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Research article
Jiang-Lin Liao
Jiangxi Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3013-8823
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Background: High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence.
Results: After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (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). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains.
Conclusions: After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.
Keywords
Rice, Oryza sativa, High temperature, Epigenetics, Cytosine methylation
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View the published article at BMC Genomics.
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Posted 02 Jul, 2020
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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
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
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On 07 Jan, 2020
First submitted
On 04 Jan, 2020
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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.
Version 2
Posted 02 Jul, 2020
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
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, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence.
Results: After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (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). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains.
Conclusions: After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying 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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