Datensatz

Zusammenfassung

Variation in DNA sequence underlies the evolutionary process, and establishing the relationship between sequence polymorphisms and phenotypic effects is a fundamental challenge in modern biology. A critical first step towards this goal is the identification of genetic diversity in species and populations. Among multicellular organisms, a comprehensive inventory of sequence polymorphism currently exists only for humans. In Arabidopsis thaliana, analysis of sequence diversity has typically been limited to a small number of carefully selected loci that together comprise only a small fraction of the genome, and a comprehensive description of sequence polymorphism from a core set of ecotypes across the entire genome has been lacking (although see presentation by Magnus Nordborg at this meeting). We are using a high-density oligonucleotide array approach to generate array-based sequence for 20 A. thaliana ecotypes that were chosen to maximize both sequence diversity and utility for the A. thaliana research community. This approach allows ~ 50% of bases in the A. thaliana reference genome sequence (Columbia accession) to be called for each ecotype. The resulting dataset, which will consist of about 55-60 Mb of euchromatic sequence per ecotype, will allow the identification of much of the common single nucleotide polymorphism present in A. thaliana. In addition, analysis of pilot data suggests that deletion polymorphisms of greater than several hundred bp in size in A. thaliana can also be recovered using the array-based approach. We will describe the ecotypes for sequencing that have been chosen in consultation with Magnus Nordborg and co-workers. We will summarize initial sequence data for the 20 ecotypes for about 400 kb of test array data that has been selected in collaboration with Joe Ecker and co-workers. We will also present a preliminary analysis of the complete array-based sequence for two ecotypes. The complete sequence dataset for all 20 ecotypes will be generated by Fall of 2005, and we will discuss plans for sequence analysis as well as for the release of this large genomic sequence dataset to the A. thaliana research community.