Metabolome and Transcriptome Analysis Revealed the Pivotal Role of Exogenous Melatonin in Enhancing Salt Tolerance in Vitis vinifera L.

Vitis vinifera L. possesses high economic value, but its growth and yield are seriously affected by salt stress. Though melatonin (MT) has been widely reported to enhance tolerance towards abiotic stresses in plants, the regulatory role melatonin plays in resisting salt tolerance in grapevines has scarcely been studied. Here, we observed the phenotypes under the treatment of different melatonin concentrations, and then transcriptome and metabolome analyses were performed. A total of 457 metabolites were detected in CK- and MT-treated cell cultures at 1 WAT (week after treatment) and 4 WATs. Exogenous melatonin treatment significantly increased the endogenous melatonin content while down-regulating the flavonoid content. To be specific, the melatonin content was obviously up-regulated, while the contents of more than a dozen flavonoids were down-regulated. Auxin response genes and melatonin synthesis-related genes were regulated by the exogenous melatonin treatment. WGCNA (weighted gene coexpression network analysis) identified key salt-responsive genes; they were directly or indirectly involved in melatonin synthesis and auxin response. The synergistic effect of salt and melatonin treatment was investigated by transcriptome analysis, providing additional evidence for the stress-alleviating properties of melatonin through auxin-related pathways. The present study explored the impact of exogenous melatonin on grapevines' ability to adapt to salt stress and provided novel insights into enhancing their tolerance to salt stress.

Metabolomics and Transcriptomics Revealed a Comprehensive Understanding of the Biochemical and Genetic Mechanisms Underlying the Color Variations in Chrysanthemums.

Flower color is an important characteristic of ornamental plants and is determined by various chemical components, including anthocyanin. In the present study, combined metabolomics and transcriptomics analysis was used to explore color variations in the chrysanthemums of three cultivars, of which the color of JIN is yellow, FEN is pink, and ZSH is red. A total of 29 different metabolites, including nine anthocyanins, were identified in common in the three cultivars. Compared with the light-colored cultivars, all of the nine anthocyanin contents were found to be up-regulated in the dark-colored ones. The different contents of pelargonidin, cyanidin, and their derivates were found to be the main reason for color variations. Transcriptomic analysis showed that the color difference was closely related to anthocyanin biosynthesis. The expression level of anthocyanin structural genes, including DFR, ANS, 3GT, 3MaT1, and 3MaT2, was in accordance with the flower color depth. This finding suggests that anthocyanins may be a key factor in color variations among the studied cultivars. On this basis, two special metabolites were selected as biomarkers to assist in chrysanthemum breeding for color selection.

Effects of exogenous glycine betaine and cycloleucine on photosynthetic capacity, amino acid composition, and hormone metabolism in Solanum melongena L.

Although exogenous glycine betaine (GB) and cycloleucine (Cyc) have been reported to affect animal cell metabolism, their effects on plant growth and development have not been studied extensively. Different concentrations of exogenous glycine betaine (20, 40, and 60 mmol L-1) and cycloleucine (10, 20, and 40 mmol L-1), with 0 mmol L-1 as control, were used to investigate the effects of foliar spraying of betaine and cycloleucine on growth, photosynthesis, chlorophyll fluorescence, Calvin cycle pathway, abaxial leaf burr morphology, endogenous hormones, and amino acid content in eggplant. We found that 40 mmol L-1 glycine betaine had the best effect on plant growth and development; it increased the fresh and dry weight of plants, increased the density of abaxial leaf hairs, increased the net photosynthetic rate and Calvin cycle key enzyme activity of leaves, had an elevating effect on chlorophyll fluorescence parameters, increased endogenous indoleacetic acid (IAA) content and decreased abscisic acid (ABA) content, and increased glutamate, serine, aspartate, and phenylalanine contents. However, cycloleucine significantly inhibited plant growth; plant apical dominance disappeared, plant height and dry and fresh weights decreased significantly, the development of abaxial leaf hairs was hindered, the net photosynthetic rate and Calvin cycle key enzyme activities were inhibited, the endogenous hormones IAA and ABA content decreased, and the conversion and utilization of glutamate, arginine, threonine, and glycine were affected. Combined with the experimental results and plant growth phenotypes, 20 mmol L-1 cycloleucine significantly inhibited plant growth. In conclusion, 40 mmol L-1 glycine betaine and 20 mmol L-1 cycloleucine had different regulatory effects on plant growth and development.

