A bittersweet symphony: genetic insights into cider apple fruit quality

Many traditional cider apples (Malus domestica) have unique chemotypic traits that impact the sensory profile and fermentation characteristics of the final product. In particular, cider apples may have greater polyphenol, organic acid, and sugar concentration than fresh-market apples. Despite historic importance and a growing market in many parts of the world, the genetic basis underlying cider apple fruit quality remains poorly understood. Therefore, few functional genetic markers have been successfully adapted for cider apple breeding. Using a genome-wide association study on 253 cider apple accessions from the USDA Malus collection, we identified 19 significant marker-trait associations for fruit quality traits. Notably, we identified a distinct marker on chromosome 15 that was 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. Using these 2 loci, we were able to distinguish between cider apple groups, especially for bittersweet apples. A major locus on chromosome 1 was linked to the ratio of glucose and sucrose. This locus could be targeted to select genotypes with increased glucose content, which could improve fermentation kinetics. Overall, these results provide a robust genetic analysis focusing on quality traits in a cider-specific germplasm, laying the foundation for identifying apple cultivars with desirable attributes for cider production from germplasm collections and for making marker-assisted selections within breeding programs.