Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato

Discovery of steroidal alkaloid metabolites and their accumulation in pigs after short-term tomato consumption

Studies suggest steroidal alkaloids contribute to the health properties of tomato-rich diets. Untargeted studies have detected tomato steroidal alkaloid metabolites in plasma, tissues, and urine, but concentrations remain unknown. Here we utilize UHPLC-MS/MS to characterize 31 steroidal alkaloid metabolites representing 10 unique masses, and a validated UHPLC-MS method to quantify them in blood plasma. In a two-week parallel-arm study, piglets (n = 20) were fed diets containing 10 % tomato powder or a macronutrient-matched control. Concentrations averaged to 107.7 nmol/L plasma, comprising of phase I (66 %) and phase II (4.5 %) metabolites. Primary phase I metabolites were hydroxylated isomers. MS/MS fragments (m/z 253, 271, 289) in conjunction with analysis of diet profile provided higher confidence when identifying hydroxylated metabolites. These results are the first to report quantitative levels of steroidal alkaloid metabolites in plasma, contributing to an understanding of physiologically relevant concentrations. This data is useful for contextualizing research on the health benefits of tomatoes.

Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato fruits and seeds

Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintain plasma membrane sterol homeostasis throughout plant growth and development. Ester formation in plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the composition of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favours a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit tolerance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.

The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites

Capsicum (pepper) is among the most economically important species worldwide, and its fruits accumulate specialized metabolites with essential roles in plant environmental interaction and human health benefits as well as in conferring their unique taste. However, the genetics underlying differences in metabolite presence/absence and/or accumulation remain largely unknown. In this study, we carried out a genome-wide association study as well as generating and characterizing a novel backcross inbred line mapping population to determine the genetic architecture of the pepper metabolome. This genetic analysis provided over 1,000 metabolic quantitative trait loci (mQTL) for over 250 annotated metabolites. We identified 92 candidate genes involved in various mQTLs. Among the identified loci, we described and validated a gene cluster of eleven UDP-glycosyltransferases (UGTs) involved in monomeric capsianoside biosynthesis. We additionally constructed the gene-by-gene-based biosynthetic pathway of pepper capsianoside biosynthesis, including both core and decorative reactions. Given that one of these decorative pathways, namely the glycosylation of acyclic diterpenoid glycosides, contributes to plant resistance, these data provide new insights and breeding resources for pepper. They additionally provide a blueprint for the better understanding of the biosynthesis of species-specific natural compounds in general.

The natural variance of Arabidopsis secondary metabolism on extended darkness

In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0-and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the Zenodo database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.

Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat

Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.

Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum)

Rutin, a flavonoid rich in buckwheat, is important for human health and plant resistance to external stresses. The hydrolysis of rutin to quercetin underlies the bitter taste of Tartary buckwheat. In order to identify rutin hydrolysis genes, a 200 genotypes mini-core Tartary buckwheat germplasm resource was re-sequenced with 30-fold coverage depth. By combining the content of the intermediate metabolites of rutin metabolism with genome resequencing data, metabolite genome-wide association analyses (GWAS) eventually identified a glycosyl hydrolase gene FtGH1, which could hydrolyse rutin to quercetin. This function was validated both in Tartary buckwheat overexpression hairy roots and in vitro enzyme activity assays. Mutation of the two key active sites, which were determined by molecular docking and experimentally verified via overexpression in hairy roots and transient expression in tobacco leaves, exhibited abnormal subcellular localization, suggesting functional changes. Sequence analysis revealed that mutation of the FtGH1 promoter in accessions of two haplotypes might be necessary for enzymatic activity. Co-expression analysis and GWAS revealed that FtbHLH165 not only repressed FtGH1 expression, but also increased seed length. This work reveals a potential mechanism behind rutin metabolism, which should provide both theoretical support in the study of flavonoid metabolism and in the molecular breeding of Tartary buckwheat.

Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality

Classically fruit ripening and development was studied using genetic approaches, with understanding of metabolic changes that occurred in concert largely focused on a handful of metabolites including sugars, organic acids, cell wall components, and phytohormones. The advent and widespread application of metabolomics has, however, led to far greater understanding of metabolic components that play a crucial role not only in this process but also in influencing the organoleptic and nutritive properties of the fruits. Here we review how the study of natural variation, mutants, transgenics, and gene-edited fruits has led to a considerable increase in our understanding of these aspects. We focus on fleshy fruits such as tomato but also review berries, receptacle fruits, and stone-bearing fruits. Finally, we offer a perspective as to how comparative analyses and machine learning will likely further improve our comprehension of the functional importance of various metabolites in the future.

