Establishment of a comprehensive germplasm collection of chate melon informed with whole-genome sequence and phenotypic data

The species Cucumis melo L. includes several minor crops, such as the chate melon (C. melo subsp. melo var. chate), found in Apulia (Southern Italy) as a relic of its former wider cultivation, spanning from the time of Ancient Egypt to the Middle Ages. Recently, the consumption of chate melon has been gaining popularity both inside and outside the regional boundaries as a substitute for cucumber. Here, we describe the collection and characterization of fifteen open-pollinated, farmer-maintained chate melon populations, known by the folk names "meloncella", "spuredda" and " cucummaru", which are representative of the germplasm cultivated in Salento (Southern Apulia). Whole-genome resequencing of population DNA pools was performed to investigate genetic diversity within and between populations. A high level of variation was found in terms of heterozygosity. Notably, the lowest heterozygosity was associated with the population known as meloncella striata, characterized by deep grooves on the pepo and more widely distributed in commerce, indicating a greater selective pressure exerted by farmers. A total of 1,352 alleles were found to be fixed privately in the populations under study, including 170 private alleles fixed in the meloncella striata population, which are valuable for its traceability. Replicated field trials enabled the selection of superior populations based on key agronomic and commercial traits, including fruit number per plant, fruit shape, yield per plant, and earliness. Overall, this study secures the chate melon gene pool from further genetic erosion. Additionally, genomic and phenotypic data reported here offer a basis for utilizing the chate melon gene in breeding and for introducing this crop into mainstream agrifood systems.