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...
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Online Access: | http://dx.doi.org/10.1534/genetics.107.072231 https://academic.oup.com/genetics/article-pdf/176/4/2357/49404585/genetics2357.pdf |
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croxfordunivpr:10.1534/genetics.107.072231 2024-05-12T08:05:57+00:00 Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata Kamau, Esther Charlesworth, Brian Charlesworth, Deborah 2007 http://dx.doi.org/10.1534/genetics.107.072231 https://academic.oup.com/genetics/article-pdf/176/4/2357/49404585/genetics2357.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Genetics volume 176, issue 4, page 2357-2369 ISSN 1943-2631 Genetics journal-article 2007 croxfordunivpr https://doi.org/10.1534/genetics.107.072231 2024-04-18T08:16:54Z 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. Article in Journal/Newspaper Iceland Oxford University Press Genetics 176 4 2357 2369 |
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Genetics Kamau, Esther Charlesworth, Brian Charlesworth, Deborah Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
topic_facet |
Genetics |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Kamau, Esther Charlesworth, Brian Charlesworth, Deborah |
author_facet |
Kamau, Esther Charlesworth, Brian Charlesworth, Deborah |
author_sort |
Kamau, Esther |
title |
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
title_short |
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
title_full |
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
title_fullStr |
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
title_full_unstemmed |
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata |
title_sort |
linkage disequilibrium and recombination rate estimates in the self-incompatibility region of arabidopsis lyrata |
publisher |
Oxford University Press (OUP) |
publishDate |
2007 |
url |
http://dx.doi.org/10.1534/genetics.107.072231 https://academic.oup.com/genetics/article-pdf/176/4/2357/49404585/genetics2357.pdf |
genre |
Iceland |
genre_facet |
Iceland |
op_source |
Genetics volume 176, issue 4, page 2357-2369 ISSN 1943-2631 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/genetics.107.072231 |
container_title |
Genetics |
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176 |
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4 |
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2357 |
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2369 |
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1798848339109740544 |