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

• Published in: Genetics
• Main Authors: Kamau, Esther, Charlesworth, Brian, Charlesworth, Deborah
• Format: Article in Journal/Newspaper
• Language: English
• Published: Silverchair Information Systems 2007
• Subjects: Iceland
• Online Access: https://doi.org/10.1534/genetics.107.072231; https://pubmed.ncbi.nlm.nih.gov/17565949; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950637/

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.