Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

Spatio-temporal dynamics of the metabolome of climacteric fruit during ripening and post-harvest storage

Fruit quality traits are determined to a large extent by their metabolome. The metabolite content of climacteric fruit changes drastically during ripening and post-harvest storage, and has been investigated extensively. However, the spatial distribution of metabolites and how it changes in time has received much less attention as fruit are usually considered as homogenous plant organs. Yet, spatio-temporal changes of starch, which is hydrolyzed during ripening, has been used for a long time as a ripening index. As vascular transport of water, and hence convective transport of metabolites, slows down in mature fruit and even stalls after detachment, spatio-temporal changes in their concentration are probably affected by diffusive transport of gaseous molecules that act as substrate (O2), inhibitor (CO2), or regulator (ethylene and NO) of the metabolic pathways that are active during climacteric ripening. In this review, we discuss such spatio-temporal changes of the metabolome and how they are affected by transport of metabolic gases and gaseous hormones. As there are currently no techniques available to measure the metabolite distribution repeatedly by non-destructive means, we introduce reaction-diffusion models as an in silico tool to compute it. We show how the different components of such a model can be integrated and used to better understand the role of spatio-temporal changes of the metabolome in ripening and post-harvest storage of climacteric fruit that is detached from the plant, and discuss future research needs.

Low-temperature adaptation and preservation revealed by changes in physiological-biochemical characteristics and proteome expression patterns in post-harvest Hami melon during cold storage

The proteome and its time-dependent effects reveal the importance of stress response (including expression regulation of heat-shock proteins) and fatty acid metabolism in cold adaptation and preservation of Hami melon. To better understand the molecular mechanism of how Hami melons respond to low-temperature stress, this study investigated the relevant physiological characteristics, catalytic antibody activity, and quantitative proteomics of Hami melon (Jiashi muskmelon) during low-temperature storage. Jiashi muskmelon was stored inside two refrigerators set at 21 °C (control group) and 3 °C, respectively, for 24 days. Low-temperature storage led to a significantly reduced decay rate, weight loss rate, and loss of relative conductivity. It also maintained fruit firmness, inhibited the production rate of malondialdehyde and H₂O₂, and induced over-expression of antioxidant enzyme and ATPase. A total of 1064 differentially expressed proteins (DEPs) were identified during low-temperature storage. Stimulation response was the main process in response to low-temperature. To further verify the proteome data, we selected four heat-shock proteins (HSP) displaying relatively high expression levels. Real-time fluorescence PCR results confirmed that HmHSP90 I, HmHSP90 II, HmHSP70, and HmsHSP were significantly up-regulated upon low-temperature induction. These proteins may protect the Hami melon from physiological and cellular damage due to the low-temperature stress by acting alone or synergistically. Additionally, the main enrichment term of the fatty acid metabolism-related DEPs was fatty acid beta oxidation at 21 °C in contrast to fatty acid biosynthesis processes at 3 °C. It is speculated that Hami melon enhances low-temperature adaptability by slowing down the oxidative degradation of fatty acids and synthesizing new fatty acids at low temperatures. This study provides new insights into the mechanism of low-temperature adaptation and preservation in post-harvest Hami melon during cold storage.

Evaluation of ORAC, IR and NMR metabolomics for predicting ripening stage and variety in melon (Cucumis melo L.)

A combination of FTIR- and NMR-based metabolomics approaches coupled to multivariate data analysis techniques was used for the first time to characterize and explore the metabolic changes along the ripening of two Spanish melon landraces (Jimbee N and Jimbee XL). Furthermore, the fatty acids profile and the antioxidant capacity were investigated by GC-FID and ORAC method, respectively. Despite FTIR was able to identify changes in the sugars content between fruits of different maturity stages, it failed to discriminate between both varieties, being exceeded by NMR in both situations. Increased fruit maturation led to an increase of sucrose, fatty acids and β-carotene, accompanied by a decrease of glucose, fructose, citrate, amino acids, and polyphenols (which were positively correlated with fruits antioxidant activity).

Metabolite profile of African horned cucumber (Cucumis metuliferus E. May. Ex Naudin) fruit grown under differing environmental conditions

Plant metabolites are known as biological compounds that are essential to the growth and development of a plant and have a direct impact on yield and biochemical constituents of plants. For this study, the objective was to conduct primary metabolomics analysis using liquid chromatography mass spectrometry. African horned cucumber fruits were harvested from plants grown under pots experiment (greenhouse, shade net and open field), soil types (loamy soil and sandy loam) and three water stress levels (no water stress-100%-3L, moderate water stress-75%-2L, and severe water stress-35%-1L) during 2017/18 and 2018/19 seasons. Results showed that the treatment of no water stress combined with sandy loam under shade net environment, significantly increased asparagine content from 10 × 10⁶ to 80 × 10⁶ peak intensity. The treatment of no water stress, in combination with sandy loam soil under open field environment increased 4-hydroxyproline from 10 × 10⁶ to 90 × 10⁶ peak intensity compared to other treatments. It can be deduced that the treatment combination of (no water stress and moderate water stress) and all soil types, under greenhouse environment increased most metabolites content of the fruit when compared to other treatments. Therefore, it subsequently has potential to affect fruit quality such as taste and other biochemical constituents.