Changes in growth, physiology, and photosynthetic capacity of spinach (Spinacia oleracea L.) under different nitrate levels.

Nitrate content is an essential indicator of the quality of vegetables but can cause stress at high levels. This study aimed to elucidate the regulatory mechanisms of nitrate stress tolerance in spinach (Spinacia oleracea L.). We studied the effects of exogenous application of 15 (control), 50, 100, 150, 200, and 250 mM NO3- on spinach growth, physiology, and photosynthesis. The results showed that all the nitrate treatments inhibited the growth of the aerial parts of spinach compared to the control. In contrast, low nitrate levels (50 and 100 mM) promoted spinach root formation, but this effect was inhibited at high levels (150, 200, and 250 mM). Treatment with 150 mM NO3- significantly decreased the root growth vigor. Low nitrate levels increased the chlorophyll content in spinach leaves, whereas high levels had the opposite effect. High nitrate levels also weakened the net photosynthetic rate (Pn), the actual photochemical efficiency of PSII Y(II), and increased non-photochemical quenching (NPQ), reducing photosynthetic performance. Nitrate stress increased the activity of nitrate reductase (NR) and promoted the accumulation of nitrate in spinach leaves, exceeding the health-tolerance limit for nitrate in vegetables, highlighting the necessity of mitigating nitrate stress to ensure food safety. Starting with the 150 mM NO3- treatment, the proline and malondialdehyde content in spinach leaves and roots increased significantly as the nitrate levels increased. Treatment with 150 mM NO3- significantly increased soluble protein and flavonoid contents, while the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) were significantly reduced in leaves. However, spinach could resist nitrate stress by regulating the synthesis of osmoregulatory substances such as proline, thus showing some nitrate tolerance. These results provide insights into the physiological regulatory mechanisms of nitrate stress tolerance and its mitigation in spinach, an essential vegetable crop.

Exogenous Proline Enhances Systemic Defense against Salt Stress in Celery by Regulating Photosystem, Phenolic Compounds, and Antioxidant System.

This study aimed to explore how exogenous proline induces salinity tolerance in celery. We analyzed the effects of foliar spraying with 0.3 mM proline on celery growth, photosystem, phenolic compounds, and antioxidant system under salt stress (100 mM NaCl), using no salt stress and no proline spraying as control. The results showed that proline-treated plants exhibited a significant increase in plant biomass due to improved growth physiology, supported by gas exchange parameters, chlorophyll fluorescence, and Calvin cycle enzyme activity (Ketosasaccharide-1,5-diphosphate carboxylase and Fructose-1,6-diphosphate aldolase) results. Also, proline spraying significantly suppressed the increase in relative conductivity and malondialdehyde content caused by salt stress, suggesting a reduction in biological membrane damage. Moreover, salt stress resulted in hydrogen peroxide, superoxide anions and 4-coumaric acid accumulation in celery, and their contents were reduced after foliar spraying of proline. Furthermore, proline increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the content of non-enzymatic antioxidants (reduced ascorbic acid, glutathione, caffeic acid, chlorogenic acid, total phenolic acids, and total flavonoids). Additionally, proline increased the activity of key enzymes (ascorbate oxidase, ascorbate peroxidase, glutathione reductase, and dehydroascorbate reductase) in the ascorbic acid-glutathione cycle, activating it to counteract salt stress. In summary, exogenous proline promoted celery growth under salt stress, enhanced photosynthesis, increased total phenolic acid and flavonoid contents, and improved antioxidant capacity, thereby improving salt tolerance in celery.

Moderate Salinity of Nutrient Solution Improved the Nutritional Quality and Flavor of Hydroponic Chinese Chives (Allium tuberosum Rottler).

