DNA methylation affects freezing tolerance in winter rapeseed by mediating the expression of genes related to JA and CK pathways
Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezi...
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| Published in | Frontiers in genetics Vol. 13; p. 968494 |
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| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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17.08.2022
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| Abstract | Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezing stress. Therefore, in this study, the whole-genome DNA methylation map and transcriptome expression profiles of freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained. The genome-wide methylation assay exhibited lower levels of methylation in gene-rich regions. DNA methylation was identified in three genomic sequence contexts including CG, CHG and CHH, of which CG contexts exhibited the highest methylation levels (66.8%), followed by CHG (28.6%) and CHH (9.5%). Higher levels of the methylation were found in upstream 2 k and downstream 2 k of gene regions, whereas lowest levels were in the gene body regions. In addition, 331, 437, and 1720 unique differentially methylated genes (DMGs) were identified in three genomic sequence contexts in 17NS under freezing stress compared to the control. Function enrichment analysis suggested that most of enriched DMGs were involved in plant hormones signal transduction, phenylpropanoid biosynthesis and protein processing pathways. Changes of genes expression in signal transduction pathways for cytokinin (CK) and jasmonic acid (JA) implied their involvement in freezing stress responses. Collectively, these results suggested a critical role of DNA methylation in their transcriptional regulation in winter rapeseed under freezing stress. |
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| AbstractList | Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezing stress. Therefore, in this study, the whole-genome DNA methylation map and transcriptome expression profiles of freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained. The genome-wide methylation assay exhibited lower levels of methylation in gene-rich regions. DNA methylation was identified in three genomic sequence contexts including CG, CHG and CHH, of which CG contexts exhibited the highest methylation levels (66.8%), followed by CHG (28.6%) and CHH (9.5%). Higher levels of the methylation were found in upstream 2 k and downstream 2 k of gene regions, whereas lowest levels were in the gene body regions. In addition, 331, 437, and 1720 unique differentially methylated genes (DMGs) were identified in three genomic sequence contexts in 17NS under freezing stress compared to the control. Function enrichment analysis suggested that most of enriched DMGs were involved in plant hormones signal transduction, phenylpropanoid biosynthesis and protein processing pathways. Changes of genes expression in signal transduction pathways for cytokinin (CK) and jasmonic acid (JA) implied their involvement in freezing stress responses. Collectively, these results suggested a critical role of DNA methylation in their transcriptional regulation in winter rapeseed under freezing stress. Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezing stress. Therefore, in this study, the whole-genome DNA methylation map and transcriptome expression profiles of freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained. The genome-wide methylation assay exhibited lower levels of methylation in gene-rich regions. DNA methylation was identified in three genomic sequence contexts including CG, CHG and CHH, of which CG contexts exhibited the highest methylation levels (66.8%), followed by CHG (28.6%) and CHH (9.5%). Higher levels of the methylation were found in upstream 2 k and downstream 2 k of gene regions, whereas lowest levels were in the gene body regions. In addition, 331, 437, and 1720 unique differentially methylated genes (DMGs) were identified in three genomic sequence contexts in 17NS under freezing stress compared to the control. Function enrichment analysis suggested that most of enriched DMGs were involved in plant hormones signal transduction, phenylpropanoid biosynthesis and protein processing pathways. Changes of genes expression in signal transduction pathways for cytokinin (CK) and jasmonic acid (JA) implied their involvement in freezing stress responses. Collectively, these results suggested a critical role of DNA methylation in their transcriptional regulation in winter rapeseed under freezing stress.Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezing stress. Therefore, in this study, the whole-genome DNA methylation map and transcriptome expression profiles of freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained. The genome-wide methylation assay exhibited lower levels of methylation in gene-rich regions. DNA methylation was identified in three genomic sequence contexts including CG, CHG and CHH, of which CG contexts exhibited the highest methylation levels (66.8%), followed by CHG (28.6%) and CHH (9.5%). Higher levels of the methylation were found in upstream 2 k and downstream 2 k of gene regions, whereas lowest levels were in the gene body regions. In addition, 331, 437, and 1720 unique differentially methylated genes (DMGs) were identified in three genomic sequence contexts in 17NS under freezing stress compared to the control. Function enrichment analysis suggested that most of enriched DMGs were involved in plant hormones signal transduction, phenylpropanoid biosynthesis and protein processing pathways. Changes of genes expression in signal transduction pathways for cytokinin (CK) and jasmonic acid (JA) implied their involvement in freezing stress responses. Collectively, these results suggested a critical role of DNA methylation in their transcriptional regulation in winter rapeseed under freezing stress. |
| Author | Zheng, Guoqiang Dong, Xiaoyun Wei, Jiaping Shen, Yingzi Wang, Ying Li, Hui Cui, Junmei Liu, Zigang Zhu, Yajing Tian, Haiyan |
| AuthorAffiliation | 1 State Key Laboratory of Aridland Crop Science , Lanzhou , China 4 Economic Crop Research Institute , Henan Academy of Agricultural Sciences , Zhengzhou , China 3 College of Agronomy , Gansu Agricultural University , Lanzhou , China 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement , Nanjing Agricultural University , Nanjing , China |
| AuthorAffiliation_xml | – name: 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement , Nanjing Agricultural University , Nanjing , China – name: 4 Economic Crop Research Institute , Henan Academy of Agricultural Sciences , Zhengzhou , China – name: 1 State Key Laboratory of Aridland Crop Science , Lanzhou , China – name: 3 College of Agronomy , Gansu Agricultural University , Lanzhou , China |
| Author_xml | – sequence: 1 givenname: Jiaping surname: Wei fullname: Wei, Jiaping – sequence: 2 givenname: Yingzi surname: Shen fullname: Shen, Yingzi – sequence: 3 givenname: Xiaoyun surname: Dong fullname: Dong, Xiaoyun – sequence: 4 givenname: Yajing surname: Zhu fullname: Zhu, Yajing – sequence: 5 givenname: Junmei surname: Cui fullname: Cui, Junmei – sequence: 6 givenname: Hui surname: Li fullname: Li, Hui – sequence: 7 givenname: Guoqiang surname: Zheng fullname: Zheng, Guoqiang – sequence: 8 givenname: Haiyan surname: Tian fullname: Tian, Haiyan – sequence: 9 givenname: Ying surname: Wang fullname: Wang, Ying – sequence: 10 givenname: Zigang surname: Liu fullname: Liu, Zigang |
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| ContentType | Journal Article |
| Copyright | Copyright © 2022 Wei, Shen, Dong, Zhu, Cui, Li, Zheng, Tian, Wang and Liu. Copyright © 2022 Wei, Shen, Dong, Zhu, Cui, Li, Zheng, Tian, Wang and Liu. 2022 Wei, Shen, Dong, Zhu, Cui, Li, Zheng, Tian, Wang and Liu |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Yang Yuting, Ninxia Unversity, China Reviewed by: Jianfang Li, Guangzhou Laboratory, China Edited by: Yuchen Yang, School of Ecology, Sun Yat-sen University, China This article was submitted to Plant Genomics, a section of the journal Frontiers in Genetics |
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| SubjectTerms | differentially methylated genes DNA methylation freezing stress Genetics transcriptome winter rapeseed |
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| Title | DNA methylation affects freezing tolerance in winter rapeseed by mediating the expression of genes related to JA and CK pathways |
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