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

作者：Libo Xing, Youmei Li, Siyan Qi, Chenguang Zhang, Wenchun Ma, Xiya Zuo, Jiayan Liang, Cai Gao, Jia Pen, Kamran Shah, Dong Zhang, Na An, Caiping Zhao, Mingyu Han, Juan Zhao · 发表于：Plant and Cell Physiology · 年份：2019 · DOI：10.1093/pcp/pcz080 · 被引用次数：60 · 研究领域：Plant Molecular Biology Research、Plant Physiology and Cultivation Studies、Plant Reproductive Biology

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 nonexpressed 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 indi...