1. Lewis-Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey 08544, USA
2. These authors contributed equally to this work.
3. Present address: Department of Molecular Genetics, Genomics and Microbiology, Louis-Pasteur University and CNRS, UMR7156, Strasbourg 67083, France.

Correspondence to: Leonid Kruglyak¹ Correspondence and requests for materials should be addressed to L.K. (Email: leonid@genomics.princeton.edu).

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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