A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought

Introduction

Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources.

Methods

In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads.

Results

The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production.

Discussion

Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.

Water saving irrigation mediates bioactive pigments metabolism and storage capacity in tomato fruit

Tomato fruit consumption is influenced by flavor and nutrient quality. In the present study, we investigate the impact of water saving irrigation (WSI) as a pre-harvest management on flavor and nutrient quality of tomato fruit. Our results demonstrate that WSI-treated tomato fruit exhibited improved sensory scores as assessed by a taste panel, accompanied by elevated levels of SlGLK2 expression, sugars, acids, and carotenoid contents compared to non-treated fruit. Notably, WSI treatment significantly enhanced the development of chloroplast and plastoglobulus in chromoplast, which served as carotenoid storage sites and upregulated the expression of carotenoid biosynthetic genes. Furthermore, integrated transcriptome and metabolome analysis revealed heightened expression of sugar and flavonoid metabolism pathways in WSI-treated tomato fruit. Remarkably, the master regulator SlMYB12 displayed a substantially increased expression due to WSI. These findings suggest that WSI is an effective and sustainable approach to enhance the pigments metabolism and storage capacity as well as the organoleptic characteristics and nutritional value of tomato fruit, offering a win-win solution for both water conservation and quality improvement in agro-food production.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Synthetic biology identifies the minimal gene set required for paclitaxel biosynthesis in a plant chassis

The diterpenoid paclitaxel (Taxol) is a chemotherapy medication widely used as a first-line treatment against several types of solid cancers. The supply of paclitaxel from natural sources is limited. However, missing knowledge about the genes involved in several specific metabolic steps of paclitaxel biosynthesis has rendered it difficult to engineer the full pathway. In this study, we used a combination of transcriptomics, cell biology, metabolomics, and pathway reconstitution to identify the complete gene set required for the heterologous production of paclitaxel. We identified the missing steps from the current model of paclitaxel biosynthesis and confirmed the activity of most of the missing enzymes via heterologous expression in Nicotiana benthamiana. Notably, we identified a new C4β-C20 epoxidase that could overcome the first bottleneck of metabolic engineering. We used both previously characterized and newly identified oxomutases/epoxidases, taxane 1β-hydroxylase, taxane 9α-hydroxylase, taxane 9α-dioxygenase, and phenylalanine-CoA ligase, to successfully biosynthesize the key intermediate baccatin III and to convert baccatin III into paclitaxel in N. benthamiana. In combination, these approaches establish a metabolic route to taxoid biosynthesis and provide insights into the unique chemistry that plants use to generate complex bioactive metabolites.

Plant Metabolomics: Current Initiatives and Future Prospects

Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.

Quantifying the impact of dynamic plant-environment interactions on metabolic regulation

A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.

Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits

In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.

Natural variation of respiration-related traits in plants

Plant respiration is one of the greatest global metabolic fluxes, but rates of respiration vary massively both within different cell types as well as between different individuals and different species. Whilst this is well known, few studies have detailed population-level variation of respiration until recently. The last 20 years have seen a renaissance in studies of natural variance. In this review, we describe how experimental breeding populations and collections of large populations of accessions can be used to determine the genetic architecture of plant traits. We further detail how these approaches have been used to study the rate of respiration per se as well as traits that are intimately associated with respiration. The review highlights specific breakthroughs in these areas but also concludes that the approach should be more widely adopted in the study of respiration per se as opposed to the more frequently studied respiration-related traits.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase

Strawberry (Fragaria × ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F₁ population derived from parental lines 'Candonga' and 'Senga Sengana', adapted to distinct Southern and Northern European areas. To account for environmental effects, the F₁ and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A), and the chloroplast-located AsA transporter gene FaPHT4;4(7C) might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A) inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A) was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

