Development and validation of high-resolution melting and TaqMan assays for a fruit shape-associated SNP in peach (Prunus persica)

Introduction Fruit shape is an important quality and breeding trait in peach ( Prunus persica ), and molecular markers associated with this trait could facilitate selection before fruit phenotypes can be evaluated. Methods In this study, high-resolution melting (HRM) and TaqMan assays were developed and evaluated for genotyping an A/T single-nucleotide polymorphism (SNP) associated with fruit shape in peach. Whole-genome resequencing (WGS) data from 445 peach germplasm accessions were used to evaluate the relationship between the target SNP genotype and fruit shape. Results Among these, all 423 accessions with the AA genotype bore round fruit, whereas all 22 accessions with the AT genotype bore flat fruit. The HRM assay clearly discriminated the AA and AT genotypes on the basis of distinct melting profiles, and the HRM genotypes were fully concordant with the corresponding WGS genotypes across all 445 accessions. The HRM marker was further validated in 744 progenies derived from nine peach breeding populations, in which the HRM-based genotype classifications were consistent with the observed round and flat fruit phenotypes. In addition, a TaqMan assay targeting the same A/T polymorphism clearly discriminated the AA and AT genotypes in 20 representative peach accessions, indicating that this fruit shape-associated SNP can also be genotyped with an allele-specific probe-based assay. Discussion Together, these results show that both the HRM and TaqMan assays can effectively discriminate the observed genotypes at the fruit shape-associated SNP, and the validation of the HRM marker across germplasm accessions and breeding populations supports its potential application in marker-assisted selection for fruit shape in peach breeding.