Special Issue "Fruit Metabolism and Metabolomics"

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: 30 November 2019.

Special Issue Editors

Guest Editor
Dr. Annick Moing

INRA, UMR 1332 Fruit Biology and Pathology, Centre INRA de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, France
Website | E-Mail
Interests: Plant metabolomics; fruit metabolism; biomarker metabolites; proton NMR metabolomic profiling; metabolomic data combination
Guest Editor
Dr. Sonia Osorio

Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071, Málaga, Spain
Website | E-Mail
Interests: Fruit quality; post-harvest; biotechnology; genomics; metabolomics
Guest Editor
Dr. Pierre Pétriacq

Univ. Bordeaux, UMR 1332 Fruit Biology and Pathology, Centre INRA de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, France
Website 1 | Website 2 | E-Mail
Interests: Plant biochemistry; redox metabolism; mass spectrometry

Special Issue Information

Dear Colleagues,

Fruit development and ripening are complex and highly coordinated developmental processes that yields flavorful tissues for organisms that consume and disperse the associated seeds. Fruits are economically important and crucial for human nutrition and health due to their content in sugars, organic acids, pigments, volatiles and nutraceutical compounds.

In recent years, there have been dramatic improvements in the knowledge of different aspects of fruit metabolism. Specifically, high-throughput metabolomics technologies have provided the quantitation of metabolite levels across various biological processes allowing the identification of the genes underpinning fruit development and ripening. A collection of papers is required to review the current understanding of temperate and tropical fruit metabolism using metabolomics for basic research or practical applications.

This Special Issue will include, but not be limited to, articles and reviews about different aspects of fruit metabolism, including primary and specialized metabolisms, and postharvest. The effect of genotype, biotic or abiotic environment and their interaction on metabolomic profiles and metabolism are within the scope of the present topic. Studies of fruit lipidomics or a combination of genomics or other omics with metabolomics are also welcomed.

Dr. Annick Moing
Dr. Sonia Osorio
Dr. Pierre Pétriacq
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • Fruit metabolomics
  • Developmental metabolomics
  • Spatial metabolomics
  • Lipidomics
  • Fruit metabolomic profiling
  • Central metabolism
  • Specialized metabolism
  • Mass spectrometry
  • Nuclear magnetic resonance spectroscopy
  • Omics data integration

Published Papers (1 paper)

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Open AccessArticle
Metabolomic Variability of Different Genotypes of Cashew by LC-Ms and Correlation with Near-Infrared Spectroscopy as a Tool for Fast Phenotyping
Metabolites 2019, 9(6), 121; https://doi.org/10.3390/metabo9060121
Received: 6 May 2019 / Revised: 18 June 2019 / Accepted: 20 June 2019 / Published: 25 June 2019
PDF Full-text (11064 KB) | HTML Full-text | XML Full-text | Supplementary Files
The objective of the present work was to develop an advanced fast phenotyping tool to explore the cashew apple compositions from different genotypes, based on a portable near-infrared (MicroNIR) spectroscopy. This will be in addition to associating the variability of the respective cashew [...] Read more.
The objective of the present work was to develop an advanced fast phenotyping tool to explore the cashew apple compositions from different genotypes, based on a portable near-infrared (MicroNIR) spectroscopy. This will be in addition to associating the variability of the respective cashew apple pulps with the genotypes by ultra-performance liquid chromatography (UPLC), coupled with high-resolution mass spectrometry (HRMS). The NIR analysis is a non-destructive, low-cost procedure that provides prompt results, while considering the morphology of different cashew apples (shape, size, and color). The UPLC-HRMS analysis is characterized by specific bioactive compounds, such as the derivatives of hydroxybutanoic acid, galloyl, and flavonoids. Furthermore, both techniques allowed the identification of a group of accessions, which presented similarities among the chemical profiling. However, to improve the understanding of cashew chemical and physical variability, further variables related to the cashew apple composition, such as edaphoclimatic conditions, should be considered for future studies. These approaches lead to the conclusion that these two tools are useful for the maintenance of BAG-Caju (Cashew Germplasm Bank) and for the cashew-breeding program. Full article
(This article belongs to the Special Issue Fruit Metabolism and Metabolomics)

