Harvest maturity significantly affects the quality of apple fruit in post‐harvest storage process. Although the regulatory mechanisms underlying fruit ripening have been studied, the associated epigenetic modifications remain unclear. Thus, we compared the DNA methylation changes and the transcriptional responses of mature fruit (MF) and immature fruit (NF). There were significant correlations between DNA methylation and gene expression. Moreover, the sugar contents (sucrose, glucose, and fructose) were higher in MF than in NF, whereas the opposite pattern was detected for the starch content. The expression‐level differences were due to DNA methylations and ultimately resulted in diverse fruit textures and ripeness. Furthermore, the higher ethylene, auxin, and abscisic acid levels in MF than in NF, which influenced the fruit texture and ripening, were associated with multiple differentially expressed genes in hormone synthesis, signaling, and response pathways (ACS, ACO, ZEP, NCED, and ABA2) that were regulated by DNA methylations. Multiple transcription factor genes involved in regulating fruit ripening and quality via changes in DNA methylation were identified, including MIKCC‐type MADS‐box genes and fruit ripening‐related genes (NAP, SPL, WRKY, and NAC genes). These findings reflect the diversity in the epigenetic regulation of gene expression and may be relevant for elucidating the epigenetic regulatory mechanism underlying the ripening and quality of apple fruit with differing harvest maturity.

中文翻译：

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不同采收成熟度苹果果实品质和成熟度的表观基因组调控机制

采收成熟度显着影响苹果采后贮藏过程中的品质。尽管已经研究了果实成熟的调控机制，但相关的表观遗传修饰仍不清楚。因此，我们比较了成熟果实（MF）和未成熟果实（NF）的DNA甲基化变化和转录反应。 DNA甲基化与基因表达之间存在显着相关性。此外，MF 中的糖含量（蔗糖、葡萄糖和果糖）高于 NF 中的含量，而淀粉含量则检测到相反的模式。表达水平的差异是由于 DNA 甲基化造成的，最终导致了不同的水果质地和成熟度。此外，MF 中的乙烯、生长素和脱落酸水平高于 NF，这影响了果实的质地和成熟，与激素合成、信号传导和响应途径中多个差异表达的基因有关。ACS、ACO、ZEP、NCED， 和ABA2）受 DNA 甲基化调节。鉴定出多个通过 DNA 甲基化变化参与调节果实成熟和品质的转录因子基因，包括 MIKCC-类型MADS盒基因和果实成熟相关基因（小憩,声压级,WRKY， 和NAC基因）。这些发现反映了基因表达表观遗传调控的多样性，可能有助于阐明不同采收成熟度苹果果实成熟和品质的表观遗传调控机制。