Comparative RNA-sequencing and DNA methylation analyses of apple (Malus domestica Borkh.) buds with diverse flowering capabilities reveal novel insights into the regulatory mechanisms of flower bud formation.
Comparative RNA-sequencing and DNA methylation analyses of apple (Malus domestica Borkh.) buds with diverse flowering capabilities reveal novel insights into the regulatory mechanisms of flower bud formation.
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对具有不同开花能力的苹果芽进行比较 RNA 测序和 DNA 甲基化分析，揭示了对花芽形成调控机制的新见解。
DOI：
10.1093/pcp/pcz080
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发表时间：
2019-08
影响因子：
4.9
通讯作者：
Juan Zhao
中科院分区：
文献类型：
--
作者：
Libo Xing;Siyan Qi;Youmei Li;Chenguang Zhang;Wenchun Ma;Xiya Zuo;Jiayan Liang;Cai Gao;Pen Jia;Kamran Shah;Dong Zhang;Na An;Caiping Zhao;Mingyu Han;Juan Zhao
在植物中，DNA甲基化（即染色质修饰）对包括生长、发育和开花在内的各种生物过程都很重要。由于富士苹果树为互生果树，成熟期长，花蕾质量差，我们利用不同开花能力的花蕾类型来研究影响花蕾形成的表观遗传调控机制。我们研究了选定的苹果芽类型的DNA甲基化变化和转录反应。我们观察到，在苹果基因组中，CG、CHG和CHH序列的甲基化率分别约为79.5%、67.4%和23.7%。对于每个序列背景，差异甲基化区域在分析的苹果芽类型中表现出不同的甲基化模式。全球甲基化和转录分析显示，非表达基因或低水平表达的基因在基因体区域高度甲基化，表明基因体甲基化与基因表达呈负相关。此外，启动子甲基化的基因比启动子未甲基化的基因表达更高，这表明启动子甲基化与基因表达呈正相关。此外，开花相关基因（如SOC1、AP1和SPLs）和一些转录因子基因（如GATA、bHLH、bZIP和WOX）在距芽中高表达（开花率最高），但与基因体区域的低甲基化水平相关。研究结果表明，在不同开花能力的苹果花蕾中，DNA甲基化与基因表达之间存在潜在的相关性，表明表观遗传调控机制影响了苹果花蕾的形成。
In plants, DNA methylation (i.e., chromatin modification) is important for various biological processes, including growth, development, and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4%, and 23.7% of the CG, CHG, and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that non-expressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g., SOC1, AP1, and SPLs) and some transcription factor genes (e.g., GATA, bHLH, bZIP, and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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