title: Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana.
abstract: Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima's D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.
authors.affiliation: Department of Genetics, Lund University, Sölvegatan 29, S-223 62 Lund, Sweden.
authors.forename: Jenny
authors.initials: J
authors.lastname: Hagenblad
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D003198:Computer Simulation; D035264:Flowers / Q000235:genetics / Q000254:growth & development*; D005787:Gene Frequency; D017343:Genes, Plant; D014644:Genetic Variation; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic