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Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response

Epigenetic mechanisms in crops have emerged as a fundamental factor in plant adaptation and acclimation to biotic and abiotic stresses. Among described epigenetic mechanisms, DNA methylation has been defined as the most studied epigenetic modification involved in several developmental processes. It...

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Autores principales: Gallo‐Franco, Jenny Johana, Ghneim‐Herrera, Thaura, Tobar‐Tosse, Fabian, Romero, Miguel, Chaura, Juliana, Quimbaya, Mauricio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9414936/
https://www.ncbi.nlm.nih.gov/pubmed/36051226
http://dx.doi.org/10.1002/pld3.430
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author Gallo‐Franco, Jenny Johana
Ghneim‐Herrera, Thaura
Tobar‐Tosse, Fabian
Romero, Miguel
Chaura, Juliana
Quimbaya, Mauricio
author_facet Gallo‐Franco, Jenny Johana
Ghneim‐Herrera, Thaura
Tobar‐Tosse, Fabian
Romero, Miguel
Chaura, Juliana
Quimbaya, Mauricio
author_sort Gallo‐Franco, Jenny Johana
collection PubMed
description Epigenetic mechanisms in crops have emerged as a fundamental factor in plant adaptation and acclimation to biotic and abiotic stresses. Among described epigenetic mechanisms, DNA methylation has been defined as the most studied epigenetic modification involved in several developmental processes. It has been shown that contrasting methylation marks are associated with gene expression variations between cultivated and wild crop species. In this study, we analyzed single‐base resolution methylome maps for Oryza sativa (a cultivated species) and Oryza glumaepatula (a wild species) genotypes grown under control conditions. Our results showed that overall, genome‐wide methylation profiles are mainly conserved between both species, nevertheless, there are several differentially methylated regions with species‐specific methylation patterns. In addition, we analyzed the association of identified DNA methylation marks in relation with Aluminum‐tolerance levels of studied genotypes. We found several differentially methylated regions (DMRs) and DMR‐associated genes (DAGs) that are linked with Al tolerance. Some of these DAGs have been previously reported as differentially expressed under Al exposure in O. sativa . Complementarily a Transposable Elements (TE) analysis revealed that specific aluminum related genes have associated‐TEs potentially regulated by DNA methylation. Interestingly, the DMRs and DAGs between Al‐tolerant and susceptible genotypes were different between O. sativa and O. glumaepatula, suggesting that methylation patterns related to Al responses are unique for each rice species. Our findings provide novel insights into DNA methylation patterns in wild and cultivated rice genotypes and their possible role in the regulation of plant stress responses.
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spelling pubmed-94149362022-08-31 Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response Gallo‐Franco, Jenny Johana Ghneim‐Herrera, Thaura Tobar‐Tosse, Fabian Romero, Miguel Chaura, Juliana Quimbaya, Mauricio Plant Direct Original Research Epigenetic mechanisms in crops have emerged as a fundamental factor in plant adaptation and acclimation to biotic and abiotic stresses. Among described epigenetic mechanisms, DNA methylation has been defined as the most studied epigenetic modification involved in several developmental processes. It has been shown that contrasting methylation marks are associated with gene expression variations between cultivated and wild crop species. In this study, we analyzed single‐base resolution methylome maps for Oryza sativa (a cultivated species) and Oryza glumaepatula (a wild species) genotypes grown under control conditions. Our results showed that overall, genome‐wide methylation profiles are mainly conserved between both species, nevertheless, there are several differentially methylated regions with species‐specific methylation patterns. In addition, we analyzed the association of identified DNA methylation marks in relation with Aluminum‐tolerance levels of studied genotypes. We found several differentially methylated regions (DMRs) and DMR‐associated genes (DAGs) that are linked with Al tolerance. Some of these DAGs have been previously reported as differentially expressed under Al exposure in O. sativa . Complementarily a Transposable Elements (TE) analysis revealed that specific aluminum related genes have associated‐TEs potentially regulated by DNA methylation. Interestingly, the DMRs and DAGs between Al‐tolerant and susceptible genotypes were different between O. sativa and O. glumaepatula, suggesting that methylation patterns related to Al responses are unique for each rice species. Our findings provide novel insights into DNA methylation patterns in wild and cultivated rice genotypes and their possible role in the regulation of plant stress responses. John Wiley and Sons Inc. 2022-08-26 /pmc/articles/PMC9414936/ /pubmed/36051226 http://dx.doi.org/10.1002/pld3.430 Text en © 2022 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Original Research
Gallo‐Franco, Jenny Johana
Ghneim‐Herrera, Thaura
Tobar‐Tosse, Fabian
Romero, Miguel
Chaura, Juliana
Quimbaya, Mauricio
Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title_full Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title_fullStr Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title_full_unstemmed Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title_short Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response
title_sort whole‐genome dna methylation patterns of oryza sativa (l.) and oryza glumaepatula (steud) genotypes associated with aluminum response
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9414936/
https://www.ncbi.nlm.nih.gov/pubmed/36051226
http://dx.doi.org/10.1002/pld3.430
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