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Genetics, Vol. 163, 79-89, January 2003, Copyright © 2003

Genetic Diversity in Yeast Assessed With Whole-Genome Oligonucleotide Arrays

Elizabeth A. Winzelera, Cristian I. Castillo-Davisb, Guy Oshiroa, David Lianga, Daniel R. Richardsc, Yingyao Zhoua, and Daniel L. Hartlb
a Genomics Institute of the Novartis Research Foundation, San Diego, California 92121,
b Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
c Department of Genetics, Stanford University School of Medicine, Stanford, California 95307

Corresponding author: Elizabeth A. Winzeler, The Scripps Research Institute, 10550 Torrey Pines Rd., La Jolla, CA 92037.

Communicating editor: M. JOHNSTON

The availability of a complete genome sequence allows the detailed study of intraspecies variability. Here we use high-density oligonucleotide arrays to discover 11,115 single-feature polymorphisms (SFPs) existing in one or more of 14 different yeast strains. We use these SFPs to define regions of genetic identity between common laboratory strains of yeast. We assess the genome-wide distribution of genetic variation on the basis of this yeast population. We find that genome variability is biased toward the ends of chromosomes and is more likely to be found in genes with roles in fermentation or in transport. This subtelomeric bias may arise through recombination between nonhomologous sequences because full-gene deletions are more common in these regions than in more central regions of the chromosome.




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