Genetic mapping of maize metabolites using high-throughput mass profiling

Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of plants with augmented nutritional value. To identify genetic factors related to the metabolic composition in maize, we generated mass profiles of 198 recombinant inbred lines (RILs) and their parents (B73 and Mo17) using direct-injection electrospray ionization mass spectrometry (DLI-ESI MS). Mass profiling allowed the correct clustering of samples according to genotype. We quantified 71 mass features from grains and 236 mass features from leaf extracts. For the corresponding ions, we identified tissue-specific metabolic 'Quantitative Trait Loci' (mQTLs) distributed across the maize genome. These genetic regions could regulate multiple metabolite biosynthesis pathways. Our findings demonstrate that DLI-ESI MS has sufficient analytical resolution to map mQTLs. These identified genetic loci will be helpful in metabolite-focused maize breeding. Mass profiling is a powerful tool for detecting mQTLs in maize and enables the high-throughput screening of loci responsible for metabolite biosynthesis.

Untargeted Proteomics and Metabolomics Analysis of Plant Organ Development

Our understanding of major developmental transitions in plants and animals has been transformed by the emergence of omics technologies. The majority of leaf growth research has been conducted at the transcriptional level. Although historically understudied, alterations at the protein and metabolite levels have begun to gain traction in recent years. Here, we present a protocol for metabolite and protein extraction followed by untargeted metabolomics and proteomics analysis of the growing leaves.

Selenium Application Enhances the Accumulation of Flavones and Anthocyanins in Bread Wheat (Triticum aestivum L.) Grains

Selenium (Se) biofortification in wheat reduces the risk of Se deficiency in humans. Se biofortification increases the concentration of Se and anthocyanins in wheat grains. However, it is unknown whether Se biofortification can enhance flavonoids other than anthocyanins and the mechanism underlying flavonoid accumulation in wheat grains. Here, foliar application of selenite solution in wheat was conducted 10 days after flowering. Metabolite profiling and transcriptome sequencing were performed in Se-treated grains. A significant increase in the total contents of Se, anthocyanins, and flavonoids was observed in Se-treated mature grains. Twenty-seven significantly increased flavonoids were identified in Se-treated immature grains. The significant accumulation of flavones (tricin, tricin derivatives, and chrysoeriol derivatives) was detected, and six anthocyanins, dihydroquercetin (the precursor for anthocyanin biosynthesis) and catechins were also increased. Integrated analysis of metabolites and transcriptome revealed that Se application enhanced the biosynthesis of flavones, dihydroquercetin, anthocyanins, and catechins by increasing the expression levels of seven key structural genes in flavonoid biosynthesis (two TaF3Hs, two TaDFRs, one TaF3'5'H, one TaOMT, and one TaANR). Our findings shed new light on the molecular mechanism underlying the enhancement in flavonoid accumulation by Se supplementation and pave the way for further enhancing the nutritional value of wheat grains.

Identification of a Hydroxygallic Acid Derivative, Zingibroside R1 and a Sterol Lipid as Potential Active Ingredients of Cuscuta chinensis Extract That Has Neuroprotective and Antioxidant Effects in Aged Caenorhabditis elegans

We examined the effects of the extracts from two traditional Chinese medicine plants, Cuscuta chinensis and Eucommia ulmoides, on the healthspan of the model organism Caenorhabditis elegans. C. chinensis increased the short-term memory and the mechanosensory response of aged C. elegans. Furthermore, both extracts improved the resistance towards oxidative stress, and decreased the intracellular level of reactive oxygen species. Chemical analyses of the extracts revealed the presence of several bioactive compounds such as chlorogenic acid, cinnamic acid, and quercetin. A fraction from the C. chinensis extract enriched in zingibroside R1 improved the lifespan, the survival after heat stress, and the locomotion in a manner similar to the full C. chinensis extract. Thus, zingibroside R1 could be (partly) responsible for the observed health benefits of C. chinensis. Furthermore, a hydroxygallic acid derivative and the sterol lipid 4-alpha-formyl-stigmasta-7,24(241)-dien-3-beta-ol are abundantly present in the C. chinensis extract and its most bioactive fraction, but hardly in E. ulmoides, making them good candidates to explain the overall healthspan benefits of C. chinensis compared to the specific positive effects on stress resistance by E. ulmoides. Our findings highlight the overall anti-aging effects of C. chinensis in C. elegans and provide first hints about the components responsible for these effects.

