Traditional cider apples are typically classified by their sugar, acid, and phenolic composition and concentration, which all impact the sensory profile and fermentation characteristics of the final beverage. Despite the practical importance of these traits, the genetic basis underlying cider apple fruit quality remains poorly understood and few functional genetic markers have been successfully adapted for cider apple breeding. Using a genome-wide association study (GWAS) on 253 cider apple accessions from the USDA-Plant Genetic Resources Unit Malus collection held in Geneva, NY, we found 19 significant marker-trait associations for titratable acidity, pH, total polyphenols, and non-structural carbohydrates. Notably, we identified a distinct marker on chromosome 15 strongly associated with total polyphenols, a key determinant of bitterness and astringency. A major association on chromosome 16, near the Ma1 locus, explained a substantial proportion of the phenotypic variance for titratable acidity and pH, confirming the importance of this region. Significant marker-trait associations were detected for sugar concentration on chromosomes 1, 6, 8, and 10. Further analysis confirmed identification of favorable alleles for titratable acidity, total polyphenols, glucose and sucrose concentration. These results provide a foundation for identifying apple cultivars with desirable phenotypic traits for cider production from germplasm collections and for making marker assisted selections within breeding programs.
