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Research article
Jiang-Lin Liao
Jiangxi Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3013-8823
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
High temperatures are detrimental to rice yield and quality, especially at night. Due to the predicted increases in global warming, it is imperative that crops are able to adapt to high night temperatures (HNTs) in the near future. DNA methylation is a potential mechanism for controlling gene activity and cellular phenotype under adversely environment without changing nucleotide sequence.
Results
Here, we reported that few CG and CHG contexts but CHH context in rice genome was strongly induced by HNT to occur cytosine methylation variation between two coisogenic rice strains with significant difference in heat tolerance. Methylation variations occurred mainly on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, two basal transcriptional factor TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31 were fully demethylated in the downstream 358-359 bp and 2-60 bp under HNT in the heat-tolerant strain, respectively. Various genes involved in ABA-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694), were induced by HNT to occur methylation variation on successive cytosines in the gene promoter regions of the heat-tolerant strain. Varidation among the typical heat-tolerant group and heat-sensitive group of rice germplasms, methylation rate of the cytosines in gene promoter region for gene PPR was higher and gene expression was suppressed in the heat-sensitive group, comparing to the heat-tolerant group.
Conclusions
The CHH context in rice genome was the main context type to occur cytosine methylation variation under HNT between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes related to abscisic acid-related oxidation and ROS scavenging contributes to rice heat tolerance. These findings provide bases to explain the molecular mechanisms behind rice heat tolerance.
Keywords
Rice, Oryza sativa, High temperature, Epigenetics, Cytosine methylation
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Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Reviewer #1 agreed
On 01 Jul, 2020
Editor assigned
On 30 Jun, 2020
Reviewers invited
Invitations sent on 30 Jun, 2020
Submission checks complete
On 29 Jun, 2020
Editor invited
On 29 Jun, 2020
Version 1
Posted 16 Jan, 2020
No comments provided
Editorial decision: Major revision
On 01 Jun, 2020
Review #2 received
Received 28 May, 2020
Reviewer #2 agreed
On 07 May, 2020
Review #1 received
Received 19 Mar, 2020
Reviewer #1 agreed
On 05 Mar, 2020
Reviewers invited
Invitations sent on 30 Jan, 2020
Editor invited
On 13 Jan, 2020
Editor assigned
On 08 Jan, 2020
Submission checks complete
On 07 Jan, 2020
First submitted
On 04 Jan, 2020
Metrics
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PDF Downloads: ...
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Jiang-Lin Liao
Jiangxi Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3013-8823
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Reviewer #1 agreed
On 01 Jul, 2020
Editor assigned
On 30 Jun, 2020
Reviewers invited
Invitations sent on 30 Jun, 2020
Submission checks complete
On 29 Jun, 2020
Editor invited
On 29 Jun, 2020
Version 1
Posted 16 Jan, 2020
No comments provided
Editorial decision: Major revision
On 01 Jun, 2020
Review #2 received
Received 28 May, 2020
Reviewer #2 agreed
On 07 May, 2020
Review #1 received
Received 19 Mar, 2020
Reviewer #1 agreed
On 05 Mar, 2020
Reviewers invited
Invitations sent on 30 Jan, 2020
Editor invited
On 13 Jan, 2020
Editor assigned
On 08 Jan, 2020
Submission checks complete
On 07 Jan, 2020
First submitted
On 04 Jan, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background
High temperatures are detrimental to rice yield and quality, especially at night. Due to the predicted increases in global warming, it is imperative that crops are able to adapt to high night temperatures (HNTs) in the near future. DNA methylation is a potential mechanism for controlling gene activity and cellular phenotype under adversely environment without changing nucleotide sequence.
Results
Here, we reported that few CG and CHG contexts but CHH context in rice genome was strongly induced by HNT to occur cytosine methylation variation between two coisogenic rice strains with significant difference in heat tolerance. Methylation variations occurred mainly on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, two basal transcriptional factor TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31 were fully demethylated in the downstream 358-359 bp and 2-60 bp under HNT in the heat-tolerant strain, respectively. Various genes involved in ABA-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694), were induced by HNT to occur methylation variation on successive cytosines in the gene promoter regions of the heat-tolerant strain. Varidation among the typical heat-tolerant group and heat-sensitive group of rice germplasms, methylation rate of the cytosines in gene promoter region for gene PPR was higher and gene expression was suppressed in the heat-sensitive group, comparing to the heat-tolerant group.
Conclusions
The CHH context in rice genome was the main context type to occur cytosine methylation variation under HNT between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes related to abscisic acid-related oxidation and ROS scavenging contributes to rice heat tolerance. These findings provide bases to explain the molecular mechanisms behind rice heat tolerance.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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