Genetic dissection of apricot fruit skin color (Prunus armeniaca L.) using SNP and SSR molecular markers

Fruit skin color is a key quality trait in apricot, strongly influencing consumer preference and market value. However, phenotypic evaluation of this trait is time-consuming and highly dependent on environmental conditions and harvest timing. This study aimed to develop reliable molecular markers associated with apricot skin color to support marker-assisted selection in breeding programs. A major skin color QTL located on chromosome 3 was explored, leading to the identification of an AP2/ERF domain-containing gene involved in carotenoid regulation. Within this gene, both SNP and SSR polymorphisms were characterized. High-resolution melting (HRM) analysis validated a highly significant SNP associated with fruit skin color in a segregating 'Goldrich' × 'Currot' population and in a panel of 57 apricot cultivars. The HRM-based SNP marker accurately discriminated between orange- and yellow-skinned fruits, reaching 100% efficiency in the segregating population and 89.5% in the cultivar set. In parallel, SSR markers developed within the AP2/ERF gene revealed allelic variation associated with skin color, with one SSR marker achieving an efficiency of 93.9%. Allelic and protein sequence reconstruction demonstrated that variation in polyalanine tract length and non-synonymous amino acid substitutions generate functional diversity in the AP2/ERF protein. Notably, this analysis indicated that a marker based on SNP4 (S3_22924316), which directly affects the protein sequence, may provide enhanced discriminatory power. comparable to that previously observed for the SSR-based marker. Overall, these results provide both mechanistic insight into apricot color regulation and practical molecular tools for efficient breeding.

The online version contains supplementary material available at 10.1007/s11032-026-01674-5.