Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus
Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (<i>Oryza sativa</i> L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to i...
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MDPI AG
2020-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/16/5753 |
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| author | Linying Li Yuqing He Xueying Zhang Hehong Zhang Zongtao Sun Junmin Li Gaojie Hong |
| author_facet | Linying Li Yuqing He Xueying Zhang Hehong Zhang Zongtao Sun Junmin Li Gaojie Hong |
| author_sort | Linying Li |
| collection | DOAJ |
| description | Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (<i>Oryza sativa</i> L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified in CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. Additionally, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 102 genes with positive correlation and 71 genes with negative correlation between methylation level at promoter regions and gene expression. Key genes associated with maintaining DNA methylation in rice were analyzed by RT-qPCR and indicated that <i>OsDMT702</i> might be responsible for the global increase of DNA methylation level in rice under RBSDV stress. Our results suggest important roles of rice DNA methylation in response to RBSDV and provide potential target genes for rice antiviral immunity. |
| first_indexed | 2024-03-10T17:38:29Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T17:38:29Z |
| publishDate | 2020-08-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4e5a182022674e259fd94c2d6e73561f2023-11-20T09:46:28ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-08-012116575310.3390/ijms21165753Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf VirusLinying Li0Yuqing He1Xueying Zhang2Hehong Zhang3Zongtao Sun4Junmin Li5Gaojie Hong6College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, ChinaThe State Key Laboratory Breeding Base for Sustainable Control of Pests and Disease, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaThe State Key Laboratory Breeding Base for Sustainable Control of Pests and Disease, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaThe State Key Laboratory Breeding Base for Sustainable Control of Pests and Disease, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, ChinaRice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice (<i>Oryza sativa</i> L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified in CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. Additionally, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 102 genes with positive correlation and 71 genes with negative correlation between methylation level at promoter regions and gene expression. Key genes associated with maintaining DNA methylation in rice were analyzed by RT-qPCR and indicated that <i>OsDMT702</i> might be responsible for the global increase of DNA methylation level in rice under RBSDV stress. Our results suggest important roles of rice DNA methylation in response to RBSDV and provide potential target genes for rice antiviral immunity.https://www.mdpi.com/1422-0067/21/16/5753DNA methylationriceRBSDVdifferentially methylated genesgene expression |
| spellingShingle | Linying Li Yuqing He Xueying Zhang Hehong Zhang Zongtao Sun Junmin Li Gaojie Hong Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus International Journal of Molecular Sciences DNA methylation rice RBSDV differentially methylated genes gene expression |
| title | Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus |
| title_full | Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus |
| title_fullStr | Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus |
| title_full_unstemmed | Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus |
| title_short | Alterations of Rice (<i>Oryza sativa</i> L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus |
| title_sort | alterations of rice i oryza sativa i l dna methylation patterns associated with gene expression in response to rice black streaked dwarf virus |
| topic | DNA methylation rice RBSDV differentially methylated genes gene expression |
| url | https://www.mdpi.com/1422-0067/21/16/5753 |
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