Coffee berry and green bean chemistry - Opportunities for improving cup quality and crop circularity

Coffee cup quality is primarily determined by the type and variety of green beans chosen and the roasting regime used. Furthermore, green coffee beans are not only the starting point for the production of all coffee beverages but also are a major source of revenue for many sub-tropical countries. Green bean quality is directly related to its biochemical composition which is influenced by genetic and environmental factors. Post-harvest, on-farm processing methods are now particularly recognised as being influential to bean chemistry and final cup quality. However, research on green coffee has been limited and results are fragmented. Despite this, there are already indications that multiple factors play a role in determining green coffee chemistry - including plant cultivation/fruit ripening issues and ending with farmer practices and post-harvest storage conditions. Here, we provide the first overview of the knowledge determined so far specifically for pre-factory, green coffee composition. In addition, the potential of coffee waste biomass in a biobased economy context for the delivery of useful bioactives is described as this is becoming a topic of growing relevance within the coffee industry. We draw attention to a general lack of consistency in experimentation and reporting and call for a more intensive and united effort to build up our knowledge both of green bean composition and also how perturbations in genetic and environmental factors impact bean chemistry, crop sustainability and ultimately, cup quality.

Strawberry sweetness and consumer preference are enhanced by specific volatile compounds

Breeding crops for improved flavor is challenging due to the high cost of sensory evaluation and the difficulty of connecting sensory experience to chemical composition. The main goal of this study was to identify the chemical drivers of sweetness and consumer liking for fresh strawberries (Fragaria × ananassa). Fruit of 148 strawberry samples from cultivars and breeding selections were grown and harvested over seven years and were subjected to both sensory and chemical analyses. Each panel consisted of at least 100 consumers, resulting in more than 15,000 sensory data points per descriptor. Three sugars, two acids and 113 volatile compounds were quantified. Consumer liking was highly associated with sweetness intensity, texture liking, and flavor intensity, but not sourness intensity. Partial least square analyses revealed 20 volatile compounds that increased sweetness perception independently of sugars; 18 volatiles that increased liking independently of sugars; and 15 volatile compounds that had positive effects on both. Machine learning-based predictive models including sugars, acids, and volatiles explained at least 25% more variation in sweetness and liking than models accounting for sugars and acids only. Volatile compounds such as γ-dodecalactone; 5-hepten-2-one, 6-methyl; and multiple medium-chain fatty acid esters may serve as targets for breeding or quality control attributes for strawberry products. A genetic association study identified two loci controlling ester production, both on linkage group 6 A. Co-segregating makers in these regions can be used for increasing multiple esters simultaneously. This study demonstrates a paradigm for improvement of fruit sweetness and flavor in which consumers drive the identification of the most important chemical targets, which in turn drives the discovery of genetic targets for marker-assisted breeding.

Comparative Metabolic Profiling in Pulp and Peel of Green and Red Pitayas (Hylocereus polyrhizus and Hylocereus undatus) Reveals Potential Valorization in the Pharmaceutical and Food Industries

Pitaya (Hylocereus genus) is a popular plant with exotic and nutritious fruit, which has widespread uses as a source of nutrients and raw materials in the pharmaceutical industry. However, the potential of pitaya peel as a natural source of bioactive compounds has not yet fully been explored. Recent advances in metabolomics have paved the way for understanding and evaluating the presence of diverse sets of metabolites in different plant parts. This study is aimed at exploring the diversity of primary and secondary metabolites in two commercial varieties of pitaya, i.e., green pitaya (Hylocereus undatus) and red pitaya (Hylocereus polyrhizus). A total of 433 metabolites were identified using a widely targeted metabolomic approach and classified into nine known diverse classes of metabolites, including flavonoids, amino acids and its derivatives, alkaloids, tannins, phenolic acids, organic acids, nucleotides and derivatives, lipids, and lignans. Red pitaya peel and pulp showed relatively high accumulation of metabolites viz. alkaloids, amino acids and its derivatives, and lipids. Differential metabolite landscape of pitaya fruit indicated the presence of key bioactive compounds, i.e., L-tyrosine, L-valine, DL-norvaline, tryptophan, γ-linolenic acid, and isorhamnetin 3-O-neohesperidoside. The findings in this study provide new insight into the broad spectrum of bioactive compounds of red and green pitaya, emphasizing the valorization of the biowaste pitaya peel as raw material for the pharmaceutical and food industries.

Metabolome and Transcriptome Integration Reveals Insights Into Flavor Formation of 'Crimson' Watermelon Flesh During Fruit Development

Metabolites have been reported as the main factor that influences the fruit flavor of watermelon. But the comprehensive study on the dynamics of metabolites during the development of watermelon fruit is not up-to-date. In this study, metabolome and transcriptome datasets of 'Crimson' watermelon fruit at four key developmental stages were generated. A total of 517 metabolites were detected by ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry and gas chromatography-solid-phase microextraction-mass spectrometry. Meanwhile, by K-means clustering analysis, the total differentially expressed genes were clustered in six classes. Integrating transcriptome and metabolome data revealed similar expression trends of sugars and genes involved in the glycolytic pathway, providing molecular insights into the formation of taste during fruit development. Furthermore, through coexpression analysis, we identified five differentially expressed ADH (alcohol dehydrogenase) genes (Cla97C01G013600, Cla97C05G089700, Cla97C01G001290, Cla97C05G095170, and Cla97C06G118330), which were found to be closely related to C9 alcohols/aldehydes, providing information for the formation of fruit aroma. Our findings establish a metabolic profile during watermelon fruit development and provide insights into flavor formation.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Simple Summary

This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health.

