title: Linkage disequilibrium and recombination rate estimates in the self-incompatibility region of Arabidopsis lyrata.
abstract: Genetic diversity is unusually high at loci in the S-locus region of the self-incompatible species of the flowering plant, Arabidopsis lyrata, not just in the S loci themselves, but also at two nearby loci. In a previous study of a single natural population from Iceland, we attributed this elevated polymorphism to linkage disequilibrium (LD) between variants at loci close to the S locus and the S alleles, which are maintained in the population by balancing selection. With the four S-flanking loci whose diversity we previously studied, we could not determine the extent of the region linked to the S loci in which neutral sites are affected. We also could not exclude the possibility of a population bottleneck, or of admixture, as causes of the LD. We have now studied four more distant loci flanking the S-locus region, and more populations, and we analyze the results using a theoretical model of the effect of balancing selection on diversity at linked neutral sites within and between different functional S-allelic classes. In the model, diversity is a function of the number of selectively maintained alleles and the recombination distances from the selectively maintained sites. We use the model to estimate the number of different functional S alleles, their turnover rate, and recombination rates between the S-locus region and other loci. Our estimates suggest that there is a small region of very low recombination surrounding the S-locus region.
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, W. Mains Road, Edinburgh, United Kingdom.
authors.forename: Esther
authors.initials: E
authors.lastname: Kamau
authors.forename: Brian
authors.initials: B
authors.lastname: Charlesworth
authors.forename: Deborah
authors.initials: D
authors.lastname: Charlesworth
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D014644:Genetic Variation; D005828:Genetics, Population; D007055:Iceland; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic
chemical_list: D017931:DNA Primers; D018744:DNA, Plant