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Identification Of Bioactive Phytochemicals In Mulberries
Authors: Gilda D’Urso1, Jurriaan J. Mes2, Paola Montoro1, Robert D. Hall3,4, Ric C.H. de Vos3
Affiliations: 1Department of Pharmacy, University of Salerno, Fisciano, Italy.
2Business Unit Fresh Food and Chains, Wageningen Food & Biobased Research, Wageningen University and Research, The Netherlands
3Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research, The Netherlands
4Department of Plant Physiology, Wageningen University and Research, The Netherlands
Abstract: Mulberries are consumed as both fresh and processed fruits and are used in traditional medicines to combat several diseases, especially Type II diabetes. Here we studied the metabolite compositions of aqueous-methanol extracts from ripe fruits of both white (Morus alba) and black (Morus nigra) mulberries, using reversed-phase HPLC coupled to high resolution  mass spectrometry (LC-MS), and related these to their antioxidant and α-glucosidase inhibitory activities in vitro. Based on accurate masses, fragmentation data, absorbance spectra and retention times, 36 compounds mainly representing phenolic compounds and amino sugar acids were identified. While the antioxidant activity was highest in M. nigra, the α-glucosidase inhibitory activities were similar. Both bioactivities were mostly resistant to in vitro gastrointestinal digestion. To identify compounds responsible for the α-glucosidase inhibitory activity, we combined LC-MS with 96-well-format fractionation followed by bioactivity testing of individual fractions; compounds responsible for the antioxidant activities were identified using HPLC with an online antioxidant detection system. We thus determined iminosugars and phenolic compounds in both M. alba and M. nigra, and anthocyanins in M. nigra as the key α-glucosidase inhibitors, while anthocyanins in M. nigra and both phenylpropanoids and flavonols M. alba were the key antioxidants in mulberries.

TitleExploring the metabolomics and transcriptomes data of the Solanum pennellii introgression line population: a novel insight into tomato metabolism
Authors: Anastasiya Kuhalskaya 1, Micha Wijesingha Ahchige 2, Yariv Brotman 1, Saleh Alseekh2*
Affiliations: 1 Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
2 Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
Abstract: Here, we will used our previously published data on lipids, primary and secondary metabolites in combinations with phenotypic data for fruit pericarp of the Solanum pennellii introgression lines to construct metabolite-metabolite and metabolite-phenotypic trait correlation networks. This will enable us to identify yet unknown association between those branches of metabolism. We will also use gene clusters and orthologues search approaches to investigate the genomic organization of specific metabolic pathways. We will reconstruct the transcriptional network of leaf and fruit ILs fusing global expression data available from those tissues. Combining those data will yield a new set of candidate genes participating in biosynthesis and regulation of the tomato metabolome.

TitleMetabolomic tools to elucidate metabolic changes during fruit senescence and postharvest
Authors: Delphine M Pott1, Jose G Vallarino1*, Sonia Osorio1*
Affiliations: 1Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Málaga, Spain.
Abstract: Metabolic changes occurring in senescent fruits during their postharvest shelf life lead to a general deterioration of quality attributes, including flavour and firmness decrease and ‘off aroma’ generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry, which mostly consists of cold temperature storage and the use of modified atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly known. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for quality traits, such as volatiles, primary and secondary metabolites, play a predominant role in the identification of the pathways affected by fruit senescence. Here, we review how metabolomic studies are helpful in characterizing the metabolic shifts occurring during postharvest and in pointing out the regulatory factors underlying the last stage of fruit maturation. In particular, we will pay attention to the effects of current technologies used in the postharvest industry on metabolite content, and consequently, on fruit metabolism and quality traits.

TitleNontargeted metabolite profiles and sensory properties elucidates communalities and differences of wines made with same variety but different cultivar clone.
Authors: Álvaro Cuadros-Espinoza1, Claudio Verdugo-Alegría2, Yerko Moreno2*, José G. Vallarino2*
Affiliations: 1 metaSysX GmbH, Potsdam-Golm 14476, Germany
2 Centro Tecnologico de la Vid y el Vino, Universidad de Talca, Av. Lircay s/n, Talca, Chile
Abstract: Grapes, one of the oldest agricultural crops, are cultivated to produce table fruits, dried fruits, juice and wine. The number of cépages referenced as varieties held in germplasm collections around the world is estimated at 10 000, most of them belonging to the European species Vitis vinifera L. A grapevine variety consists of an array of clones descended by vegetative propagation from a single selected vine grown from a single seedling A majority of the clones within a variety are identical, but some can show divergent genotypes and, to some extent, divergent phenotypes. The chemical composition of grape berries is varietal dependent and influenced by the environment and viticulture practices. In this study, three Vitis vinifera cv. Pinot noir clones grown under identical field conditions were subjected to nontargeted metabolite profiling analysis with UPLC-Orbitrap-MS/MS and to descriptive sensory evaluation by a trained panel. Combined metabolome and sensory data (sPLS model) revealed an important variation in the metabolome explained variation in the sensory profiles. Descriptive analysis revealed that the wines from different clones were significantly different for a number of flavour and aroma characters, particularly those related to mouth-feel. Metabolomic analysis allowed classification of the wines based on grape variety-clone with better performance that by sensory analysis. The analysis described here is rapid, inexpensive and allows the simultaneous assessment of multiple metabolites contributing to wine quality. Metabolomic analysis of wine may, therefore, offer a more affordable technique to investigate certain sensory aspects of wine.