Abstract

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

Biomarkers of intake for tropical fruits

Consumption of fruit and vegetable is a key component of a healthy and sustainable diet. However, their accurate dietary assessment remains a challenge. Due to errors in self-reporting methods, the available dietary information is usually biased. Biomarkers of intake constitute objective tools to better reflect the usual or recent consumption of different foods, including fruits and vegetables. Partners of The Food Biomarker Alliance (FoodBall) Project have undertaken the task of reviewing the available literature on putative biomarkers of tropical fruit intake. The identified candidate biomarkers were subject to validation evaluation using eight biological and chemical criteria. This publication presents the current knowledge on intake biomarkers for 17 tropical fruits including banana, mango, and avocado as the most widely consumed ones. Candidate biomarkers were found only for banana, avocado, and watermelon. An array of banana-derived metabolites has been reported in human biofluids, among which 5-hydroxyindole-acetic acid, dopamine sulfate, methoxyeugenol glucuronide, salsolinol sulfate, 6-hydroxy-1-methyl-1,2,3,4-tetrahydro-β-carboline-sulfate, and other catecholamine metabolites. Their validation is still at an early stage, with insufficient data on dose-response relationship. Perseitol and mannoheptulose have recently been reported as candidate biomarkers for avocado intake, while the amino acid citrulline has been associated with watermelon intake. Additionally, the examination of food composition data revealed some highly specific phytochemicals, which metabolites after absorption may be further studied as putative BFI for one or several tropical fruits. To make the field move forward, untargeted metabolomics, as a data-driven explorative approach, will have to be applied in both intervention and observational studies to discover putative BFIs, while their full validation and the establishment of dose-response calibration curves will require quantification methods at a later stage.

UV-B Radiation Largely Promoted the Transformation of Primary Metabolites to Phenols in Astragalus mongholicus Seedlings

: Ultraviolet-B (UV-B) radiation (280-320 nm) may induce photobiological stress in plants, activate the plant defense system, and induce changes of metabolites. In our previous work, we found that between the two Astragalus varieties prescribed by the Chinese Pharmacopoeia, Astragalus mongholicus has better tolerance to UV-B. Thus, it is necessary to study the metabolic strategy of Astragalus under UV-B radiation further. In the present study, we used untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-mass spectrometry (LC-MS techniques) to investigate the profiles of primary and secondary metabolic. The profiles revealed the metabolic response of Astragalus to UV-B radiation. We then used real-time polymerase chain reaction (RT-PCR) to obtain the transcription level of relevant genes under UV-B radiation (UV-B supplemented in the field, λmax = 313 nm, 30 W, lamp-leaf distance = 60 cm, 40 min·day-1), which annotated the responsive mechanism of phenolic metabolism in roots. Our results indicated that supplemental UV-B radiation induced a stronger shift from carbon assimilation to carbon accumulation. The flux through the phenylpropanoids pathway increased due to the mobilization of carbon reserves. The response of metabolism was observed to be significantly tissue-specific upon the UV-B radiation treatment. Among phenolic compounds, C6C1 carbon compounds (phenolic acids in leaves) and C6C3C6 carbon compounds (flavones in leaves and isoflavones in roots) increased at the expense of C6C3 carbon compounds. Verification experiments show that the response of phenolics in roots to UV-B is activated by upregulation of relevant genes rather than phenylalanine. Overall, this study reveals the tissues-specific alteration and mechanism of primary and secondary metabolic strategy in response to UV-B radiation.

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Metabolic profiling and scavenging activities of developing circumscissile fruit of psyllium (Plantago ovata Forssk.) reveal variation in primary and secondary metabolites

BACKGROUND

Developing fruit is considered as an excellent model to study the complex network of metabolites which are altered rapidly during development.

RESULTS

Metabolomics revealed that developing psyllium fruit is a rich source of primary metabolites (ω-3 and ω-6 fatty acids and amino-acids), secondary metabolites and natural antioxidants. Eidonomy and anatomy confirmed that psyllium fruit followed five stages of development. Total lipids and fatty acids were synthesized differentially; saturated fatty acids (FAs) increased, whereas total polyunsaturated FAs decreased with increasing developmental stage. The unsaturation index and degree of unsaturation showed a catenary curve. Principal component analysis confirmed a significant shift in the FA profile from bud initiation to the maturation stage. Similarly, a similar level of total amino acids was present at different developmental stage following a temporal biosynthesis pathway. Total phenolic and flavonoid contents decreased in tandem with fruit development. Twenty-two different metabolites were identified, and metabolic changes were also observed during fruit development. Six metabolites were detected exclusively in the flowering stage, whereas two were detected in each of early and maturity stages of development. The metabolites apigenin and kaempferol were detected ubiquitously in all developmental stages. Time-dependent metabolomics revealed a shift in metabolite biosynthesis.

CONCLUSION

During fruit development, metabolites, FAs, amino acids, total phenolics, total flavonoids, antioxidants and scavenging activities changed progressively and were co-ordinately linked to each other. As a future perspective, further studies will focus on the validation of identified metabolites, which integrated with transcriptomics data and will reveal the metabolic regulatory network of development psyllium fruit.

Central Metabolism Is Tuned to the Availability of Oxygen in Developing Melon Fruit

Respiration of bulky plant organs such as fleshy fruits depends on oxygen (O₂) availability and often decreases with O₂ concentration to avoid anoxia, but the relationship between O₂ diffusional resistance and metabolic adjustments remains unclear. Melon fruit (Cucumis melo L.) was used to study relationships between O₂ availability and metabolism in fleshy fruits. Enzyme activities, primary metabolites and O₂ partial pressure were quantified from the periphery to the inner fruit mesocarp, at three stages of development. Hypoxia was gradually established during fruit development, but there was no strong oxygen gradient between the outer- and the inner mesocarp. These trends were confirmed by a mathematical modeling approach combining O₂ diffusion equations and O₂ demand estimates of the mesocarp tissue. A multivariate analysis of metabolites, enzyme activities, O₂ demand and concentration reveals that metabolite gradients and enzyme capacities observed in melon fruits reflect continuous metabolic adjustments thus ensuring a timely maturation of the mesocarp. The present results suggest that the metabolic adjustments, especially the tuning of the capacity of cytochrome c oxidase (COX) to O₂-availability that occurs during growth development, contribute to optimizing the O₂-demand and avoiding the establishment of an O₂ gradient within the flesh.

