS

Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping.

RESULTS

NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance.

CONCLUSION

After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.

Comparative Metabolic Response between Cucumber ( Cucumis sativus) and Corn ( Zea mays) to a Cu(OH)2 Nanopesticide

Due to their unique properties, copper-based nanopesticides are emerging in the market. Thus, understanding their effect on crop plants is very important. Metabolomics can capture a snapshot of cellular metabolic responses to a stressor. We selected maize and cucumber as model plants for exposure to different doses of Cu(OH)₂ nanopesticide. GC-TOF-MS-based metabolomics was employed to determine the metabolic responses of these two species. Results revealed significant differences in metabolite profile changes between maize and cucumber. Furthermore, the Cu(OH)₂ nanopesticide induced metabolic reprogramming in both species, but in different manners. In maize, several intermediate metabolites of the glycolysis pathway and tricarboxylic acid cycle (TCA) were up-regulated, indicating the energy metabolism was activated. In addition, the levels of aromatic compounds (4-hydroxycinnamic acid and 1,2,4-benzenetriol) and their precursors (phenylalanine, tyrosine) were enhanced, indicating the activation of shikimate-phenylpropanoid biosynthesis in maize leaves, which is an antioxidant defense-related pathway. In cucumber, arginine and proline metabolic pathways were the most significantly altered pathway. Both species exhibited altered levels of fatty acids and polysaccharides, suggesting the cell membrane and cell wall composition may change in response to Cu(OH)₂ nanopesticide. Thus, metabolomics helps to deeply understand the differential response of these plants to the same nanopesticide stressor.

Identification and validation of genomic regions influencing kernel zinc and iron in maize

KEY MESSAGE

Genome-wide association study (GWAS) on 923 maize lines and validation in bi-parental populations identified significant genomic regions for kernel-Zinc and-Iron in maize. Bio-fortification of maize with elevated Zinc (Zn) and Iron (Fe) holds considerable promise for alleviating under-nutrition among the world's poor. Bio-fortification through molecular breeding could be an economical strategy for developing nutritious maize, and hence in this study, we adopted GWAS to identify markers associated with high kernel-Zn and Fe in maize and subsequently validated marker-trait associations in independent bi-parental populations. For GWAS, we evaluated a diverse maize association mapping panel of 923 inbred lines across three environments and detected trait associations using high-density Single nucleotide polymorphism (SNPs) obtained through genotyping-by-sequencing. Phenotyping trials of the GWAS panel showed high heritability and moderate correlation between kernel-Zn and Fe concentrations. GWAS revealed a total of 46 SNPs (Zn-20 and Fe-26) significantly associated (P ≤ 5.03 × 10-05) with kernel-Zn and Fe concentrations with some of these associated SNPs located within previously reported QTL intervals for these traits. Three double-haploid (DH) populations were developed using lines identified from the panel that were contrasting for these micronutrients. The DH populations were phenotyped at two environments and were used for validating significant SNPs (P ≤ 1 × 10-03) based on single marker QTL analysis. Based on this analysis, 11 (Zn) and 11 (Fe) SNPs were found to have significant effect on the trait variance (P ≤ 0.01, R2 ≥ 0.05) in at least one bi-parental population. These findings are being pursued in the kernel-Zn and Fe breeding program, and could hold great value in functional analysis and possible cloning of high-value genes for these traits in maize.

Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars

Metabolic composition is known to exert influence on several important agronomic traits, and metabolomics, which represents the chemical composition in a cell, has long been recognized as a powerful tool for bridging phenotype-genotype interactions. In this work, sixteen truly representative sugarcane Brazilian varieties were selected to explore the metabolic networks in buds and culms, the tissues involved in the vegetative propagation of this species. Due to the fact that bud sprouting is a key trait determining crop establishment in the field, the sprouting potential among the genotypes was evaluated. The use of partial least square discriminant analysis indicated only mild differences on bud outgrowth potential under controlled environmental conditions. However, primary metabolite profiling provided information on the variability of metabolic features even under a narrow genetic background, typical for modern sugarcane cultivars. Metabolite-metabolite correlations within and between tissues revealed more complex patterns for culms in relation to buds, and enabled the recognition of key metabolites (e.g., sucrose, putrescine, glutamate, serine, and myo-inositol) affecting sprouting ability. Finally, those results were associated with the genetic background of each cultivar, showing that metabolites can be potentially used as indicators for the genetic background.

Combined Drought and Heat Activates Protective Responses in Eucalyptus globulus That Are Not Activated When Subjected to Drought or Heat Stress Alone

Aiming to mimic a more realistic field condition and to determine convergent and divergent responses of individual stresses in relation to their combination, we explored physiological, biochemical, and metabolomic alterations after drought and heat stress imposition (alone and combined) and recovery, using a drought-tolerant Eucalyptus globulus clone. When plants were exposed to drought alone, the main responses included reduced pre-dawn water potential (Ψpd) and gas exchange. This was accompanied by increases in malondialdehyde (MDA) and total glutathione, indicative of oxidative stress. Abscisic acid (ABA) levels increased while the content of jasmonic acid (JA) fell. Metabolic alterations included reductions in the levels of sugar phosphates accompanied by increases in starch and non-structural carbohydrates. Levels of α-glycerophosphate and shikimate were also reduced while free amino acids increased. On the other hand, heat alone triggered an increase in relative water content (RWC) and Ψpd. Photosynthetic rate and pigments were reduced accompanied by a reduction in water use efficiency. Heat-induced a reduction of salicylic acid (SA) and JA content. Sugar alcohols and several amino acids were enhanced by the heat treatment while starch, fructose-6-phosphate, glucose-6-phosphate, and α-glycerophosphate were reduced. Contrary to what was observed under drought, heat stress activated the shikimic acid pathway. Drought-stressed plants subject to a heat shock exhibited a sharp decrease in gas exchange, Ψpd and JA, no alterations in electrolyte leakage, MDA, starch, and pigments and increased glutathione pool in relation to control. Comparing this with drought stress alone, subjecting drought stressed plants to an additional heat stress alleviated Ψpd and MDA, maintained an increased glutathione pool and reduced starch content and non-structural carbohydrates. A novel response triggered by the combined stress was the accumulation of cinnamate. Regarding recovery, most of the parameters affected by each stress condition reversed after re-establishment of control growing conditions. These results highlight that the combination of drought and heat provides significant protection from more detrimental effects of drought-stressed eucalypts, confirming that combined stress alter plant metabolism in a novel manner that cannot be extrapolated by the sum of the different stresses applied individually.

