Phenotypic Characterization and DNA Fingerprinting of Tianbao Melon Using Genome-Wide SNPs

The Tianbao melon (Cucumis melo subsp. agrestis) is a highly valued regional horticultural crop, yet its sustainable development is severely constrained by a narrow genetic base and widespread varietal admixture in the market. In this study, a panel of 32 Tianbao melon accessions was systematically evaluated by integrating field-based phenotypic assessment with genome-wide single-nucleotide polymorphism (SNP) analysis via whole-genome resequencing. Phenotypic analysis based on ten quantitative traits revealed low overall morphological variability, indicating limited discriminatory power of morphological traits alone. In contrast, 173,497 high-quality SNPs uncovered substantial hidden genetic differentiation, partitioning the accessions into four distinct genotypic groups. Notably, accessions TB-17 and TB-27, though nearly indistinguishable morphologically, exhibited clear genetic divergence in both phylogenetic and principal component analyses. Furthermore, a panel of 20 core SNPs with conserved flanking sequences was selected, generating unique molecular fingerprint profiles for all 32 accessions and achieving high discriminatory resolution (pairwise differences ranging from 10 to 13 SNPs). These findings demonstrate that the integration of phenotypic and genome-wide SNP data provides a robust framework for genetic diversity assessment and DNA fingerprinting in Tianbao melon, offering a scientific basis for cultivar identification, intellectual property protection, and precision breeding to support sustainable development of the regional melon industry.