A metabolomics-based approach for the evaluation of off-tree ripening conditions and different postharvest treatments in mangosteen (Garcinia mangostana)

INTRODUCTION

Metabolomics is an important tool to support postharvest fruit development and ripening studies. Mangosteen (Garcinia mangostana L.) is a tropical fruit with high market value but has short shelf-life during postharvest handling. Several postharvest technologies have been applied to maintain mangosteen fruit quality during storage. However, there is no study to evaluate the metabolite changes that occur in different harvesting and ripening condition. Additionally, the effect of postharvest treatment using a metabolomics approach has never been studied in mangosteen.

OBJECTIVES

The aims of this study were to evaluate the metabolic changes between different harvesting and ripening condition and to evaluate the effect of postharvest treatment in mangosteen.

METHODS

Mangosteen ripening stage were collected with several different conditions ("natural on-tree", "random on-tree" and "off-tree"). The metabolite changes were investigated for each ripening condition. Additionally, mangosteen fruit was harvested in stage 2 and was treated with several different treatments (storage at low temperature (LT; 12.3 ± 1.4 °C) and stress inducer treatment (methyl jasmonate and salicylic acid) in comparison with control treatment (normal temperature storage) and the metabolite changes were monitored over the course of 10 days after treatment. The metabolome data obtained from gas chromatography coupled with mass spectrometry were analyzed by multivariate analysis, including hierarchical clustering analysis, principal component analysis, and partial to latent squares analysis.

RESULTS

"On-tree" ripening condition showed the progression of ripening process in accordance with the accumulation of some aroma precursor metabolites in the flesh part and pectin breakdown in the peel part. Interestingly, similar trend was found in the "off-tree" ripening condition although the progression of ripening process observed through color changes occurred much faster compared to "on-tree" ripening. Additionally, low-temperature treatment is shown as the most effective treatment to prolong mangosteen shelf-life among all postharvest treatments tested in this study compared to control treatment. After postharvest treatment, a total of 71 and 65 metabolites were annotated in peel and flesh part of mangosteen, respectively. Several contributed metabolites (xylose, galactose, galacturonic acid, glucuronate, glycine, and rhamnose) were decreased after treatment in the peel part. However, low-temperature treatment did not show any significant differences compared to a room temperature treatment in the flesh part.

CONCLUSIONS

Our findings clearly indicate that there is a similar trend of metabolic changes between on-tree and off-tree ripening conditions. Additionally, postharvest treatment directly or indirectly influences many metabolic processes (cell-wall degrading process, sweet-acidic taste quality) during postharvest treatment.

Food intake biomarkers for apple, pear, and stone fruit

Fruit is a key component of a healthy diet. However, it is still not clear whether some classes of fruit may be more beneficial than others and whether all individuals whatever their age, gender, health status, genotype, or gut microbiota composition respond in the same way to fruit consumption. Such questions require further observational and intervention studies in which the intake of a specific fruit can be precisely assessed at the population and individual levels. Within the Food Biomarker Alliance Project (FoodBAll Project) under the Joint Programming Initiative “A Healthy Diet for a Healthy Life”, an ambitious action was undertaken aiming at reviewing existent literature in a systematic way to identify validated and promising biomarkers of intake for all major food groups, including fruits. This paper belongs to a series of reviews following the same BFIRev protocol and is focusing on biomarkers of pome and stone fruit intake. Selected candidate biomarkers extracted from the literature search went through a validation process specifically developed for food intake biomarkers.

Answering biological questions by analysis of the strawberry metabolome

BACKGROUND

The qualitative and quantitative analysis of all low molecular weight metabolites within a biological sample, known as the metabolome, provides powerful insights into their roles in biological systems and processes. The study of all the chemical structures, concentrations, and interactions of the thousands of metabolites is called metabolomics. However present state of the art methods and equipment can only analyse a small portion of the numerous, structurally diverse groups of chemical substances found in biological samples, especially with respect to samples of plant origin with their huge diversity of secondary metabolites. Nevertheless, metabolite profiling and fingerprinting techniques have been applied to the analysis of the strawberry metabolome since their early beginnings.

AIM

The application of metabolomics and metabolite profiling approaches within strawberry research was last reviewed in 2011. Here, we aim to summarize the latest results from research of the strawberry metabolome since its last review with a special emphasis on studies that address specific biological questions.

KEY SCIENTIFIC CONCEPTS

Analysis of strawberry, and other fruits, requires a plethora of analytical methods and approaches encompassing the analysis of primary and secondary metabolites, as well as capturing and quantifying volatile compounds that are related to aroma as well as fruit development, function and plant-to-plant communication. The success and longevity of metabolite and volatile profiling approaches in fruit breeding relies upon the ability of the approach to uncover biologically meaningful insights. The key concepts that must be addressed and are reviewed include: gene function analysis and genotype comparison, analysis of environmental effects and plant protection, screening for bioactive compounds for food and non-food uses, fruit development and physiology as well as fruit sensorial quality. In future, the results will facilitate fruit breeding due to the identification of metabolic QTLs and candidate genes for fruit quality and consumer preference.