Comparative physiological and metabolomics analysis of wheat (Triticum aestivum L.) following post-anthesis heat stress

Genetic improvement for stress tolerance requires a solid understanding of biochemical processes involved with different physiological mechanisms and their relationships with different traits. The objective of this study was to demonstrate genetic variability in altered metabolic levels in a panel of six wheat genotypes in contrasting temperature regimes, and to quantify the correlation between those metabolites with different traits. In a controlled environment experiment, heat stress (35:28 ± 0.08°C) was initiated 10 days after anthesis. Flag leaves were collected 10 days after heat treatment to employ an untargeted metabolomics profiling using LC-HRMS based technique called IROA. High temperature stress produced significant genetic variations for cell and thylakoid membrane damage, and yield related traits. 64 known metabolites accumulated 1.5 fold of higher or lower due to high temperature stress. In general, metabolites that increased the most under heat stress (L-tryptophan, pipecolate) showed negative correlation with different traits. Contrary, the metabolites that decreased the most under heat stress (drummondol, anthranilate) showed positive correlation with the traits. Aminoacyl-tRNA biosysnthesis and plant secondary metabolite biosynthesis pathways were most impacted by high temperature stress. The robustness of metabolic change and their relationship with phenotypes renders those metabolites as potential bio-markers for genetic improvement.

Genomics-Enabled Next-Generation Breeding Approaches for Developing System-Specific Drought Tolerant Hybrids in Maize

Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems. With advent of novel genomics and breeding tools, the way of doing breeding has been tremendously changed in the last two decades. Drought tolerance is a combination of several component traits with a quantitative mode of inheritance. Rapid DNA and RNA sequencing tools and high-throughput SNP genotyping techniques, trait mapping, functional characterization, genomic selection, rapid generation advancement, and other tools are now available to understand the genetics of drought tolerance and to accelerate the breeding cycle. Informatics play complementary role by managing the big-data generated from the large-scale genomics and breeding experiments. Genome editing is the latest technique to alter specific genes to improve the trait expression. Integration of novel genomics, next-generation breeding, and informatics tools will accelerate the stress breeding process and increase the genetic gain under different production systems.

Metabolomics and proteomics reveal drought-stress responses of leaf tissues from spring-wheat

To reveal the integrative biochemical networks of wheat leaves in response to water deficient conditions, proteomics and metabolomics were applied to two spring-wheat cultivars (Bahar, drought-susceptible; Kavir, drought-tolerant). Drought stress induced detrimental effects on Bahar leaf proteome, resulting in a severe decrease of total protein content, with impairments mainly in photosynthetic proteins and in enzymes involved in sugar and nitrogen metabolism, as well as in the capacity of detoxifying harmful molecules. On the contrary, only minor perturbations were observed at the protein level in Kavir stressed leaves. Metabolome analysis indicated amino acids, organic acids, and sugars as the main metabolites changed in abundance upon water deficiency. In particular, Bahar cv showed increased levels in proline, methionine, arginine, lysine, aromatic and branched chain amino acids. Tryptophan accumulation via shikimate pathway seems to sustain auxin production (indoleacrylic acid), whereas glutamate reduction is reasonably linked to polyamine (spermine) synthesis. Kavir metabolome was affected by drought stress to a less extent with only two pathways significantly changed, one of them being purine metabolism. These results comprehensively provide a framework for better understanding the mechanisms that govern plant cell response to drought stress, with insights into molecules that can be used for crop improvement projects.

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.

IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

Metabolic analyses reveal different mechanisms of leaf color change in two purple-leaf tea plant (Camellia sinensis L.) cultivars

Purple-leaf tea plants, as anthocyanin-rich cultivars, are valuable materials for manufacturing teas with unique colors or flavors. In this study, a new purple-leaf cultivar "Zixin" ("ZX") was examined, and its biochemical variation and mechanism of leaf color change were elucidated. The metabolomes of leaves of "ZX" at completely purple, intermediately purple, and completely green stages were analyzed using ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS). Metabolites in the flavonoid biosynthetic pathway remained at high levels in purple leaves, whereas intermediates of porphyrin and chlorophyll metabolism and carotenoid biosynthesis exhibited high levels in green leaves. In addition, fatty acid metabolism was more active in purple leaves, and steroids maintained higher levels in green leaves. Saponin, alcohol, organic acid, and terpenoid-related metabolites also changed significantly during the leaf color change process. Furthermore, the substance changes between "ZX" and "Zijuan" (a thoroughly studied purple-leaf cultivar) were also compared. The leaf color change in "Zijuan" was mainly caused by a decrease in flavonoids/anthocyanins. However, a decrease in flavonoids/anthocyanins, an enhancement of porphyrin, chlorophyll metabolism, carotenoid biosynthesis, and steroids, and a decrease in fatty acids synergistically caused the leaf color change in "ZX". These findings will facilitate comprehensive research on the regulatory mechanisms of leaf color change in purple-leaf tea cultivars.