Sodium chloride (NaCl), as a eustressor, can trigger relevant pathways to cause plants to produce a series of metabolites, thus improving the quality of crops to a certain extent. However, there are few reports on the improvement of nutrient quality and flavor of hydroponic Chinese chives (Allium tuberosum Rottler) by sodium chloride. In this study, five NaCl concentrations were used to investigate the dose-dependent effects on growth, nutritional quality and flavor in Chinese chives. The results show that 10 mM NaCl had no significant effect on the growth of Chinese chives, but significantly decreased the nitrate content by 40% compared with 0 mM NaCl treatment, and the content of soluble protein and vitamin C was increased by 3.6% and 2.1%, respectively. In addition, a total of 75 volatile compounds were identified among five treatments using headspace solid-phase microextraction gas chromatography/mass spectrometry (HS-SPME/GC-MS). Compared with the 0 mM NaCl treatment, 10 mM NaCl had the greatest effect on the quantity and content of volatile compounds, with the total content increased by 27.8%. Furthermore, according to the odor activity values (OAVs) and odor description, there were 14 major aroma-active compounds (OAVs > 1) in Chinese chives. The "garlic and onion" odor was the strongest among the eight categories of aromas, and its highest value was observed in the 10 mM NaCl treatment (OAVs = 794).Taken together, adding 10 mM NaCl to the nutrient solution could improve the nutritional quality and flavor of Chinese chives without affecting their normal growth.

Co-silencing of ABA receptors (SlRCAR) reveals interactions between ABA and ethylene signaling during tomato fruit ripening.

The ripening of fleshy fruits is highly dependent on the regulation of endogenous hormones, including ethylene, abscisic acid (ABA) and other phytohormones. However, the regulatory mechanism of ABA signaling and its interaction with ethylene signaling in fruit ripening are still unclear. In this study, multi-gene interference (RNAi) was applied to silence the ABA receptor genes in tomato for screening the specific receptors that mediate ABA signaling during fruit ripening. The results indicated that the ABA receptors, including SlRCAR9, SlRCAR12, SlRCAR11, and SlRCAR13, participate in the regulation of tomato fruit ripening. Comparative analysis showed that SlRCAR11 and SlRCAR13 play more important roles in mediating ABA signaling during tomato fruit ripening. Co-silencing of the four genes encoding these receptors could weaken the ethylene biosynthesis and signaling pathway at the early stage of tomato fruit ripening, leading to delayed fruit ripening. Meanwhile, co-silencing enhanced fruit firmness, and altered the shelf-life and susceptibility to Botrytis cinerea of the transgenic fruits. Furthermore, blocking ABA signaling did not affect the ability of ethylene to induce fruit ripening, whereas the block may inhibit the effectiveness of ABA in promoting fruit ripening. These results suggested that ABA signaling may be located upstream of ethylene signaling in regulating fruit ripening. Our findings provide a new insight into the complex regulatory network of phytohormones in regulating fruit ripening in tomato.

Effect of Methyl Jasmonate Treatment on Primary and Secondary Metabolites and Antioxidant Capacity of the Substrate and Hydroponically Grown Chinese Chives.

Hydroponic culture has become a commercial planting model for leafy vegetables, herbs, and other plants with medicinal value. Methyl jasmonate (MeJA) is involved in primary and secondary plant metabolism; moreover, it regulates plant bioactive compounds and enhances the nutritional and medicinal value of plants. We performed targeted metabolomic analysis of the primary and secondary metabolites in substrate-grown and hydroponic Chinese chive leaves sprayed with MeJA (0, 300, 500, and 800 µM). Using ultra-performance liquid chromatography (UPLC), UPLC tandem mass spectrometry, and chemometric tools, and analyzed the antioxidant activity of these plants. We identified the biomarkers of amino acids (serine, proline, lysine, and arginine) and phenolic compounds (4-coumaric acid and protocatechuic acid) using chemometric tools to distinguish between substrate-grown and hydroponic Chinese chives treated with MeJA. MeJA (500 µM) treatment significantly increased the total sugar and amino acid (essential and non-essential amino acids and sulfur-containing amino acids) contents of hydroponically grown Chinese chives. However, the changes in total sugar and amino acid contents in Chinese chive grown in substrates showed the opposite trend. The organic acid content of hydroponically grown Chinese chives treated with MeJA decreased significantly, whereas that of substrate-grown plants treated with 300 µM MeJA increased significantly. Further, MeJA treatment significantly increased the phenolic content of substrate-grown Chinese chives. Treatment with 800 µM MeJA significantly increased the carotenoid content of substrate-grown Chinese chives and the phenolic content of hydroponic Chinese chives. In addition, the 500 µM MeJA treatment significantly increased the antioxidant activity of Chinese chives in both substrate-grown and hydroponic cultures, and promoted the accumulation of nutrients and bioactive substances. This treatment also improved the flavor quality of these plants and their nutritional and medicinal value. Thus, the results suggested that MeJA-treated plants could be used as value-added horticultural products.