Genetic diversity of strawberry germplasm using metabolomic biomarkers

High-throughput metabolomics technologies can provide the quantification of metabolites levels across various biological processes in different tissues, organs and species, allowing the identification of genes underpinning these complex traits. Information about changes of metabolites during strawberry development and ripening processes is key to aiding the development of new approaches to improve fruit attributes. We used network-based methods and multivariate statistical approaches to characterize and investigate variation in the primary and secondary metabolism of seven domesticated and seven wild strawberry fruit accessions at three different fruit development and ripening stages. Our results demonstrated that Fragaria sub-species can be identified solely based on the gathered metabolic profiles. We also showed that domesticated accessions displayed highly similar metabolic changes due to shared domestication history. Differences between domesticated and wild accessions were detected at the level of metabolite associations which served to rank metabolites whose regulation was mostly altered in the process of domestication. The discovery of comprehensive metabolic variation among strawberry accessions offers opportunities to probe into the genetic basis of variation, providing insights into the pathways to relate metabolic variation with important traits.

Putting primary metabolism into perspective to obtain better fruits

Background

One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits.

Scope

Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening.

Conclusions

Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.

Differential metabolism of L-phenylalanine in the formation of aromatic volatiles in melon (Cucumis melo L.) fruit

Studies on the active pathways and the genes involved in the biosynthesis of L-phenylalanine-derived volatiles in fleshy fruits are sparse. Melon fruit rinds converted stable-isotope labeled L-phe into more than 20 volatiles. Phenylpropanes, phenylpropenes and benzenoids are apparently produced via the well-known phenylpropanoid pathway involving phenylalanine ammonia lyase (PAL) and being (E)-cinnamic acid a key intermediate. Phenethyl derivatives seemed to be derived from L-phe via a separate biosynthetic route not involving (E)-cinnamic acid and PAL. To explore for a biosynthetic route to (E)-cinnamaldehyde in melon rinds, soluble protein cell-free extracts were assayed with (E)-cinnamic acid, CoA, ATP, NADPH and MgSO₄, producing (E)-cinnamaldehyde in vitro. In this context, we characterized CmCNL, a gene encoding for (E)-cinnamic acid:coenzyme A ligase, inferred to be involved in the biosynthesis of (E)-cinnamaldehyde. Additionally we describe CmBAMT, a SABATH gene family member encoding a benzoic acid:S-adenosyl-L-methionine carboxyl methyltransferase having a role in the accumulation of methyl benzoate. Our approach leads to a more comprehensive understanding of L-phe metabolism into aromatic volatiles in melon fruit.

Characterization of a Potential Ripening Regulator, SlNAC3, from Solanum Lycopersicum

NAC (for NAM, ATAF1-2, and CUC2) proteins are one of the largest transcription factor families in plants. They have various functions and are closely related to developmental processes of fruits. Tomato (Solanum lycopersicum) is a model plant for studies of fruit growth patterns. In this study, the functional characteristics and action mechanisms of a new NAC-type transcription factor, SlNAC3 (SGN-U568609), were examined to determine its role in tomato development and ripening. The SlNAC3 protein was produced by prokaryotic expression and used to immunize New Zealand white rabbits to obtain a specific polyclonal antibody against SlNAC3. By co-immunoprecipitation and MALDI-TOF-MS assays, we showed that there was an interaction between the SlNAC3 protein and Polygalacturonase-2 (PG-2), which is related to the ripening and softening of fruit. Chromatin immunoprecipitation assays revealed the genome of the highly stress-tolerant Solanum pennellii chromosome 10 (sequence ID, HG975449.1), further demonstrating that SlNAC3 is a negative regulator of drought and salinity stress resistance in tomato, consistent with previous reports. These results indicate that SlNAC3 is not only involved in abiotic stress, but also plays a necessary role in mediating tomato ripening.

Plant metabolism as studied by NMR spectroscopy

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.

The peach HECATE3-like gene FLESHY plays a double role during fruit development

Tight control of cell/tissue identity is essential for a correct and functional organ patterning, an important component of overall fruit development and eventual maturation and ripening. Despite many investigations regarding the molecular determinants of cell identity in fruits of different species, a useful model able to depict the regulatory networks governing this relevant part of fruit development is still missing. Here we described the peach fruit as a system to link the phenotype of a slow ripening (SR) selection to an altered transcriptional regulation of genes involved in determination of mesocarp cell identity providing insight toward molecular regulation of fruit tissue formation. Morpho-anatomical observations and metabolomics analyses performed during fruit development on the reference cultivar Fantasia, compared to SR, revealed that the mesocarp of SR maintained typical immaturity traits (e.g. small cell size, high amino acid contents and reduced sucrose) throughout development, along with a strong alteration of phenylpropanoid contents, resulting in accumulation of phenylalanine and lignin. These findings suggest that the SR mesocarp is phenotypically similar to a lignifying endocarp. To test this hypothesis, the expression of genes putatively involved in determination of drupe tissues identity was assessed. Among these, the peach HEC3-like gene FLESHY showed a strongly altered expression profile consistent with pit hardening and fruit ripening, generated at a post-transcriptional level. A double function for FLESHY in channelling the phenylpropanoid pathway to either lignin or flavour/aroma is suggested, along with its possible role in triggering auxin-ethylene cross talk at the start of ripening.

