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Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

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Abstract

Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K=6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances.

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Acknowledgements

This work was funded by the German Ministry of Science (BMBF) as part of the GABI project (#0312275A) to T. A. and by the Emmy-Noether program of the Deutsche Forschungsgemeinschaft (Schm 1354-2/2) to K. J. S. We are grateful to Henriette Ringys-Beckstein, Maik Zehnsdorf and Melanie Lück for excellent technical assistance. We also thank K. Bachmann, M. Clauss, B. Haubold, M. Koornneef, A. Lawton-Rauh, T. Mitchell-Olds, S. Ramos-Onsins and E. Wheeler for discussions and comments on an earlier version of the manuscript.

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Authors and Affiliations

  1. Max-Planck-Institute of Chemical Ecology, Jena, Germany

    Karl J. Schmid

  2. University of Potsdam, Germany and Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany

    Ottó Törjék, Rhonda Meyer & Thomas Altmann

  3. Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany

    Heike Schmuths

  4. University of Nottingham, Loughborough, UK

    Heike Schmuths

  5. Institute of Geobotany and Botanical Gardens, Martin-Luther-University, Halle, Germany

    Matthias H. Hoffmann

  6. Department of Genetics and Evolution, Max-Planck-Institute of Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany

    Karl J. Schmid

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  1. Karl J. Schmid
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Correspondence to Karl J. Schmid.

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Communicated by O. Savolainen

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Schmid, K.J., Törjék, O., Meyer, R. et al. Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers. Theor Appl Genet 112, 1104–1114 (2006). https://doi.org/10.1007/s00122-006-0212-7

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  • DOI: https://doi.org/10.1007/s00122-006-0212-7

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