Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China.
Int J Mol Sci. 2024 Oct 16;25(20):11100. doi: 10.3390/ijms252011100.
Plant grafting using dwarfing rootstocks is one of the important cultivation measures in the sweet cherry () industry. In this work, we aimed to explore the effects of the dwarfing rootstock "Pd1" () on sweet cherry 'Shuguang2' scions by performing morphological observations using the paraffin slice technique, detecting GA (gibberellin) and IAA (auxin) contents using UPLC-QTRAP-MS (ultra-performance liquid chromatography coupled with a hybrid triple quadrupole-linear ion trap mass spectrometer), and implementing integration analyses of the epigenome and transcriptome using whole-genome bisulfite sequencing and transcriptome sequencing. Anatomical analysis indicated that the cell division ability of the SAM (shoot apical meristem) in dwarfing plants was reduced. Pd1 rootstock significantly decreased the levels of GAs and IAA in sweet cherry scions. Methylome analysis showed that the sweet cherry genome presented 15.218.6%, 59.8861.55%, 28.0933.78%, and 2.995.28% methylation at total C, CG, CHG, and CHH sites, respectively. Shoot tips from dwarfing plants exhibited a hypermethylated pattern mostly due to increased CHH methylation, while leaves exhibited a hypomethylated pattern. According to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, DMGs (differentially methylated genes) and DEGs (differentially expressed genes) were enriched in hormone-related GO terms and KEGG pathways. Global correlation analysis between methylation and transcription revealed that mCpG in the gene body region enhanced gene expression and mCHH in the region near the TSS (transcription start site) was positively correlated with gene expression. Next, we found some hormone-related genes and TFs with significant changes in methylation and transcription, including , , , , , , and . This study presents a methylome map of the sweet cherry genome, revealed widespread DNA methylation alterations in scions caused by dwarfing rootstock, and obtained abundant genes with methylation and transcription alterations that are potentially involved in rootstock-induced growth changes in sweet cherry scions. Our findings can lay a good basis for further epigenetic studies on sweet cherry dwarfing and provide valuable new insight into understanding rootstock-scion interactions.
利用矮化砧木进行植物嫁接是甜樱桃（）产业中的重要栽培措施之一。在这项工作中，我们旨在通过石蜡切片技术进行形态观察，使用 UPLC-QTRAP-MS（超高效液相色谱-串联三重四极杆-线性离子阱质谱）检测 GA（赤霉素）和 IAA（生长素）含量，并对全基因组亚硫酸氢盐测序和转录组测序进行整合分析，来探索矮化砧木“Pd1”（）对甜樱桃品种“曙光 2 号”接穗的影响。解剖分析表明，矮化砧木 SAM（茎尖分生组织）的细胞分裂能力降低。Pd1 根砧显著降低了甜樱桃接穗中 GA 和 IAA 的含量。甲基组分析表明，甜樱桃基因组在总 C、CG、CHG 和 CHH 位点的甲基化水平分别为 15.2%18.6%、59.88%61.55%、28.09%33.78%和 2.99%5.28%。矮化砧木的茎尖表现出超甲基化模式，主要是由于 CHH 甲基化增加，而叶片表现出低甲基化模式。根据 GO（基因本体论）和 KEGG（京都基因与基因组百科全书）分析，DMGs（差异甲基化基因）和 DEGs（差异表达基因）在激素相关的 GO 术语和 KEGG 途径中富集。甲基化和转录的全局相关性分析表明，基因体区域的 mCpG 增强了基因表达，而 TSS（转录起始位点）附近区域的 mCHH 与基因表达呈正相关。接下来，我们发现一些激素相关基因和转录因子的甲基化和转录发生了显著变化，包括、、、、、、和。本研究提供了甜樱桃基因组的甲基组图谱，揭示了矮化砧木引起接穗中广泛的 DNA 甲基化改变，并获得了大量与甲基化和转录改变相关的基因，这些基因可能参与甜樱桃接穗中由砧木诱导的生长变化。我们的研究结果为甜樱桃矮化的进一步表观遗传学研究奠定了良好的基础，并为理解砧木-接穗相互作用提供了新的见解。