Effects of Preharvest Methyl Jasmonate and Salicylic Acid Treatments on Growth, Quality, Volatile Components, and Antioxidant Systems of Chinese Chives.

Methyl jasmonate (MeJA) and salicylic acid (SA) regulate the production of biologically active compounds in plants and stimulate the accumulation of plant aromatic substances. However, the underlying mechanisms of how MeJA and SA influence characteristic flavor compounds and the antioxidant activity of vegetables are poorly understood. Five MeJA and SA concentrations were used to investigate the dose-dependent effects of these phytohormones on the dry and fresh weight; chlorophyll abundance; the contents of vitamin C, soluble protein, and sugar, nitrate, total phenols, flavonoids, volatile components, and enzymatically produced pyruvic acid; and antioxidant activity in Chinese chive. We found that MeJA and SA at concentrations of 500 and 150 µM, respectively, significantly increased the levels of total chlorophyll, phenols and flavonoids, vitamin C, and volatile components and significantly reduced the accumulation of nitrate. In addition, compared with the control, 500 µM of MeJA significantly increased the soluble sugar and protein content, and 150 µM SA significantly increased the dry and fresh weight of Chinese chive. Furthermore, these concentrations of MeJA and SA significantly increased the enzymatic pyruvate content and the amount of sulfide and aromatic volatile compounds and improved the characteristic flavor compounds. The 2,2-diphenyl-1-picrylhydrazyl radical scavenging capacity, Trolox-equivalent antioxidant capacity, and ferric-reducing antioxidant capacity were significantly improved after a preharvest treatment with 500 µM MeJA and 150 µM SA, which could improve the antioxidant activity, thus improving the postharvest quality and preservation characteristics of Chinese chives. Taken together, a preharvest treatment with 500 µM MeJA and 150 µM SA is optimal to improve the growth, quality, antioxidant activity, and flavor of Chinese chive, thereby enhancing its commercial value.

Tomato transcriptional repressor MYB70 directly regulates ethylene-dependent fruit ripening.

Ethylene is a key plant hormone controlling the ripening of climacteric fruits, and several transcription factors acting as important regulators of fruit ripening have been identified in tomato (Solanum lycopersicum), a model for climacteric fruits. The vast majority of these transcription factors are transcriptional activators, however, and the associated transcriptional regulatory mechanisms of most regulators are unclear. Here, we report on a tomato transcriptional repressor (termed SlMYB70) that negatively regulates fruit ripening by directly modulating ethylene biosynthesis. As an EAR motif-containing MYB transcription factor-encoding gene, SlMYB70 displayed a ripening-associated expression pattern and was responsive to ethylene. RNA interference (RNAi)-mediated repression of SlMYB70 accelerated fruit ripening, but overexpression of SlMYB70 delayed fruit ripening. Ethylene production was noticeably increased and decreased in SlMYB70-RNAi and SlMYB70-overexpressing lines, respectively, compared with wild-type tomatoes. SlMYB70 was proven to be a transcriptional repressor, dependent on the EAR repression motif, and to repress the transcription of two ethylene biosynthesis genes in fruit ripening, namely SlACS2 and SlACO3. The promoters of SlACS2 and SlACO3 are directly bound by SlMYB70, which was verified using a combination of yeast one-hybrid chromatin immunoprecipitation quantitative polymerase chain reaction and electrophoretic mobility shift assays. These results suggest that SlMYB70 negatively regulates fruit ripening via the direct transcriptional repression of ethylene biosynthesis genes, which provides insights into the ethylene-mediated key regulatory hierarchy in climacteric fruit ripening, and also highlights different types of transcriptional regulation of fruit ripening.

SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits.