Suppression of tomato SlNAC1 transcription factor delays fruit ripening

Fruit ripening is a complex process involving many physiological and biochemical changes, including those for ethylene, carotenoid, and cell wall metabolism. Tomato (Solanum lycopersicum) serves as a research model for fruit development and ripening because it possesses numerous favorable genetic features. In this study, SlNAC1 was cloned. An antisense (AS) vector was constructed and transferred to tomato to further explore the function of SlNAC1. The results showed that AS fruits exhibited delayed ripening and a deeper red appearance when these fruits were fully ripened. Fully ripened AS fruits also produced higher total carotenoid and lycopene contents than those of the wild-type (WT) line. Ethylene production of AS fruits was delayed but occurred to a higher extent than that of WT fruits. The softening of AS fruits was slower than that of WT fruits. Endogenous abscisic acid (ABA) level in AS-4 fruits was lower than that in WT fruits. Exogenous ABA accelerated the softening of AS fruits. Furthermore, AS fruits demonstrated up-regulated expression of genes related to lycopene and ethylene biosynthesis but down-regulated expression of genes related to cell wall metabolism and ABA synthesis. Therefore, SlNAC1 is likely implicated in fruit ripening.

Metabolomics-Based Analysis of Banana and Pear Ingestion on Exercise Performance and Recovery

Bananas and pears vary in sugar and phenolic profiles, and metabolomics was utilized to measure their influence on exercise performance and recovery. Male athletes (N = 20) cycled for 75 km while consuming water (WATER), bananas (BAN), or pears (PEAR) (0.6 g carbohydrate/kg each hour) in randomized order. UPLC-MS/MS and the library of purified standards maintained by Metabolon (Durham, NC) were used to analyze metabolite shifts in pre- and postexercise (0-h, 1.5-h, 21-h) blood samples. Performance times were 5.0% and 3.3% faster during BAN and PEAR versus WATER (P = 0.018 and P = 0.091, respectively), with reductions in cortisol, IL-10, and total leukocytes, and increases in blood glucose, insulin, and FRAP. Partial Least Square Discriminant Analysis (PLS-DA) showed a distinct separation between trials immediately (R(2)Y = 0.877, Q(2)Y = 0.457) and 1.5-h postexercise (R(2)Y = 0.773, Q(2)Y = 0.441). A total of 107 metabolites (primarily lipid-related) increased more than 2-fold during WATER, with a 48% and 52% reduction in magnitude during BAN and PEAR recovery (P < 0.001). Increases in metabolites unique to BAN and PEAR included fructose and fruit constituents, and sulfated phenolics that were related to elevated FRAP. These data indicate that BAN and PEAR ingestion improves 75-km cycling performance, attenuates fatty acid utilization and oxidation, and contributes unique phenolics that augment antioxidant capacity.

Metabolic profiling reveals ethylene mediated metabolic changes and a coordinated adaptive mechanism of 'Jonagold' apple to low oxygen stress

Apples are predominantly stored in controlled atmosphere (CA) storage to delay ripening and prolong their storage life. Profiling the dynamics of metabolic changes during ripening and CA storage is vital for understanding the governing molecular mechanism. In this study, the dynamics of the primary metabolism of 'Jonagold' apples during ripening in regular air (RA) storage and initiation of CA storage was profiled. 1-Methylcyclopropene (1-MCP) was exploited to block ethylene receptors and to get insight into ethylene mediated metabolic changes during ripening of the fruit and in response to hypoxic stress. Metabolic changes were quantified in glycolysis, the tricarboxylic acid (TCA) cycle, the Yang cycle and synthesis of the main amino acids branching from these metabolic pathways. Partial least square discriminant analysis of the metabolic profiles of 1-MCP treated and control apples revealed a metabolic divergence in ethylene, organic acid, sugar and amino acid metabolism. During RA storage at 18°C, most amino acids were higher in 1-MCP treated apples, whereas 1-aminocyclopropane-1-carboxylic acid (ACC) was higher in the control apples. The initial response of the fruit to CA initiation was accompanied by an increase of alanine, succinate and glutamate, but a decline in aspartate. Furthermore, alanine and succinate accumulated to higher levels in control apples than 1-MCP treated apples. The observed metabolic changes in these interlinked metabolites may indicate a coordinated adaptive strategy to maximize energy production.

Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions

The control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. Physiological differences between the basal and mature region of wheat (Triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. Fourier Transform Infrared (FT-IR) spectroscopy confirmed the suitability and phenotypic reproducibility of the leaf growth conditions. Principal Component-Discriminant Function Analysis (PC-DFA) revealed distinct clustering between base, and tip sections of the developing wheat leaf, and from plants grown in the presence or absence of nitrate. Gas Chromatography-Time of Flight/Mass Spectrometry (GC-TOF/MS) combined with multivariate and univariate analyses, and Bayesian network (BN) analysis, distinguished different tissues and confirmed the physiological switch from high rates of respiration to photosynthesis along the leaf. The operation of nitrogen metabolism impacted on the levels and distribution of amino acids, organic acids and carbohydrates within the wheat leaf. In plants grown in the presence of nitrate there was reduced levels of a number of sugar metabolites in the leaf base and an increase in maltose levels, possibly reflecting an increase in starch turnover. The value of using this combined metabolomics analysis for further functional investigations in the future are discussed.

Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network

Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.

