中国农业科学 ›› 2024, Vol. 57 ›› Issue (24): 4825-4838.doi: 10.3864/j.issn.0578-1752.2024.24.001

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

高温胁迫下芝麻全基因组甲基化差异及关联基因表达分析

苏小雨(), 谭政委, 李春明, 李磊, 鲁丹丹, 余永亮, 董薇, 安素妨, 杨青, 孙瑶, 许兰杰, 杨红旗, 梁慧珍()   

  1. 河南省农业科学院中药材研究所/河南省中药材资源保护与利用重点实验室,郑州 450002
  • 收稿日期:2024-08-04 接受日期:2024-09-30 出版日期:2024-12-16 发布日期:2024-12-23
  • 通信作者:
    梁慧珍,E-mail:
  • 联系方式: 苏小雨,E-mail:suxiaoyu_2014@163.com。
  • 基金资助:
    国家自然科学基金青年基金(32301952); 财政部和农业农村部:国家现代农业产业技术体系(CARS-21); 河南省杰出外籍科学家工作室(GZS2024025)

Analysis of Genome-Wide Methylation Differences and Associated Gene Expression of Sesame Varieties Under High Temperature Stress

SU XiaoYu(), TAN ZhengWei, LI ChunMing, LI Lei, LU DanDan, YU YongLiang, DONG Wei, AN SuFang, YANG Qing, SUN Yao, XU LanJie, YANG HongQi, LIANG HuiZhen()   

  1. Institute of Chinese Herbal Medicines, Henan Academy of Agricultural Sciences/Provincial Key Laboratory of Conservation and Utilization of Traditional Chinese Medicine Resources, Zhengzhou 450002
  • Received:2024-08-04 Accepted:2024-09-30 Published:2024-12-16 Online:2024-12-23

摘要:

【目的】探究高温胁迫下不同耐热型芝麻品种全基因组DNA甲基化差异及其与关联基因表达的关系,以深入理解DNA甲基化在芝麻响应高温胁迫中的调控机制,为芝麻耐热性育种提供理论依据。【方法】选取郑太芝3号(耐热型)和山东白芝麻(敏感型)2个芝麻品种作为试验材料,在高温(41 ℃)和对照(30 ℃)条件下培养10 d。采用纳米孔测序技术(nanopore sequencing)对2种芝麻品种的基因组DNA进行甲基化测序,并通过转录组测序分析关联基因的表达变化。使用Minimap 2软件进行参考基因组序列比对,Tombo软件检测5mC、CpG和6mA甲基化位点,并基于基因组分割方法检测差异甲基化区域(DMRs)。最后,对DMRs关联的差异表达基因(DMR-DEGs)进行GO、COG和KEGG功能注释及通路分析。【结果】在高温胁迫下,郑太芝3号和山东白芝麻的全基因组DNA甲基化模式发生显著变化。郑太芝3号的m6A和胞嘧啶甲基化(mC)含量均有所增加,而山东白芝麻则呈现下降趋势。全基因组范围内共鉴定出621个(郑太芝3号)和374个(山东白芝麻)DMRs,主要分布在启动子和基因间区域。进一步分析发现,这些DMRs与113个(郑太芝3号)和56个(山东白芝麻)差异表达基因(DMR-DEGs)显著相关,且去甲基化的DMRs与基因表达上调密切相关。功能注释结果显示,这些DMR-DEGs主要参与碳水化合物运输和代谢、翻译后修饰、蛋白质转换、信号转导和次生代谢产物生物合成等生物学过程。【结论】揭示了高温胁迫下不同耐热型芝麻品种全基因组DNA甲基化差异及其与关联基因表达的关系。耐热型芝麻郑太芝3号在高温胁迫下通过增加DNA甲基化水平来调控相关基因的表达,而敏感型芝麻山东白芝麻则表现出甲基化水平下降的趋势。特别是CpG位点的甲基化动态变化在调控芝麻高温胁迫响应中起重要作用。

关键词: 芝麻, 高温胁迫, 耐热性, DNA甲基化, 基因表达

Abstract:

【Objective】This study aimed to explore the differences in genome-wide DNA methylation patterns and their relationships with associated gene expression in different heat-tolerant sesame varieties under high temperature stress, in order to gain a deeper understanding of the regulatory mechanisms of DNA methylation in sesame's response to high temperature stress, and to provide a theoretical basis for heat tolerance breeding in sesame. 【Method】Two sesame varieties, Zhengtaizhi 3 (heat-tolerant) and Shandong White Sesame (heat-sensitive), were selected as experimental materials and cultivated under high temperature (41 ℃) and control (30 ℃) conditions for 10 days. Nanopore sequencing technology was used to conduct methylation sequencing of the genomic DNA of these two sesame varieties, and transcriptome sequencing was performed to analyze changes in the expression of associated genes. Minimap 2 software was utilized for reference genome sequence alignment, and Tombo software was employed to detect 5mC, CpG, and 6mA methylation sites. Differentially methylated regions (DMRs) were identified based on a genome segmentation approach. Finally, functional annotation and pathway analysis of DMR-associated differentially expressed genes (DMR-DEGs) were conducted using GO, COG, and KEGG databases. 【Result】Under high temperature stress, significant changes were observed in the genome-wide DNA methylation patterns of both Zhengtaizhi 3 and Shandong White Sesame. Specifically, the m6A and cytosine methylation (mC) contents of Zhengtaizhi 3 increased, while those of Shandong White Sesame decreased. A total of 621 DMRs (Zhengtaizhi 3) and 374 DMRs (Shandong White Sesame) were identified across the entire genome, mainly distributed in promoter and intergenic regions. Further analysis revealed that these DMRs were significantly associated with 113 DMR-DEGs (Zhengtaizhi 3) and 56 DMR-DEGs (Shandong White Sesame), respectively, and that demethylated DMRs were closely related to upregulated gene expression. Functional annotation results indicated that these DMR-DEGs were primarily involved in biological processes such as carbohydrate transport and metabolism, posttranslational modification, protein turnover, signal transduction, and secondary metabolite biosynthesis. 【Conclusion】This study revealed the differences in genome-wide DNA methylation patterns and their relationships with associated gene expression in different heat-tolerant sesame varieties under high temperature stress. Zhengtaizhi 3, a heat-tolerant sesame variety, regulated the expression of related genes by increasing DNA methylation levels under high temperature stress, while Shandong White Sesame, a heat-sensitive variety, exhibited a decreasing trend in methylation levels. In particular, the dynamic changes in CpG site methylation played a crucial role in regulating sesame's response to high temperature stress. These findings provide new insights and theoretical support for understanding the mechanisms of sesame heat tolerance and for heat tolerance breeding.

Key words: sesame, high temperature stress, heat tolerance, DNA methylation, gene expression