Whole-genome sequencing and phenotyping of neglected and underutilized vegetable melons from the Salento diversity centre (Southern Italy)

The species <i>Cucumis melo</i> L. includes two neglected and underutilized vegetable crops, cucumber melon (<i>C. melo</i> subsp. <i>melo</i> var. <i>chate</i>) and snake melon (<i>C. melo</i> subsp. <i>melo</i> var. <i>flexuosus</i>). In particular, cucumber melon was highly popular in Mediterranean civilizations during Antiquity and the Middle Ages, whereas today its cultivation is mostly confined to the Salento area of southern Italy. Here, we describe the collection and characterization of thirteen cucumber melon and two snake melon populations from Salento. Whole-genome resequencing of DNA pools was performed to investigate genetic diversity within and among populations. The cucumber melon population UBGCMC111, most widely cultivated and marketed, exhibited the lowest heterozygosity, possibly reflecting more intense selection by farmers. Hierarchical clustering revealed genetic divergence of UBGCMC111 and UBGCMC053, the latter originating from a unique area of Salento with linguistic and cultural ties to Greek heritage. Despite some unique patterns of variation, snake melons clustered together with cucumber melons, suggesting overall genetic similarity. A total of 1,307 alleles were fixed and private to different populations under study, potentially valuable for their traceability. Some of them were associated with genes possibly underlying deeply grooved and pale green pepo phenotypes of the populations UBGCMC111 and UBGCMC124, respectively. Replicated field trials enabled germplasm characterization and the selection of agronomically superior populations. Overall, this study safeguards valuable <i>C. melo</i> genetic diversity from further genetic erosion. Additionally, it provides genomic and phenotypic data laying a foundation for integrating unexplored genetic resources into mainstream agrifood systems and breeding programs.