Genetic Analysis and Fingerprint Construction for Thick-Skinned Melon (Cucumis melo subsp. melo) Based on InDel Markers

Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’ is an F1 hybrid derived from a cross between two Hami melon inbred lines, ‘M06-1-3’ and ‘M15-3’. This study utilized resequencing data derived from the bi-parents of ‘Dongfangmi No.4’ to identify 557,878 insertion and deletion (InDel) variations across the entire genome. Thirty-nine highly polymorphic InDel markers were screened to conduct a genetic analysis of 40 representative cultivated varieties, with marker MS108 specifically distinguishing ‘Dongfangmi No.4’ from the other 39 cultivated varieties. Genetic analysis revealed a high level of genetic diversity within the population (average observed heterozygosity Ho = 0.313, Shannon index I = 0.528), and polymorphic information content (PIC) analysis indicated that 54% of the markers (21/39) were highly polymorphic. Principal component analysis (PCA) and clustering demonstrated significant genetic differentiation between cantaloupe and Hami melons, as well as between cantaloupe and honeydew. In contrast, the genetic boundaries between Hami melons and honeydew were obscured due to frequent germplasm exchange. Ultimately, seven core InDel markers were selected to construct the DNA fingerprinting map, successfully achieving complete differentiation of 40 varieties. This marker system provides an effective molecular tool for melon variety identification, intellectual property protection, and breeding.