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

1
INRAE, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Bordeaux Metabolome Facility MetaboHUB, Centre INRAE de Nouvelle Aquitaine - Bordeaux, 33140 Villenave d’Ornon, France
2
The James Hutton Institute, Environmental & Biochemical Sciences, Invergowrie, Dundee, DD2 5DA Scotland, UK
3
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
4
Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
5
Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
6
Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Dto. Química Orgánica, Córdoba 5000, Argentina
7
CONICET, ICYTAC (Instituto de Ciencia y Tecnologia de Alimentos Córdoba), Córdoba 5000, Argentina
8
Institute of Plant Science, Agricultural Research Organization—Volcani Center, Rishon LeZiyyon 7515101, Israel
9
Newe Ya‘ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel
10
Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
11
Department of Plant and Environmental Sciences & Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
12
Business Unit Bioscience, Wageningen University & Research, Post Box 16, 6700AA, Wageningen, Netherlands
13
Department of Plant Physiology, Wageningen University & Research, Laboratory of Plant Physiology, Post Box 16, 6700AA, Wageningen, Netherlands
*
Author to whom correspondence should be addressed.
These authors have contributed equally to this work.
Metabolites 2020, 10(3), 121; https://doi.org/10.3390/metabo10030121
Received: 27 February 2020 / Revised: 19 March 2020 / Accepted: 20 March 2020 / Published: 24 March 2020
(This article belongs to the Special Issue Fruit Metabolism and Metabolomics)
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. View Full-Text
Keywords: genetic resources; melon; genotype by sequencing; elemental analysis; metabolome; Cucumis melo genetic resources; melon; genotype by sequencing; elemental analysis; metabolome; Cucumis melo
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Moing, A.; Allwood, J.W.; Aharoni, A.; Baker, J.; Beale, M.H.; Ben-Dor, S.; Biais, B.; Brigante, F.; Burger, Y.; Deborde, C.; Erban, A.; Faigenboim, A.; Gur, A.; Goodacre, R.; Hansen, T.H.; Jacob, D.; Katzir, N.; Kopka, J.; Lewinsohn, E.; Maucourt, M.; Meir, S.; Miller, S.; Mumm, R.; Oren, E.; Paris, H.S.; Rogachev, I.; Rolin, D.; Saar, U.; Schjoerring, J.K.; Tadmor, Y.; Tzuri, G.; de Vos, R.C.; Ward, J.L.; Yeselson, E.; Hall, R.D.; Schaffer, A.A. Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity. Metabolites 2020, 10, 121.

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