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

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

Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives

Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important root crops cultivated worldwide. Because of its adaptability, high yield potential, and nutritional value, sweetpotato has become an important food crop, particularly in developing countries. To ensure adequate crop yields to meet increasing demand, it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting factors. The highly heterozygous hexaploid genome of I. batatas complicates genetic studies and limits improvement of sweetpotato through traditional breeding. However, application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop improvement. In this review, we discuss the genomics resources that are available for sweetpotato, including the current reference genome, databases, and available bioinformatics tools. We systematically review the current state of knowledge on the polyploid genetics of sweetpotato, including studies of its origin and germplasm diversity and the associated mapping of important agricultural traits. We then outline the conventional and molecular breeding approaches that have been applied to sweetpotato. Finally, we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene editing. These approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.

A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator

Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.

Recent advances in proteomics and metabolomics in plants

Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.

Autophagy modulates the metabolism and growth of tomato fruit during development

Although autophagy is a conserved mechanism operating across eukaryotes, its effects on crops and especially their metabolism has received relatively little attention. Indeed, whilst a few recent studies have used systems biology tools to look at the consequences of lack of autophagy in maize these focused on leaf tissues rather than the kernels. Here we utilized RNA interference (RNAi) to generate tomato plants that were deficient in the autophagy-regulating protease ATG4. Plants displayed an early senescence phenotype yet relatively mild changes in the foliar metabolome and were characterized by a reduced fruit yield phenotype. Metabolite profiling indicated that metabolites of ATG4-RNAi tomato leaves just exhibited minor alterations while that of fruit displayed bigger difference compared to the WT. In detail, many primary metabolites exhibited decreases in the ATG4-RNAi lines, such as proline, tryptophan and phenylalanine, while the representative secondary metabolites (quinic acid and 3-trans-caffeoylquinic acid) were present at substantially higher levels in ATG4-RNAi green fruits than in WT. Moreover, transcriptome analysis indicated that the most prominent differences were in the significant upregulation of organelle degradation genes involved in the proteasome or chloroplast vesiculation pathways, which was further confirmed by the reduced levels of chloroplastic proteins in the proteomics data. Furthermore, integration analysis of the metabolome, transcriptome and proteome data indicated that ATG4 significantly affected the lipid metabolism, chlorophyll binding proteins and chloroplast biosynthesis. These data collectively lead us to propose a more sophisticated model to explain the cellular co-ordination of the process of autophagy.

Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement

Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.

Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red-fruited clade

The tomato (Solanum spp.) clade of Solanaceae features a unique assortment of cholesterol-derived steroidal alkaloids. However, little quantitative data exists reporting the profile and concentration of these alkaloids across diverse fruit germplasm. To address the lack of knowledge regarding the chemical diversity, concentration, and genetic architecture controlling tomato steroidal alkaloids, we quantitatively profiled and genotyped two tomato populations representing diversity in the red-fruited clade. We grew 107 genetically diverse fresh market, processing, landrace, and wild tomato in multiple environments. Nine steroidal alkaloid groups were quantified using ultra-high performance liquid chromatography tandem mass spectrometry. The diversity panel and a biparental population segregating for high alpha-tomatine were genotyped to identify and validate quantitative trait loci (QTL) associated with steroidal alkaloids. Landraces and wild material exhibited higher alkaloid concentrations and more chemical diversity. Average total content of steroidal alkaloids, often dominated by lycoperoside F/G/esculeoside A, ranged from 1.9 to 23.3 mg 100 g^-1 fresh wt. across accessions. Landrace and wild cherry accessions distinctly clustered based on elevated concentrations of early or late-pathway steroidal alkaloids. Significant correlations were observed among alkaloids from the early and late parts of the biosynthetic pathway in a species-dependent manner. A QTL controlling multiple, early steroidal alkaloid pathway intermediates on chromosome 3 was identified by genome-wide association studies (GWAS) and validated in a backcross population. Overall, tomato steroidal alkaloids are diverse in the red-fruited clade and their biosynthesis is regulated in a coordinated manner.

Natural variance at the interface of plant primary and specialized metabolism

Plants produce a large number of diverse metabolites when they grow and develop as well as when they respond to the changing external environment. These are an important source of human nutrition and medicine. In this review we emphasized the major issues of the primary-specialized metabolic interface in plant metabolism, described the metabolic flow from primary to specialized metabolism, and the conservation and diversity of primary and specialized metabolites. At the same time, we summarized the regulatory mechanisms underpinning the dynamic balance primary and specialized metabolism based on multi-omics integration analysis, as well as the natural variation of primary and specialized metabolic pathways and genes during the plant evolution. Moreover, the discovery and optimization of the synthesis and regulation elements of various primary to specialized metabolic flows provide the possibility for precise modification and personalized customization of metabolic pathways, which will greatly promote the development of synthetic biology.

Foxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.)

BACKGROUND

Although the genome for the allotetraploid bioenergy crop switchgrass (Panicum virgatum) has been established, limitations in mutant resources have hampered in planta gene function studies toward crop optimization. Virus-induced gene silencing (VIGS) is a versatile technique for transient genetic studies. Here we report the implementation of foxtail mosaic virus (FoMV)-mediated gene silencing in switchgrass in above- and below-ground tissues and at different developmental stages.

RESULTS

The study demonstrated that leaf rub-inoculation is a suitable method for systemic gene silencing in switchgrass. For all three visual marker genes, Magnesium chelatase subunit D (ChlD) and I (ChlI) as well as phytoene desaturase (PDS), phenotypic changes were observed in leaves, albeit at different intensities. Gene silencing efficiency was verified by RT-PCR for all tested genes. Notably, systemic gene silencing was also observed in roots, although silencing efficiency was stronger in leaves (~ 63-94%) as compared to roots (~ 48-78%). Plants at a later developmental stage were moderately less amenable to VIGS than younger plants, but also less perturbed by the viral infection.

CONCLUSIONS

Using FoMV-mediated VIGS could be achieved in switchgrass leaves and roots, providing an alternative approach for studying gene functions and physiological traits in this important bioenergy crop.

2-oxoglutarate-dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum

Solanum steroidal glycoalkaloids (SGAs) are renowned defence metabolites exhibiting spectacular structural diversity. Genes and enzymes generating the SGA precursor pathway, SGA scaffold and glycosylated forms have been largely identified. Yet, the majority of downstream metabolic steps creating the vast repertoire of SGAs remain untapped. Here, we discovered that members of the 2-OXOGLUTARATE-DEPENDENT DIOXYGENASE (2-ODD) family play a prominent role in SGA metabolism, carrying out three distinct backbone-modifying oxidative steps in addition to the three formerly reported pathway reactions. The GLYCOALKALOID METABOLISM34 (GAME34) enzyme catalyses the conversion of core SGAs to habrochaitosides in wild tomato S. habrochaites. Cultivated tomato plants overexpressing GAME34 ectopically accumulate habrochaitosides. These habrochaitoside enriched plants extracts potently inhibit Puccinia spp. spore germination, a significant Solanaceae crops fungal pathogen. Another 2-ODD enzyme, GAME33, acts as a desaturase (via hydroxylation and E/F ring rearrangement) forming unique, yet unreported SGAs. Conversion of bitter α-tomatine to ripe fruit, nonbitter SGAs (e.g. esculeoside A) requires two hydroxylations; while the known GAME31 2-ODD enzyme catalyses hydroxytomatine formation, we find that GAME40 catalyses the penultimate step in the pathway and generates acetoxy-hydroxytomatine towards esculeosides accumulation. Our results highlight the significant contribution of 2-ODD enzymes to the remarkable structural diversity found in plant steroidal specialized metabolism.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

The reliance of phytohormone biosynthesis on primary metabolite precursors

There is some debate as to whether phytohormone metabolites should be classified as primary or secondary metabolites. Phytohormones have profound effects on growth - a typical trait of primary metabolites - yet several of them are formed from secondary metabolite precursors. This is further exacerbated by the blurred distinction between primary and secondary metabolism. What is clearer, however, is that phytohormones display distinctive regulatory mechanisms from other metabolites. Moreover, by contrast to microbial and mammalian systems, the majority of plant metabolite receptors characterized to date are hormone receptors. Here, we provide an overview of the metabolic links between primary metabolism and phytohormone biosynthesis in an attempt to complement recent reviews covering the signaling crosstalk between elements of core metabolism and the phytohormones. In doing so, we cover the biosynthesis of both the classical metabolic phytohormones namely auxins, salicylic acid, jasmonate, ethylene, cytokinins, brassinosteroids, gibberellins and abscisic acid as well as recently described plant growth regulators which have been proposed as novel phytohormones namely strigolactones blumenols, zaxinone and β-cyclocitral as well as melatonin. For each hormone, we describe the primary metabolite precursors which fuel its synthesis, act as conjugates or in the case of 2-oxoglutarate act more directly as a co-substrate in the biosynthesis of gibberellin, auxin and salicylic acid. Furthermore, several amino acids operate as hormone conjugates, such as jasmonate-conjugates. In reviewing the biosynthesis of all the phytohormones simultaneously, the exceptional intricacy of the biochemical interplay that underpins their interaction emerges.

