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Article

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

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Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40–032 Katowice, Poland
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Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
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Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, UK
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The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Shanxi Agricultural University, Taigu, Shanxi 030801, China
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Department of Field Crops, Faculty of Agriculture, Tekirdag Namik Kemal University, Suleymanpasa 59030, Tekirdag, Turkey
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Tekirdag Anatolian High School, 59030 Suleymanpasa, Tekirdag, Turkey
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Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60–479 Poznan, Poland
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Applied Omics—Rafał Wóycicki, 31–510 Kraków, Poland
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School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
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National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EB, UK
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(18), 6700; https://doi.org/10.3390/ijms21186700
Received: 12 July 2020 / Revised: 4 September 2020 / Accepted: 9 September 2020 / Published: 13 September 2020
(This article belongs to the Special Issue Plant Genomics 2019)
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. View Full-Text
Keywords: Brachypodium; DNA methylation; drought; flowering; genome; phenomics Brachypodium; DNA methylation; drought; flowering; genome; phenomics
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MDPI and ACS Style

Skalska, A.; Stritt, C.; Wyler, M.; Williams, H.W.; Vickers, M.; Han, J.; Tuna, M.; Savas Tuna, G.; Susek, K.; Swain, M.; Wóycicki, R.K.; Chaudhary, S.; Corke, F.; Doonan, J.H.; Roulin, A.C.; Hasterok, R.; Mur, L.A.J. Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations. Int. J. Mol. Sci. 2020, 21, 6700. https://doi.org/10.3390/ijms21186700

AMA Style

Skalska A, Stritt C, Wyler M, Williams HW, Vickers M, Han J, Tuna M, Savas Tuna G, Susek K, Swain M, Wóycicki RK, Chaudhary S, Corke F, Doonan JH, Roulin AC, Hasterok R, Mur LAJ. Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations. International Journal of Molecular Sciences. 2020; 21(18):6700. https://doi.org/10.3390/ijms21186700

Chicago/Turabian Style

Skalska, Aleksandra, Christoph Stritt, Michele Wyler, Hefin W. Williams, Martin Vickers, Jiwan Han, Metin Tuna, Gulsemin Savas Tuna, Karolina Susek, Martin Swain, Rafał K. Wóycicki, Saurabh Chaudhary, Fiona Corke, John H. Doonan, Anne C. Roulin, Robert Hasterok, and Luis A.J. Mur 2020. "Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations" International Journal of Molecular Sciences 21, no. 18: 6700. https://doi.org/10.3390/ijms21186700

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