Transcriptomic Analysis Revealed the Discrepancy between Early-Ripening ‘Geneva Early’ and Late-Ripening ‘Hanfu’ Apple Cultivars during Fruit Development and Ripening

Apples (Malus × domestica Borkh.) can be categorized into early-, medium-, and late-ripening cultivars based on the length of the fruit developmental phases. The lengthening of the apple ripening period has a direct impact on its economic worth and market competitiveness, although the underlying mechanism is mostly unclear. In the current study, the development and maturation of the early-ripening ‘Geneva Early’ (GE) and late-ripening ‘Hanfu’ (HF) cultivars of apple fruit were studied using transcriptomics to detect and identify the changes of differential genes. Results showed that the two varieties had different ripening periods, but in both, the development process of fruit ripening required cell division, cell expansion, starch accumulation, and secondary metabolite accumulation. In the early stages of fruit development (G1 to G2), the GE’s fruit size was larger than HF’s, and the GO analysis revealed an enrichment in genes involved in the metabolism of fatty acids and carbon molecules. In G2 phase, the GE involved numerous regulatory factors of hormonal pathways, while in HF this phase was mainly enriched in the metabolism of sugars and carbohydrates. The results indicated that during GE development, the relevant genes regulating fruit development were expressed earlier than HF, which made fruit development enter the next development phase earlier, thereby shortening the fruit development phase. These findings contributed to an improved understanding of the molecular basis of apple ripening and provide a reliable reference for apple breeding using genomics.