Combining novel technologies with interdisciplinary basic research to enhance horticultural crops

Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.

Gains and Losses of Agricultural Food Production: Implications for the Twenty-First Century

The world food supply depends on a diminishing list of plant crops and animal livestock to not only feed the ever-growing human population but also improve its nutritional state and lower the disease burden. Over the past century or so, technological advances in agricultural and food processing have helped reduce hunger and poverty but have not adequately addressed sustainability targets. This has led to an erosion of agricultural biodiversity and balanced diets and contributed to climate change and rising rates of chronic metabolic diseases. Modern food supply chains have progressively lost dietary fiber, complex carbohydrates, micronutrients, and several classes of phytochemicals with high bioactivity and nutritional relevance. This review introduces the concept of agricultural food systems losses and focuses on improved sources of agricultural diversity, proteins with enhanced resilience, and novel monitoring, processing, and distribution technologies that are poised to improve food security, reduce food loss and waste, and improve health profiles in the near future. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos

Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.

Mining plant metabolomes: Methods, applications, and perspectives

Plants produce a variety of metabolites that are essential for plant growth and human health. To fully understand the diversity of metabolites in certain plants, lots of methods have been developed for metabolites detection and data processing. In the data-processing procedure, how to effectively reduce false-positive peaks, analyze large-scale metabolic data, and annotate plant metabolites remains challenging. In this review, we introduce and discuss some prominent methods that could be exploited to solve these problems, including a five-step filtering method for reducing false-positive signals in LC-MS analysis, QPMASS for analyzing ultra-large GC-MS data, and MetDNA for annotating metabolites. The main applications of plant metabolomics in species discrimination, metabolic pathway dissection, population genetic studies, and some other aspects are also highlighted. To further promote the development of plant metabolomics, more effective and integrated methods/platforms for metabolite detection and comprehensive databases for metabolite identification are highly needed. With the improvement of these technologies and the development of genomics and transcriptomics, plant metabolomics will be widely used in many fields.

Metabolomics and health: from nutritional crops and plant-based pharmaceuticals to profiling of human biofluids

During the past decade metabolomics has emerged as one of the fastest developing branches of “-omics” technologies. Metabolomics involves documentation, identification, and quantification of metabolites through modern analytical platforms in various biological systems. Advanced analytical tools, such as gas chromatography–mass spectrometry (GC/MS), liquid chromatography–mass spectroscopy (LC/MS), and non-destructive nuclear magnetic resonance (NMR) spectroscopy, have facilitated metabolite profiling of complex biological matrices. Metabolomics, along with transcriptomics, has an influential role in discovering connections between genetic regulation, metabolite phenotyping and biomarkers identification. Comprehensive metabolite profiling allows integration of the summarized data towards manipulation of biosynthetic pathways, determination of nutritional quality markers, improvement in crop yield, selection of desired metabolites/genes, and their heritability in modern breeding. Along with that, metabolomics is invaluable in predicting the biological activity of medicinal plants, assisting the bioactivity-guided fractionation process and bioactive leads discovery, as well as serving as a tool for quality control and authentication of commercial plant-derived natural products. Metabolomic analysis of human biofluids is implemented in clinical practice to discriminate between physiological and pathological state in humans, to aid early disease biomarker discovery and predict individual response to drug therapy. Thus, metabolomics could be utilized to preserve human health by improving the nutritional quality of crops and accelerating plant-derived bioactive leads discovery through disease diagnostics, or through increasing the therapeutic efficacy of drugs via more personalized approach. Here, we attempt to explore the potential value of metabolite profiling comprising the above-mentioned applications of metabolomics in crop improvement, medicinal plants utilization, and, in the prognosis, diagnosis and management of complex diseases.