Profiling of volatile compounds and associated gene expression and enzyme activity during fruit development in two cucumber cultivars

Changes in volatile content, as well as associated gene expression and enzyme activity in developing cucumber fruits were investigated in two Cucumis sativus L. lines (No. 26 and No. 14) that differ significantly in fruit flavor. Total volatile, six-carbon (C6) aldehyde, linolenic and linoleic acid content were higher during the early stages, whereas the nine-carbon (C9) aldehyde content was higher during the latter stages in both lines. Expression of C. sativus hydroperoxide lyase (CsHPL) mirrored 13-hydroperoxide lyase (13-HPL) enzyme activity in variety No. 26, whereas CsHPL expression was correlated with 9-hydroperoxide lyase (9-HPL) enzyme activity in cultivar No. 14. 13-HPL activity decreased significantly, while LOX (lipoxygenase) and 9-HPL activity increased along with fruit ripening in both lines, which accounted for the higher C6 and C9 aldehyde content at 0-6 day post anthesis (dpa) and 9-12 dpa, respectively. Volatile compounds from fruits at five developmental stages were analyzed by principal component analysis (PCA), and heatmaps of volatile content, gene expression and enzyme activity were constructed.

Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits

BACKGROUND

Melon (Cucumis melo) fruits exhibit phenotypic diversity in several key quality determinants such as taste, color and aroma. Sucrose, carotenoids and volatiles are recognized as the key compounds shaping the above corresponding traits yet the full network of biochemical events underlying their synthesis have not been comprehensively described. To delineate the cellular processes shaping fruit quality phenotypes, a population of recombinant inbred lines (RIL) was used as a source of phenotypic and genotypic variations. In parallel, ripe fruits were analyzed for both the quantified level of 77 metabolic traits directly associated with fruit quality and for RNA-seq based expression profiles generated for 27,000 unigenes. First, we explored inter-metabolite association patterns; then, we described metabolites versus gene association patterns; finally, we used the correlation-based associations for predicting uncharacterized synthesis pathways.

RESULTS

Based on metabolite versus metabolite and metabolite versus gene association patterns, we divided metabolites into two key groups: a group including ethylene and aroma determining volatiles whose accumulation patterns are correlated with the expression of genes involved in the glycolysis and TCA cycle pathways; and a group including sucrose and color determining carotenoids whose accumulation levels are correlated with the expression of genes associated with plastid formation.

CONCLUSIONS

The study integrates multiple processes into a genome scale perspective of cellular activity. This lays a foundation for deciphering the role of gene markers associated with the determination of fruit quality traits.

Spatial and temporal variations in mango colour, acidity, and sweetness in relation to temperature and ethylene gradients within the fruit

Managing fruit quality is complex because many different attributes have to be taken into account, which are themselves subjected to spatial and temporal variations. Heterogeneous fruit quality has been assumed to be partly related to temperature and maturity gradients within the fruit. To test this assumption, we measured the spatial variability of certain mango fruit quality traits: colour of the peel and of the flesh, and sourness and sweetness, at different stages of fruit maturity using destructive methods as well as vis-NIR reflectance. The spatial variability of mango quality traits was compared to internal variations in thermal time, simulated by a physical model, and to internal variations in maturity, using ethylene content as an indicator. All the fruit quality indicators analysed showed significant spatial and temporal variations, regardless of the measurement method used. The heterogeneity of internal fruit quality traits was not correlated with the marked internal temperature gradient we modelled. However, variations in ethylene content revealed a strong internal maturity gradient which was correlated with the spatial variations in measured mango quality traits. Nonetheless, alone, the internal maturity gradient did not explain the variability of fruit quality traits, suggesting that other factors, such as gas, abscisic acid and water gradients, are also involved.

Recent Advances in the Application of Metabolomics to Studies of Biogenic Volatile Organic Compounds (BVOC) Produced by Plant

In many plants, biogenic volatile organic compounds (BVOCs) are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and also influenced by herbivory damage and pathogen infection. Plant-produced BVOCs are receptive to many organisms, from microorganisms to human, as both airborne attractants and repellants. In addition, it is known that some BVOCs act as signals to prime a plant for the defense response in plant-to-plant communications. The compositional profiles of BVOCs can, thus, have profound influences in the physiological and ecological aspects of living organisms. Apart from that, some of them are commercially valuable as aroma/flavor compounds for human. Metabolomic technologies have recently revealed new insights in biological systems through metabolic dynamics. Here, the recent advances in metabolomics technologies focusing on plant-produced BVOC analyses are overviewed. Their application markedly improves our knowledge of the role of BVOCs in chemosystematics, ecological influences, and aroma research, as well as being useful to prove the biosynthetic mechanisms of BVOCs.

Metabolomics in melon: a new opportunity for aroma analysis

Cucumis melo fruit is highly valued for its sweet and refreshing flesh, however the flavour and value are also highly influenced by aroma as dictated by volatile organic compounds (VOCs). A simple and robust method of sampling VOCs on polydimethylsiloxane (PDMS) has been developed. Contrasting cultivars of C. melo subspecies melo were investigated at commercial maturity: three cultivars of var. Cantalupensis group Charentais (cv. Cézanne, Escrito, and Dalton) known to exhibit differences in ripening behaviour and shelf-life, as well as one cultivar of var. Cantalupensis group Ha'Ogan (cv. Noy Yisre'el) and one non-climacteric cultivar of var. Inodorus (cv. Tam Dew). The melon cultivar selection was based upon fruits exhibiting clear differences (cv. Noy Yisre'el and Tam Dew) and similarities (cv. Cézanne, Escrito, and Dalton) in flavour. In total, 58 VOCs were detected by thermal desorption (TD)-GC-MS which permitted the discrimination of each cultivar via Principal component analysis (PCA). PCA indicated a reduction in VOCs in the non-climacteric cv. Tam Dew compared to the four Cantalupensis cultivars. Within the group Charentais melons, the differences between the short, mid and long shelf-life cultivars were considerable. ¹H NMR analysis led to the quantification of 12 core amino acids, their levels were 3-10-fold greater in the Charentais melons, although they were reduced in the highly fragrant cv. Cézanne, indicating their role as VOC precursors. This study along with comparisons to more traditional labour intensive solid phase micro-extraction (SPME) GC-MS VOC profiling data has indicated that the high-throughput PDMS method is of great potential for the assessment of melon aroma and quality.

