两种开花习性差异显著的苹果品种中花发育的表观基因组调控机制

doi:10.1016/j.jia.2025.12.065

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (6): 2414-2433.DOI: 10.1016/j.jia.2025.12.065

两种开花习性差异显著的苹果品种中花发育的表观基因组调控机制

收稿日期:2024-11-13 修回日期:2025-12-31 接受日期:2025-09-25 出版日期:2026-06-20 发布日期:2026-05-06

Epigenomic regulation of flowering in apple: Insights from two contrasting cultivars

Jiahui Song^1*, Lin Li^1*, Jiahe Wang^1*, Yuqing Xia¹, Heyu Zhang¹, Jingwen Li¹, Juanjuan Ma¹, Dong Zhang¹, Jiangping Mao¹, Na An², Libo Xing^1#

¹College of Horticulture, Northwest A&F University, Yangling 712100, China
²College of Life Sciences, Northwest A&F University, Yangling 712100, China

Received:2024-11-13 Revised:2025-12-31 Accepted:2025-09-25 Online:2026-06-20 Published:2026-05-06
About author:Jiahui Song, E-mail: 2542590209@qq.com; Lin Li, E-mail: 1957491233@qq.com; Jiahe Wang, E-mail: 1028925699@qq.com; #Correspondence Libo Xing, E-mail: libo_xing@nwafu.edu.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the National Natural Science Foundation of China (32472668 and 32072522).

摘要/Abstract

摘要：

开花是木本果树生命周期中形成产量的必要前提与核心基础。尽管目前对花诱导及开花的调控机制已有较多研究，但相关表观遗传修饰的调控特征仍有待深入解析。本研究以开花习性差异显著的‘秦冠’（QA）和‘富士’（FA）苹果为试验材料，系统分析了两者腋芽全基因组水平的DNA甲基化变异及转录组响应特征。结果表明，FA在CG、CHG、CHH三种序列环境中的DNA甲基化水平分别为19.35%、62.96%和17.68%，而QA对应的甲基化水平分别为19.64%、62.49%和17.86%。不同基因区域的高甲基化或低甲基化差异甲基化区域（DMRs）数量差异，可显著调控相关基因的表达上调或下调。DNA甲基化对基因表达的调控具有双向性，其调控效应依赖于CG、CHG、CHH的序列环境，同时与甲基化位点在基因上的分布区域密切相关。此外，MIKC^c型MADS-box基因，以及光周期、年龄、赤霉素（GA）、蔗糖等多条开花通路中多个关键开花基因的转录水平，通过DNA甲基化修饰发生显著分化，这是导致QA与FA开花习性差异的重要原因。具体而言，花分生组织特征基因（FT、LEAFY、AP1、SOC1）在QA中的表达量显著高于FA，而开花抑制基因（SVP、AGL15、AGL18）的表达趋势则完全相反。同时，激素合成通路中的差异表达基因（DEGs）及其对应的差异甲基化区域（DMRs），导致两种苹果品种的多种激素水平存在显著差异，进而引发腋芽萌发及开花习性的分化。本研究结果揭示了基因表达表观遗传调控的多样性特征，为阐明苹果腋芽开花的表观遗传调控机制提供了重要理论依据。

Abstract:

Flowering is a necessary condition and basis for yield in the life cycle of woody fruit trees. Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain poorly characterized. We identified genome-wide DNA methylation changes and the transcriptional responses in axillary buds of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasting flowering behaviors. The DNA methylation levels were 19.35, 62.96 and 17.68% in FA, and 19.64, 62.49 and 17.86% in QA in the CG, CHG and CHH contexts, respectively. The number of hypermethylated and hypomethylated differentially methylated regions (DMRs) in different regions contributed to significantly up- and downregulated gene expression. DNA methylation can positively or negatively regulate gene expression depending on the CG, CHG and CHH contexts and their locations in different regions. Additionally, the huge differences in transcription of MIKC^c-type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, aging, GA and sugar) by changing DNA methylation, contributed to contrasting flowering behaviors in both QA and FA. Specifically, the floral meristem identity genes (i.e., FT, LEAFY, AP1 and SOC1) exhibited significantly higher expression in QA than FA, but the floral repressors (i.e., SVP, AGL15, and AGL18) showed the opposite trend. Significant differences in multiple hormone levels were due to differentially expressed genes (DEGs) and their DMRs in hormone synthesis pathways, leading to both contrasting axillary bud outgrowth and flowering behaviors. These findings reflect the diversity in the epigenetic regulation of gene expression and may be helpful for elucidating the epigenetic regulatory mechanism underlying the axillary bud flowering in apple.

Key words: apple trees , DMRs , RNA sequencing , axillary bud flowering , DNA methylation

Jiahui Song, Lin Li, Jiahe Wang, Yuqing Xia, Heyu Zhang, Jingwen Li, Juanjuan Ma, Dong Zhang, Jiangping Mao, Na An, Libo Xing. 两种开花习性差异显著的苹果品种中花发育的表观基因组调控机制[J]. Journal of Integrative Agriculture, 2026, 25(6): 2414-2433.

Jiahui Song, Lin Li, Jiahe Wang, Yuqing Xia, Heyu Zhang, Jingwen Li, Juanjuan Ma, Dong Zhang, Jiangping Mao, Na An, Libo Xing. Epigenomic regulation of flowering in apple: Insights from two contrasting cultivars[J]. Journal of Integrative Agriculture, 2026, 25(6): 2414-2433.

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两种开花习性差异显著的苹果品种中花发育的表观基因组调控机制

Epigenomic regulation of flowering in apple: Insights from two contrasting cultivars

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