Invited Talk: Genomic Variation and Incipient Speciation in Arabidopsis thaliana

Comprehensive polymorphism data are a prerequisite for the systematic identification of sequence variants affecting phenotypes. In the first part of my talk, I will discuss our efforts to provide a whole genome resource for the study of population level evolutionary processes in an experimentally tractable, multicellular organism, Arabidopsis thaliana. To this end, we have collaborated with Kelly Frazer and colleagues at Perlegen Sciences, and hybridized genomic DNA of 20 strains to custom microarrays that tile all possible single nucleotide polymorphisms (SNPs) along the entire genome with close to one billion (109) different oligonucleotides. The analysis of SNP distribution and haplotype maps is being carried out in collaboration with the groups of Bernhard Schölkopf (MPI for Biological Cybernetics), Gunnar Rätsch (Friedrich Miescher Laboratory), Daniel Huson (University Tübingen), Joe Ecker (Salk Institute), and Magnus Nordborg (USC). Using novel analysis methods, we identified up to 1.1 million non-redundant SNPs at various levels of precision. In addition, we predicted nearly 5% of the genome to be highly polymorphic or deleted in at least one strain. These data allow for the first time a systematic description of the types of genes that harbor major changes (e.g., stop codons or whole gene deletions) in wild populations. Although major changes are frequent, allele frequency patterns indicate that they are often associated with a fitness cost. Disease resistance (R) genes are found to be the most polymorphic class of genes.