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Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. See...

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Autores principales: Skalska, Aleksandra, Stritt, Christoph, Wyler, Michele, Williams, Hefin W., Vickers, Martin, Han, Jiwan, Tuna, Metin, Savas Tuna, Gulsemin, Susek, Karolina, Swain, Martin, Wóycicki, Rafał K., Chaudhary, Saurabh, Corke, Fiona, Doonan, John H., Roulin, Anne C., Hasterok, Robert, Mur, Luis A. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556024/
https://www.ncbi.nlm.nih.gov/pubmed/32933168
http://dx.doi.org/10.3390/ijms21186700
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author Skalska, Aleksandra
Stritt, Christoph
Wyler, Michele
Williams, Hefin W.
Vickers, Martin
Han, Jiwan
Tuna, Metin
Savas Tuna, Gulsemin
Susek, Karolina
Swain, Martin
Wóycicki, Rafał K.
Chaudhary, Saurabh
Corke, Fiona
Doonan, John H.
Roulin, Anne C.
Hasterok, Robert
Mur, Luis A. J.
author_facet Skalska, Aleksandra
Stritt, Christoph
Wyler, Michele
Williams, Hefin W.
Vickers, Martin
Han, Jiwan
Tuna, Metin
Savas Tuna, Gulsemin
Susek, Karolina
Swain, Martin
Wóycicki, Rafał K.
Chaudhary, Saurabh
Corke, Fiona
Doonan, John H.
Roulin, Anne C.
Hasterok, Robert
Mur, Luis A. J.
author_sort Skalska, Aleksandra
collection PubMed
description Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.
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spelling pubmed-75560242020-10-19 Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations Skalska, Aleksandra Stritt, Christoph Wyler, Michele Williams, Hefin W. Vickers, Martin Han, Jiwan Tuna, Metin Savas Tuna, Gulsemin Susek, Karolina Swain, Martin Wóycicki, Rafał K. Chaudhary, Saurabh Corke, Fiona Doonan, John H. Roulin, Anne C. Hasterok, Robert Mur, Luis A. J. Int J Mol Sci Article Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses. MDPI 2020-09-13 /pmc/articles/PMC7556024/ /pubmed/32933168 http://dx.doi.org/10.3390/ijms21186700 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Skalska, Aleksandra
Stritt, Christoph
Wyler, Michele
Williams, Hefin W.
Vickers, Martin
Han, Jiwan
Tuna, Metin
Savas Tuna, Gulsemin
Susek, Karolina
Swain, Martin
Wóycicki, Rafał K.
Chaudhary, Saurabh
Corke, Fiona
Doonan, John H.
Roulin, Anne C.
Hasterok, Robert
Mur, Luis A. J.
Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title_full Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title_fullStr Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title_full_unstemmed Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title_short Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
title_sort genetic and methylome variation in turkish brachypodium distachyon accessions differentiate two geographically distinct subpopulations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556024/
https://www.ncbi.nlm.nih.gov/pubmed/32933168
http://dx.doi.org/10.3390/ijms21186700
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