Understanding development and ripening of fruit crops in an 'omics' era

Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.

Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species

Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.

Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach

BACKGROUND

Maturity date (MD) is a crucial factor for marketing of fresh fruit, especially those with limited shelf-life such as peach (Prunus persica L. Batsch): selection of several cultivars with differing MD would be advantageous to cover and extend the marketing season. Aims of this work were the fine mapping and identification of candidate genes for the major maturity date locus previously identified on peach linkage group 4. To improve genetic resolution of the target locus two F2 populations derived from the crosses Contender x Ambra (CxA, 306 individuals) and PI91459 (NJ Weeping) x Bounty (WxBy, 103 individuals) were genotyped with the Sequenom and 9K Illumina Peach Chip SNP platforms, respectively.

RESULTS

Recombinant individuals from the WxBy F2 population allowed the localisation of maturity date locus to a 220 kb region of the peach genome. Among the 25 annotated genes within this interval, functional classification identified ppa007577m and ppa008301m as the most likely candidates, both encoding transcription factors of the NAC (NAM/ATAF1, 2/CUC2) family. Re-sequencing of the four parents and comparison with the reference genome sequence uncovered a deletion of 232 bp in the upstream region of ppa007577m that is homozygous in NJ Weeping and heterozygous in Ambra, Bounty and the WxBy F1 parent. However, this variation did not segregate in the CxA F2 population being the CxA F1 parent homozygous for the reference allele. The second gene was thus examined as a candidate for maturity date. Re-sequencing of ppa008301m, showed an in-frame insertion of 9 bp in the last exon that co-segregated with the maturity date locus in both CxA and WxBy F2 populations.

CONCLUSIONS

Using two different segregating populations, the map position of the maturity date locus was refined from 3.56 Mb to 220 kb. A sequence variant in the NAC gene ppa008301m was shown to co-segregate with the maturity date locus, suggesting this gene as a candidate controlling ripening time in peach. If confirmed on other genetic materials, this variant may be used for marker-assisted breeding of new cultivars with differing maturity date.

Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism

Metabolomics has emerged as a key technique of modern life sciences in recent years. Two major techniques for metabolomics in the last 10 years are gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled to mass spectrometry (LC-MS). Each platform has a specific performance detecting subsets of metabolites. GC-MS in combination with derivatisation has a preference for small polar metabolites covering primary metabolism. In contrast, reversed phase LC-MS covers large hydrophobic metabolites predominant in secondary metabolism. Here, we present an integrative metabolomics platform providing a mean to reveal the interaction of primary and secondary metabolism in plants and other organisms. The strategy combines GC-MS and LC-MS analysis of the same sample, a novel alignment tool MetMAX and a statistical toolbox COVAIN for data integration and linkage of Granger Causality with metabolic modelling. For metabolic modelling we have implemented the combined GC-LC-MS metabolomics data covariance matrix and a stoichiometric matrix of the underlying biochemical reaction network. The changes in biochemical regulation are expressed as differential Jacobian matrices. Applying the Granger causality, a subset of secondary metabolites was detected with significant correlations to primary metabolites such as sugars and amino acids. These metabolic subsets were compiled into a stoichiometric matrix N. Using N the inverse calculation of a differential Jacobian J from metabolomics data was possible. Key points of regulation at the interface of primary and secondary metabolism were identified.

Alteration of the interconversion of pyruvate and malate in the plastid or cytosol of ripening tomato fruit invokes diverse consequences on sugar but similar effects on cellular organic acid, metabolism, and transitory starch accumulation

The aim of this work was to investigate the effect of decreased cytosolic phosphoenolpyruvate carboxykinase (PEPCK) and plastidic NADP-dependent malic enzyme (ME) on tomato (Solanum lycopersicum) ripening. Transgenic tomato plants with strongly reduced levels of PEPCK and plastidic NADP-ME were generated by RNA interference gene silencing under the control of a ripening-specific E8 promoter. While these genetic modifications had relatively little effect on the total fruit yield and size, they had strong effects on fruit metabolism. Both transformants were characterized by lower levels of starch at breaker stage. Analysis of the activation state of ADP-glucose pyrophosphorylase correlated with the decrease of starch in both transformants, which suggests that it is due to an altered cellular redox status. Moreover, metabolic profiling and feeding experiments involving positionally labeled glucoses of fruits lacking in plastidic NADP-ME and cytosolic PEPCK activities revealed differential changes in overall respiration rates and tricarboxylic acid (TCA) cycle flux. Inactivation of cytosolic PEPCK affected the respiration rate, which suggests that an excess of oxaloacetate is converted to aspartate and reintroduced in the TCA cycle via 2-oxoglutarate/glutamate. On the other hand, the plastidic NADP-ME antisense lines were characterized by no changes in respiration rates and TCA cycle flux, which together with increases of pyruvate kinase and phosphoenolpyruvate carboxylase activities indicate that pyruvate is supplied through these enzymes to the TCA cycle. These results are discussed in the context of current models of the importance of malate during tomato fruit ripening.