Geographic distribution and recombination of genomic fragments on the short arm of chromosome 2 of Arabidopsis thaliana

Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene (similar to1500 bp) and a noncoding region (similar to500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, pi, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform Asian and a more variable European haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between Asian and European haplotypes occurs where they meet. Especially in the European haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNIP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern.