Leaf color mutants are key resources for uncovering the molecular mechanisms of chloroplast development and photosynthesis. Here, we identified a novel yellow-green melon mutant, ‘ygp2’, which displays yellow-green leaves and dwarfism throughout development. Genetic analysis indicated that the trait is controlled by a single recessive nuclear gene. Map-based cloning delimited the candidate region to an 805 kb interval on chromosome 11, within which only one missense mutation was identified in MELO13C_11G242690, encoding a triosephosphate isomerase (CmpdTPI). Phylogenetic analysis suggested its plastid localization, which was confirmed by transient expression of CmpdTPI-GFP in tobacco. The ‘ygp2’ mutant exhibited significantly reduced TPI enzyme activity and net photosynthetic rate. Transcriptome analysis revealed downregulation of genes related to light-harvesting complexes, cell division, and the cell cycle. These results demonstrate that the point mutation in CmpdTPI impairs chloroplast function and photosynthesis, leading to the yellow-green phenotype in melon. This study provides insight into the role of plastidial TPI in chlorophyll metabolism and chloroplast development.

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.