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

Peel is a crucial determinant of consumer preference and market value in melons, significantly influencing commercial viability. To overcome limitations in conventional breeding for melon peel color improvement, we used 'VZX' (green peel) and 'HP' (yellow peel) as parental materials to construct an F2 (n = 414) and RIL (n = 116) populations for genetic dissection and mapping. Genetic analysis revealed that green peel color is a dominant trait controlled by a single gene. Using phenotypic data and whole-genome resequencing of the RIL population, we constructed a high-density genetic landscape and identified a major-effect quantitative trait locus (QTL) spanning 77 kb (499.6-576.5 kb on chromosome 4), with a LOD score of 14.85, explaining 41.76% of peel color phenotypic variation. Bulked segregant analysis (BSA) confirmed mapping accuracy. Within this interval, 13 candidate genes were annotated via Gene annotation analysis, including EVM0008709, which encodes the APRR2 transcription factor previously associated with chlorophyll metabolism and pigment regulation in melon, watermelon, and other crops. Three foreground selection markers (RC1, RC2, and RC3) were developed based on EVM0008709 and demonstrated 100% validation accuracy in both the F2 and RIL populations. Additionally, leveraging resequencing data from 'VZX' and 'HP', we designed 204 kompetitive allele-specific PCR (KASP) markers, with 141 exhibiting robust genotyping performance for background selection. Using marker-assisted backcrossing (MABC) with 'HP' as the donor and 'VZX' as the recipient, we developed a novel yellow peel germplasm, 'YVZX', which retains the superior flesh quality of 'VZX'. This study establishes an integrated germplasm innovation pipeline spanning from gene mapping to marker development, and molecular breeding, thereby providing a reproducible technical framework for enhancement of melon quality traits. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-025-01604-x.