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Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

Abstract

Comprehensive identification of polymorphisms among individuals within a species is essential both for studying the genetic basis of phenotypic differences and for elucidating the evolutionary history of the species. Large-scale polymorphism surveys have recently been reported for human1, mouse2 and Arabidopsis thaliana3. Here we report a nucleotide-level survey of genomic variation in a diverse collection of 63 Saccharomyces cerevisiae strains sampled from different ecological niches (beer, bread, vineyards, immunocompromised individuals, various fermentations and nature) and from locations on different continents. We hybridized genomic DNA from each strain to whole-genome tiling microarrays and detected 1.89 million single nucleotide polymorphisms, which were grouped into 101,343 distinct segregating sites. We also identified 3,985 deletion events of length >200 base pairs among the surveyed strains. We analysed the genome-wide patterns of nucleotide polymorphism and deletion variants, and measured the extent of linkage disequilibrium in S. cerevisiae. These results and the polymorphism resource we have generated lay the foundation for genome-wide association studies in yeast. We also examined the population structure of S. cerevisiae, providing support for multiple domestication events as well as insight into the origins of pathogenic strains.

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Figure 1: Decay of linkage disequilibrium as a function of distance.
Figure 2: Neighbour-joining tree of 63 S. cerevisiae strains.
Figure 3: Population structure of 63 S. cerevisiae strains.

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Acknowledgements

We are grateful to all the researchers and institutions, and especially J. Fay, for sharing yeast strains. We thank K. Dolinski and J. Matese for technical support and D. Gresham for comments on the manuscript. The authors acknowledge discussions with members of the Kruglyak and Botstein laboratories. This work was supported by NIH grant R37 MH059520 and a James S. McDonnell Foundation Centennial Fellowship to L.K., and NIH grant GM071508 to the Lewis-Sigler Institute.

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Correspondence to Leonid Kruglyak.

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Schacherer, J., Shapiro, J., Ruderfer, D. et al. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458, 342–345 (2009). https://doi.org/10.1038/nature07670

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