Development and application of functional markers based on the CmAPRR2 gene for peel color improvement in Muskmelon (Cucumis melo)

Peel is a crucial trait affecting consumer preference and an important focus in melon breeding. Muskmelons display extensive genetic diversity in peel color, primarily yellow, green, and white, with additional variations in blended hues and shades. To enhance the efficiency of peel color improvement, this study constructed F ₂ and recombinant inbred line (RIL) populations from a cross between 'VZX' (green peel) and 'HP' (yellow peel) for genetic analysis and QTL mapping. In the F ₂ (n = 414) and RIL (n = 116) populations grown under protected cultivation, the green-to-yellow peel ratios were 3:1 and 1:1, respectively. Bulked Segregant Analysis (BSA) identified a significant QTL associated with peel color at the start of chromosome 4. Additionally, a high-density genetic map based on whole-genome resequencing data of the RIL population was constructed, which revealed a significant peel color-related QTL of 77 kb located at 499.6–576.5 kb of chromosome 4 with a LOD score of 14.85, explaining 41.76% of phenotypic variation. This locus overlapped with the BSA identified interval that contains 13 annotated genes, including EVM0008709 , which encodes the APRR2 transcription factor known to regulate chlorophyll metabolism and pigment accumulation in various crops. Based on the EVM0008709 , three KASP markers (RC1, RC2, and RC3) were developed and successfully guided screening of peel color phenotype in the F ₂ , RIL, and 94 inbred lines. 141 KASP markers for background selection were developed based on resequencing data of the parental lines 'VZX' and 'HP'. Using 'HP' as the donor and 'VZX' as the recipient, we performed two consecutive backcrosses followed by one selfing generation. Through foreground and background selection and traditional breeding, we obtained a novel germplasm resource ('YVZX') exhibiting yellow peel with flesh quality similar to 'VZX'. This study identified effective molecular markers and demonstrated a successful strategy for supporting melon peel color breeding.