Linkage disequilibrium and recombination rate estimates in the self-incompatibility region of Arabidopsis lyrata

• Published in: Genetics (Austin) Vol. 176; no. 4; pp. 2357 - 2369
• Main Authors: Kamau, E, Charlesworth, B, Charlesworth, D
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01.08.2007; Copyright © 2007 by the Genetics Society of America
• Subjects: Alleles; Arabidopsis; Arabidopsis - genetics; Arabidopsis lyrata; Base Sequence; DNA Primers - genetics; DNA, Plant - genetics; Estimates; Genes; Genes, Plant; genetic polymorphism; Genetic recombination; Genetic Variation; Genetics, Population; haplotypes; Iceland; Investigations; Linkage Disequilibrium; loci; Models, Genetic; Molecular Sequence Data; plant fertility; Polymorphism, Genetic; Population genetics; Recombination, Genetic; S alleles; S locus; selfing; Iceland
• ISSN: 0016-6731; 1943-2631; 1943-2631
• DOI: 10.1534/genetics.107.072231

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.