The pattern of polymorphism in Arabidopsis thaliana

Introduction

The primary goal of this project, which is a continuation of a previous collaborative project between the Bergelson, Kreitman, and Nordborg labs, is to enable genome-wide association mapping in A. thaliana by genotyping sufficiently many lines using sufficiently many markers. Based on our analyses of existing data (Nordborg et al., 2005; Aranzana et al., 2005; Zhao et al., 2007; Kim et al., 2007) we have decided to genotype on the order of 1,300 lines using a custom Affymetrix 250,000 SNP chip developed from the recently released Perlegen re-sequencing data (Clark et al., 2007; Kim et al., 2007). This represents a considerable increase in effort over the original proposal, and has been made possible by the ever-decreasing costs of genotyping and by combining forces with the Borevitz lab (supported by NIH GM073822).

Project status

• We have genotyped over 6,000 lines (including all common stock-center accessions) using 149 genome-wide SNPs.  Our primary purpose was to detect identical and heterozygous individuals, but we also sought to get a better picture of population structure.  A paper describing these data is in preparation.
• The sample for 250k SNP genotyping has been selected based on the 149-SNP data.  It will contain several large regional "population" samples as well as a geographically diverse selection of lines.  All accessions will be submitted to the stock center.  250k SNP data are being posted as soon as they become available.
• A paper describing an initial attempt at genome-wide association in preparation.  A website that allows easy access to the data and results has been developed and will soon be published.