Genetic manipulation of genes to upregulate specific branches of metabolic pathways is a method that is commonly used to improve fruit quality. However, the use of a single gene to impact several metabolic pathways is difficult. Here, we show that overexpression of the single gene SlMYB75 (SlMYB75-OE) is effective at improving multiple fruit quality traits. In these engineered fruits, the anthocyanin content reached 1.86 mg g-1 fresh weight at the red-ripe stage, and these SlMYB75-OE tomatoes displayed a series of physiological changes, including delayed ripening and increased ethylene production. In addition to anthocyanin, the total contents of phenolics, flavonoids and soluble solids in SlMYB75-OE fruits were enhanced by 2.6, 4, and 1.2 times, respectively, compared to those of wild-type (WT) fruits. Interestingly, a number of aroma volatiles, such as aldehyde, phenylpropanoid-derived and terpene volatiles, were significantly increased in SlMYB75-OE fruits, with some terpene volatiles showing more than 10 times higher levels than those in WT fruits. Consistent with the metabolic assessment, transcriptomic profiling indicated that the genes involved in the ethylene signaling, phenylpropanoid and isoprenoid pathways were greatly upregulated in SlMYB75-OE fruits. Yeast one-hybrid and transactivation assays revealed that SlMYB75 is able to directly bind to the MYBPLANT and MYBPZM cis-regulatory elements and to activate the promoters of the LOXC, AADC2 and TPS genes. The identification of SlMYB75 as a key regulator of fruit quality attributes through the transcriptional regulation of downstream genes involved in several metabolic pathways opens new avenues towards engineering fruits with a higher sensory and nutritional quality.

Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.).

FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated. The genes are clustered on ten tomato chromosomes and are categorised into two sub-classes; single and multiple domains protein gene. One of the main features of tomato FKBPs is their large fractions localized in chloroplast (in silico analysis) and clustered together phylogenetically. Tissue-specific expression analysis using available RNA-seq data revealed the spatiotemporal expression of the FKBPs, but few genes were observed with relatively high expressions in certain developmental stages. However, the quantitative expression profile of all genes under hormone stress provided a supporting evidence for their potential role in hormone signal pathways. Our prediction not only providing the foundation for better understanding the complex physiological regulation of FKBP gene family in tomato but also providing the potential aids to accelerate tolerance and survival in tomato under stressful condition.

The MADS-Box Gene SlMBP21 Regulates Sepal Size Mediated by Ethylene and Auxin in Tomato.

Normal organ size is achieved by successful co-ordination of cell proliferation and cell expansion, which are modulated by multiple factors such as ethylene and auxin. In our work, SlMBP21-RNAi (RNA interference) tomato exhibited longer sepals and improved fruit set. Histological analysis indicated that longer sepals were attributed to cell expansion. To explore how SlMBP21 regulates sepal size, we compared the transcriptomes of sepals between SlMBP21-RNAi and the wild type by RNA sequencing and found that the differentially expressed genes were dominantly related to cell expansion, ethylene and auxin, and photosynthesis. Down-regulation of SlMBP21 affected ethylene production and the free IAA and IAA-Val intensity in sepals. Hormone treatment further indicated that SlMBP21 was involved in the ethylene and auxin pathways. As reported, ethylene and auxin were important factors for cell expansion. Hence, SlMBP21 negatively regulated cell expansion to control sepal size, and ethylene and auxin may mediate this process. Additionally, the contents of Chl and the activity of ribulose-1, 5-bisphosphate carboxylase/oxygenase, the key photosynthetic enzyme, were both increased in SlMBP21-RNAi sepals, which indicated that photosynthesis might be enhanced in transgenic longer sepals. Therefore, the longer sepal, with better protection and enhanced photosynthesis, may contribute to improve fruit set. Altogether, these results suggested that SlMBP21 was a novel factor involved in organ size control. Moreover, our study provided potential application value for improving fruit set.

Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals.

The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits.

Evolutionarily Distinct BAHD N-Acyltransferases Are Responsible for Natural Variation of Aromatic Amine Conjugates in Rice.

Phenolamides (PAs) are specialized (secondary) metabolites mainly synthesized by BAHD N-acyltransferases. Here, we report metabolic profiling coupled with association and linkage mapping of 11 PAs in rice (Oryza sativa). We identified 22 loci affecting PAs in leaves and 16 loci affecting PAs in seeds. We identified eight BAHD N-acyltransferases located on five chromosomes with diverse specificities, including four aromatic amine N-acyltransferases. We show that genetic variation in PAs is determined, at least in part, by allelic variation in the tissue specificity of expression of the BAHD genes responsible for their biosynthesis. Tryptamine hydroxycinnamoyl transferase 1/2 (Os-THT1/2) and tryptamine benzoyl transferase 1/2 (Os-TBT1/2) were found to be bifunctional tryptamine/tyramine N-acyltransferases. The specificity of Os-THT1 and Os-TBT1 for agmatine involved four tandem arginine residues, which have not been identified as specificity determinants for other plant BAHD transferases, illustrating the versatility of plant BAHD transferases in acquiring new acyl acceptor specificities. With phylogenetic analysis, we identified both divergent and convergent evolution of N-acyltransferases in plants, and we suggest that the BAHD family of tryptamine/tyramine N-acyltransferases evolved conservatively in monocots, especially in Gramineae. Our work demonstrates that omics-assisted gene-to-metabolite analysis provides a useful tool for bulk gene identification and crop genetic improvement.

