WHOLE-GENOME SEQUENCING AND PHENOTYPING OF NEGLECTED AND UNDERUTILIZED VEGETABLE MELONS FROM THE SALENTO DIVERSITY CENTRE (SOUTHERN ITALY)

The species Cucumis melo L. includes two neglected and underutilized vegetable crops, cucumber melon (C. melo subsp. melo var. chate) and snake melon (C. melo subsp. melo var. flexuosus). In particular, cucumber melon was highly popular in Mediterranean civilizations during Antiquity and the Middle Ages, whereas today its cultivation is largely confined to the Apulia Region (southern Italy), especially the Salento area. Here, we describe the collection and characterization of thirteen cucumber melon and two snake melon populations from Salento, locally known as meloncella, spuredda and cucummaru. Whole-genome resequencing of DNA pools was conducted to investigate genetic diversity within and between populations. Notably, the cucumber melon population UBGCMC111, which is widely cultivated and traded, exhibited the lowest heterozygosity, likely due to strong selective pressure exerted by farmers. Genetic analyses revealed the divergence of UBGCMC111 and another population, UBGCMC053, which originates from a unique area in Salento with historical linguistic and cultural ties to Greek heritage. Despite some unique patterns of variation, the two snake melon populations clustered together with cucumber melons, suggesting an overall genetic similarity between the chate and flexuosus botanical varieties. A total of 1,307 alleles were found to be fixed and private to different populations under study, potentially valuable for their traceability. Among them, one allele, specific to the population UBGCMC111, was associated with a gene putatively involved in fruit development and morphogenesis, which might explain its characteristically deeply grooved pepos. In addition, two alleles, specific to the population UBGCMC124, were associated with genes putatively involved in photosynthesis, possibly related to its distinct pale green pepos. Replicated field trials enabled germplasm characterization for morpho-agronomic traits, and the selection of superior populations for yield potential and earliness. Overall, this study safeguards valuable C. melo genetic diversity from further genetic erosion. Additionally, it provides genomic and phenotypic data, laying a foundation for integrating largely unexplored genetic resources into mainstream agrifood systems and breeding programs.