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DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)
Ramesh S. Bhat
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1120-7088
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This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Research Notes.
Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.
Keywords
Peanut ∙ Genotypes differing for foliar disease response ∙ DNA methylome ∙ Transcriptome ∙ Differentially methylated genes ∙ expression levels of methylated genes
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Posted 26 Dec, 2019
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On 07 Jan, 2020
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On 20 Dec, 2019
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On 19 Dec, 2019
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Received 10 Dec, 2019
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Received 10 Dec, 2019
Reviewer #2 agreed
On 29 Nov, 2019
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On 22 Jul, 2019
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Reviewer #1 agreed
On 22 Jul, 2019
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This preprint is under consideration at BMC Research Notes. A preprint is 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 note
DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)
Ramesh S. Bhat
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1120-7088
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
Version 2
Posted 26 Dec, 2019
Published
On 07 Jan, 2020
No community comments so far
Editor assigned
On 20 Dec, 2019
Submission checks complete
On 19 Dec, 2019
Editor invited
On 19 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 17 Dec, 2019
Review #1 received
Received 10 Dec, 2019
Review #2 received
Received 10 Dec, 2019
Reviewer #2 agreed
On 29 Nov, 2019
Submission checks complete
On 22 Jul, 2019
Reviewers invited
Invitations sent on 22 Jul, 2019
Reviewer #1 agreed
On 22 Jul, 2019
Editor assigned
On 21 Jul, 2019
First submitted
On 20 Jul, 2019
Editor invited
On 20 Jul, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Cell Biology & Physiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Research Notes.
Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.