Population structure, genetic diversity and fruit-related traits of wild and cultivated melons based on chloroplast genome

The melon is an important fruit crop. Chloroplast genomes are widely used to analyze plant genetic diversity. The chloroplast genome was used to study melon population genetics. We identified 192 SNPs in the chloroplast genome of 348 melon tissue samples. These SNPs were mainly distributed in the large single copy and small single copy of the chloroplast genome. The two inverted repeat (IR) regions (IRa and IRb) contained almost no SNPs. The melon population structure, fruit-related traits, and genetic diversity within each group were analyzed based on these SNPs. The 192 SNPs effectively divided the melon populations into three groups: wild, thick-rind type cultivated melon, and thin-rind type cultivated melon groups, with genetic diversities of 1.12 × 10−3, 4.71 × 10−4, and 2.85 × 10−4, respectively. This study analyzed the single fruit weight, soluble solids content, flesh color value, and flesh thickness (FT) traits in the population to understand differences in important fruit-related traits, and there were remarkable differences in FT among the three groups. These results suggest the chloroplast genome can be used to study the population genetics of the melon, and they contribute to the classification and identification of core germplasm resources.