Biochemical and Volatile Compound Variation in Apple (Malus domestica) Cultivars According to Fruit Size: Implications for Quality and Breeding

Apple fruit size affects market value, yet its impact on biochemical and sensory traits is poorly understood. This study provides the first comprehensive metabolic profiling of peel and flesh across five cultivars, including red-fleshed ‘Baya Marisa’ and four white-fleshed cultivars (‘Opal’, ‘Red Boskoop’, ‘Crown Prince Rudolf’, and ‘Topaz’), in two size groups: large (>70 mm, Class I) and small (55–70 mm, Class II). Sugars and organic acids varied by cultivar but not consistently by size. White-fleshed small apples had higher flesh phenolics, suggesting a dilution effect, while ‘Baya Marisa’ showed no size-related phenolic differences, indicating potential genetic influence. VOCs were mainly aldehydes, with cultivar-specific differences outweighing size effects. Fruit maturity and controlled-atmosphere storage likely limited ester production. These findings demonstrate that fruit size influences certain biochemical traits in a cultivar-dependent manner. This study’s novelty lies in combining tissue-specific metabolite profiling with size comparisons across multiple cultivars, providing practical insights for breeders, nutritionists, and the fruit industry. This work supports size-specific quality assessment and valorization of smaller apples for fresh consumption and processing, challenging conventional market classifications based solely on size.