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

Abstract

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.

Melon Genetic Resources Characterization for Rind Volatile Profile

“…However, and interestingly, other VOCs were exclusively present in the rind such as pentadecane (also reported in melon rind by Moing et al [6]), the lipid derivative 2-hexanone or the phenolic ethylbenzene, apart from sesquiterpenes, volatiles mainly associated to rind. Other VOCS such as the BCAA related 2-methylbutanal and 3-methylbutanal, the lipid derivatives undecanal and (E)-2-pentenal, the monoterpenoid α-terpineol, the methyl ester methyl butanoate or the phenolic phenylacetaldehyde were absent in the flesh of this collection, but had been previously reported in other melons [19,24,41].…”

“…Leida et al [35] in its population structure analysis also reported high variability in Spanish types, which mainly were located in a population apart from the remaining Inodorus from other origins. Furthermore, although the complete metabolic HCA by Moing et al [6] consistently grouped together all the Inodorus accessions assayed, partial analysis with some types of compounds, especially rind semi-polar non-volatiles extracts, located the Tendral melon closer to some Cantalupensis-Reticulatus and Flexuosus genotypes than to other Inodorus, indicating that some Spanish Inodorus have chemical similarities to climacteric types.…”

“…In this sense, recent studies suggest that Momordica actually belongs to subsp. melo [6,51]. Additionally, Indian germplasm has been suggested as the origin of modern Mediterranean and Far-East melons [52].…”

“…Although a group including Conomon, Chinensis and Makuwa types has been considered in the current work, the non-climacteric Conomon and the intermediate-climacteric Makuwa can be differentiated mainly based on their ripening and sweetness [1], and classification of other metabolomics also divides these two groups [6]. In this sense, Esteras et al [5] also reported two groups based on flesh volatiles, the Conomon-Chinensis accessions (Songwhan Charmi, Paul, Shiro Uri Okayama, Nanbukin) within the non-aromatic cluster and the Makuwa accessions (Ginsen Makuwa and Baishami) mixed with Dudaim in the aromatic cluster (flesh_II-Ib and flesh_I-Ib, respectively; Figure 1).…”

“…Variation in other quality traits like nutrients content (sugars, acids and carotenoids among others) or aroma volatiles has also been reported [2][3][4][5]. Recently, Moing et al [6] analyzed a dataset of over 80,000 metabolomic and elemental features, including 282 flesh volatile metabolites, in a melon collection of 51 accessions finding that 2 of 18 metabolic classification strongly supports phylogenomics, although not completely. C. melo is divided into two subspecies [7], subsp.…”