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Originally published as Genetics Published Articles Ahead of Print on June 11, 2007.

Genetics, Vol. 176, 2357-2369, August 2007, Copyright © 2007
doi:10.1534/genetics.107.072231

Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata

Esther Kamau, Brian Charlesworth and Deborah Charlesworth1

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom

1 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Lab, King's Bldgs., W. Mains Rd., Edinburgh EH9 3JT, United Kingdom.
E-mail: deborah.charlesworth{at}ed.ac.uk

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.


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