TitleFrom vine to wine: aromas and aroma precursors metabolism in grape – an update.
Authors: Sabine Guillaumie1, Alexandre Pons2, Cornelis van Leeuwen1, Cécile Thibon2, Eric Gomès1
Affiliations:1 EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, 210 Chemin de Leysotte, F-33140  Villenave d’Ornon, France
2 EA 4577 Œnologie, Université de Bordeaux, ISVV, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France
Abstract: Grape berry is a non-climacteric fleshy fruit which human turn into quality wines thanks to winemaking techniques revealing their original diversity and organoleptic complexity. Organoleptic properties and oenological potential of grapes are tightly linked to their composition at harvest, in terms of both primary and secondary metabolites. Indeed, grapes have a highly developed secondary metabolism that produces a large array of compounds contributing to their color, taste and aroma, which can be released and bio transformed during the winemaking process. One of the components of the intrinsic grape quality is its aroma and aroma precursors content. Many of these compounds have been identified in grapes harvested at maturity or overriped. They belong to various chemical families including thiols, pyrazines, terpenoids, nor-isoprenoids, and glycosylated, glutathione-, cysteine-S-conjugates precursors. Over the past decade, combinations of analytical biochemistry, genetic mapping studies, genomic, as well as targeted and untargeted transcriptomic and metabolomics approaches have started to shed light on their biosynthetic pathways in berries. This review proposes an update on the aromas and aroma precursors metabolism during berry developmental, ripening and post-harvest phases.

Title: Cross-species comparison of fruit-metabolomics to elucidate metabolic regulation of fruit polyphenolics in the Solanaceae species

Authors: Carla Lenore F. Calumpang, Mutsumi Watanabe, Takayuki Tohge

Affiliations: Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.

Abstract: Many members of Solanaceous crops, such as tomato and eggplant, are common components of the daily human diet. Fruit polyphenolics are plant secondary metabolites known as beneficial compounds in terms of their human health benefits, as well as for their capacity to counteract plant abiotic and biotic stresses. The major phenolic compounds found in fruits of Solanaceous crops are chlorogenates, phenolamines and flavonoids that vary in terms of their quantity, physiological functions and structural diversity among and within plants. However elucidating the metabolic shifts of polyphenolic compounds during fruit development in family Solanaceae, has not yet been conducted especially at a cross-species level. Here, we performed a cross-species comparison of fruit-metabolomics to elucidate metabolic regulation of fruit polyphenolics from major Solanaceae representatives using liquid chromatography-mass spectrometry (LC-MS). We determined metabolic shifts focusing on fruit polyphenolics, during both immature and mature stages of fruit development.  Furthermore, how these patterns are influenced by the function of these polyphenols among species are discussed. Our result gives us knowledge on the metabolomics-assisted crop improvement of entire fruit crops exhibiting improved nutritive properties, as well as enhanced stress tolerance.


Title: Phytohormone and transcriptomic analysis reveals endogenous cytokinins affect kiwifruit growth under restricted carbon supply

Authors: Simona Nardozza1*, Janine Cooney2, Helen L. Boldingh2, Kati Ruppert2, Tania Trower2, Dan Jones1, Amali H. Thrimawithana1, Andrew C. Allan1,3, Annette C. Richardson4

Affiliations: 1The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand;

2PFR, Hamilton, New Zealand;

3School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand 4PFR, Kerikeri, New Zealand;


Following cell division, fruit growth is characterised by both expansion through cell volume increase, and biomass accumulation in cells. Fruit growth is limited by carbon starvation, however the mechanism controlling kiwifruit growth under restricted carbohydrate supply is poorly understood. Fruit carbon starvation usually occurs when vine leaf-to-fruit ratio is low, but it can also happen when the leaf-to-fruit ratio is optimal (e.g. high temperatures during critical fruit growth phases can substantially reduce the photosynthetic carbon supply to fruit). In a previous study on red-fleshed kiwifruit we have shown long-term carbon starvation had detrimental effects on carbohydrate and anthocyanin metabolism, as well as fruit growth. Effects on fruit growth were not immediately apparent but started 8 weeks after carbon starvation was imposed by a low leaf to fruit ratio. To elucidate the mechanisms underlying fruit growth reductions under carbon starvation, we have integrated phytohormone profiling with transcriptomic, metabolomic and developmental datasets for fruit developed under high or low carbohydrate supplies. Phytohormone profiling of the outer pericarp tissue of kiwifruit showed a significant reduction in total cytokinin concentrations in carbon starved fruit, whilst other hormones were less affected. Cytokinin concentrations were significantly and positively correlated tofruit weight measurements during growth. Principal component analysis of cytokinin concentrations in fruit at 16 weeks after mid bloom was able to discriminate between fruit based on their carbohydrate supply. Cytokinin biosynthetic genes (HMGR, IPT, CYP735A) were significantly down-regulated under carbon starvation, in agreement with metabolite data. Several genes coding for expansin proteins involved in the cell wall loosening were also down-regulated under carbon starvation. Our results suggest a role for cytokinins in driving fruit cell expansion and growth in kiwifruit.

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