Tomato fruit quality traits and metabolite content are affected by reciprocal crosses and heterosis

Heterosis occurs when the F1s outperform their parental lines for a trait. Reciprocal hybrids are obtained by changing the cross direction of parental genotypes. Both biological phenomena could affect the external and internal attributes of fleshy fruits. This work aimed to detect reciprocal effects and heterosis in tomato (Solanum lycopersicum) fruit quality traits and metabolite content. Twelve agronomic traits and 28 metabolites identified and estimated by 1H-NMR were evaluated in five cultivars grown in two environments. Given that the genotype component was more important than the phenotype, the traits were evaluated following a full diallel mating design among those cultivars, in a greenhouse. Hybrids showed a higher phenotypic diversity than parental lines. Interestingly, the metabolites, mainly amino acids, displayed more reciprocal effects and heterosis. Agronomic traits were more influenced by general combining ability (GCA) and metabolites by specific combining ability (SCA). Furthermore, the genetic distance between parental lines was not causally related to the occurrence of reciprocal effects or heterosis. Hybrids with heterosis and a high content of metabolites linked to tomato flavour and nutritious components were obtained. Our results highlight the impact of selecting a cultivar as male or female in a cross to enhance the variability of fruit attributes through hybrids as well as the possibility to exploit heterosis for fruit composition.

Genome-wide association studies: assessing trait characteristics in model and crop plants

GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.

Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants

DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms, three types of methylation—methylated CGs (mCGs), mCHGs, and mCHHs—contributed highly to variable gene expression levels among an A. thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.

The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation

The plant shikimate pathway directs bulk carbon flow toward biosynthesis of aromatic amino acids (AAAs, i.e. tyrosine, phenylalanine, and tryptophan) and numerous aromatic phytochemicals. The microbial shikimate pathway is feedback inhibited by AAAs at the first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DHS). However, AAAs generally do not inhibit DHS activities from plant extracts and how plants regulate the shikimate pathway remains elusive. Here, we characterized recombinant Arabidopsis thaliana DHSs (AthDHSs) and found that tyrosine and tryptophan inhibit AthDHS2, but not AthDHS1 or AthDHS3. Mixing AthDHS2 with AthDHS1 or 3 attenuated its inhibition. The AAA and phenylpropanoid pathway intermediates chorismate and caffeate, respectively, strongly inhibited all AthDHSs, while the arogenate intermediate counteracted the AthDHS1 or 3 inhibition by chorismate. AAAs inhibited DHS activity in young seedlings, where AthDHS2 is highly expressed, but not in mature leaves, where AthDHS1 is predominantly expressed. Arabidopsis dhs1 and dhs3 knockout mutants were hypersensitive to tyrosine and tryptophan, respectively, while dhs2 was resistant to tyrosine-mediated growth inhibition. dhs1 and dhs3 also had reduced anthocyanin accumulation under high light stress. These findings reveal the highly complex regulation of the entry reaction of the plant shikimate pathway and lay the foundation for efforts to control the production of AAAs and diverse aromatic natural products in plants.

Multi-omics analysis of early leaf development in Arabidopsis thaliana

The growth of plant organs is driven by cell division and subsequent cell expansion. The transition from proliferation to expansion is critical for the final organ size and plant yield. Exit from proliferation and onset of expansion is accompanied by major metabolic reprogramming, and in leaves with the establishment of photosynthesis. To learn more about the molecular mechanisms underlying the developmental and metabolic transitions important for plant growth, we used untargeted proteomics and metabolomics analyses to profile young leaves of a model plant Arabidopsis thaliana representing proliferation, transition, and expansion stages. The dataset presented represents a unique resource comprising approximately 4,000 proteins and 300 annotated small-molecular compounds measured across 6 consecutive days of leaf growth. These can now be mined for novel developmental and metabolic regulators of plant growth and can act as a blueprint for studies aimed at better defining the interface of development and metabolism in other species.

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Untargeted metabolomics and proteomics characterization of early leaf growth

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Translation is the primary determiner of protein abundance during early leaf growth

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12-OPDA accumulation coincides with meristem arrest

Developmental and metabolic transitions occurring during plant growth are critical for crop yield. The multi-omics dataset presented here was generated to enable the identification of novel molecular players involved in the regulation of plant growth. It comprised approximately 4,000 proteins and 300 annotated small-molecular compounds, measured across early leaf development spanning major developmental transitions. As such, the work provides a blueprint for studies aimed at better defining the interface between metabolism and development, an appreciated yet understudied research frontier across all kingdoms of life.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field

Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).