Malate accumulation and transcriptome patterns during fruit development in sweet cherry (Prunus avium L.)

Background Fruit acidity serves as a primary determinant of organoleptic quality in fleshy fruits. Malate predominates and significantly contributes to the fruit flavor profile and palatability in sweet cherry. However, the molecular mechanisms regulating malate accumulation in fruit cells of this species remain poorly understood. Results In this study, we performed quantitative profiling of TA in 97 sweet cherry cultivars at maturity, establishing a phenotyping framework for acidity classification. Temporal metabolomic analyses identified malate as the dominant organic acid throughout fruit development, exhibiting a biphasic accumulation pattern. Integrated transcriptomic profiling of high-acid and low-acid fruits across developmental stages revealed 3,643 differentially expressed genes, with functional annotation highlighting six structural genes ( PavPEPC3 , PavMDH1 , PavME1 , PavPHA5 , PavALMT1 , and PavALMT6 ) whose expression strongly correlated with malate content dynamics. Transcriptional regulatory network analysis further identified four candidate transcription factors, among which PavWRKY33 and PavbHLH149 were co-localized with a chromosome 6 quantitative trait locus (QTL)‌ associated with TA variation. Conclusion Our findings establish a comprehensive phenotyping framework for systematic acidity classification in sweet cherry, while elucidating the core genetic regulatory network governing malate accumulation. These mechanistic insights provide a robust scientific foundation for precision breeding strategies aimed at optimizing fruit quality through targeted modulation of acidity profiles.