Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (24): 4825-4838.doi: 10.3864/j.issn.0578-1752.2024.24.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

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 Online:2024-12-16 Published:2024-12-23
  • Contact: LIANG HuiZhen

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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

Table 1

qRT-PCR primers for gene"

引物名称Primer name 正向引物Forward primer (5′-3′) 反向引物Reverse primer (5′-3′)
gene.SIN_1009601 AGTTCACACACAGAGAGCGTAG TGGATCCAGTCTCTGTTTTCCG
gene.SIN_1016284 TTGCTAGACCCCCTATCTCCAA TCTTCCTCTTTGATGTCCCACG
gene.SIN_1015871 GAAGACGTGAAGGTTTGGGTTG CACCATCCTTAACCTCAGCCTT
gene.SIN_1007252 TTCCCGAAAGTAGCAGAAGCAT GAGAAGGGTGTGGAGAAATCGT
gene.SIN_1007507 TCCAGATAAGTGGAGAACGCAC TTCTCCATGCTGGCTTTGATCT
gene.SIN_1018288 GTTCCTGCCCGTTTACAGAAAC ACTCCTGTCCGAGTTTGACATC
gene.SIN_1012480 AGCAAGCTGATGGATCTGTTGA TCTTGCATTTCTCCATGGCTCT
gene.SIN_1017673 AGGCCCCAAGAAGAATCTTCAG TCTTAGCCTTACCAGAGGAGCT
gene.SIN_1015154 ATGAGAGGCACGTGATGAGTTT CACGTTTCTTCCTTCGTGTTCC
gene.SIN_1002481 CCCCAGCGCATCATATTTTCAG GGAGTATAACCTCATCGGCTGG
SiTUB TGGTGACCTCAACCACCTCAT TGACAGCGAGTTTCCTGAGATC

Fig. 1

Methylation patterns of different heat-resistant sesame under high temperature stress A: Genome distribution of different methylation sites in different heat-resistant sesame; B: Percentage of different methylation sites of different heat-resistant sesame in the same site of the whole genome"

Fig. 2

DNA methylation patterns in different gene regions"

Fig. 3

DMRs statistics of different heat-resistant sesame seeds under high temperature stress (A) and distribution of different gene regions (B)"

Fig. 4

Differential methylation-related gene expression (A) and distribution in different gene regions (B) of different heat-resistant sesame cultivars under high temperature stress DMGs: DMR related genes; DEGs: Differential genes identified by transcriptome sequencing"

Fig. 5

Expression analysis (A) and functional annotation (B) of DMR-DEGsin different heat-resistant gene regions"

Fig. 6

Analysis of DMR-DEGs expression in different heat-resistant sesame under high temperature stress"

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