Spatiotemporal distribution of phenolamides and the genetics of natural variation of hydroxycinnamoyl spermidine in rice.

Phenolamides constitute a diverse class of secondary metabolites that are found ubiquitously in plants and have been implicated to play an important role in a wide range of biological processes, such as plant development and defense. However, spatiotemporal accumulation patterns of phenolamides in rice, one of the most important crops, are not available, and no gene responsible for phenolamide biosynthesis has been identified in this species. In this study, we report the comprehensive metabolic profiling and natural variation analysis of phenolamides in a collection of rice germplasm using a liquid chromatography-mass spectrometry-based targeted metabolomics method. Spatiotemporal controlled accumulations were observed for most phenolamides, together with their differential accumulations between the two major subspecies of rice. Further metabolic genome-wide association study (mGWAS) in rice leaf and in vivo metabolic analysis of the transgenic plants identified Os12g27220 and Os12g27254 as two spermidine hydroxycinnamoyl transferases that might underlie the natural variation of levels of spermidine conjugates in rice. Our work demonstrates that gene-to-metabolite analysis by mGWAS provides a useful tool for functional gene identification and omics-based crop genetic improvement.

Spatio-temporal distribution of phenolamides and the genetics of natural variation of hydroxycinnamoyl spermidine in rice.

Phenolamides constitute a diverse class of secondary metabolites that are found ubiquitously in plants and have been implicated to play important role in a wide range of biological processes such as plant development and defense. However, spatio-temporal accumulation patterns of phenolamides in rice, one of the most important crops, are not available so far, and no gene responsible for the phenolamides biosynthesis has been identified in this species. In this report, we report here the comprehensive metabolic profiling and natural variation analysis of phenolamides in a collection of rice germplasm using an LC-MS-based targeted metabolomics method. Spatio-temporal controlled accumulations were observed for most phenolamides, together with their differential accumulations between the two major subspecies of rice. Further metabolic genome-wide association study (mGWAS) in rice leaf and the in vivo metabolic analysis of the transgenic plants identified Os12g27200 and Os12g27254 as two spermidine hydroxycinnamoyl transferases that might be underlying the natural variation of levels of spermidine conjugates in rice. Our work demonstrates 'gene-to-metabolite' analysis by mGWAS provides a useful tool for functional gene identification and omics-based crop genetic improvement.

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights.

Plants produce a variety of metabolites that have a critical role in growth and development. Here we present a comprehensive study of maize metabolism, combining genetic, metabolite and expression profiling methodologies to dissect the genetic basis of metabolic diversity in maize kernels. We quantify 983 metabolite features in 702 maize genotypes planted at multiple locations. We identify 1,459 significant locus-trait associations (P≤1.8 × 10(-6)) across three environments through metabolite-based genome-wide association mapping. Most (58.5%) of the identified loci are supported by expression QTLs, and some (14.7%) are validated through linkage mapping. Re-sequencing and candidate gene association analysis identifies potential causal variants for five candidate genes involved in metabolic traits. Two of these genes were further validated by mutant and transgenic analysis. Metabolite features associated with kernel weight could be used as biomarkers to facilitate genetic improvement of maize.

Genetic analysis of the metabolome exemplified using a rice population.

Plant metabolites are crucial for both plant life and human nutrition. Despite recent advance in metabolomics, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the rice metabolome that provided over 2,800 highly resolved metabolic quantitative trait loci for 900 metabolites. Distinct and overlapping accumulation patterns of metabolites were observed and complex genetic regulation of metabolism was revealed in two different tissues. We associated 24 candidate genes to various metabolic quantitative trait loci by data mining, including ones regulating important morphological traits and biological processes. The corresponding pathways were reconstructed by updating in vivo functions of previously identified and newly assigned genes. This study demonstrated a powerful tool and provided a vast amount of high-quality data for understanding the plasticity of plant metabolome, which may help bridge the gap between the genome and phenome.