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doi:10.1534/genetics.106.055780
A more recent version of this article appeared on June 1, 2006.
REGULAR RESEARCH PAPERS |
Linkage disequilibrium between incompatibility locus region genes in the plant Arabidopsis lyrata
Jenny Hagenblad 1, Jesper Bechsgaard 2 and Deborah Charlesworth 1*
1 University of Edinburgh
2 University of Aarhus
* To whom correspondence should be addressed. E-mail: deborah.charlesworth{at}ed.ac.uk.
Submitted on January 13, 2006
Revised on February 24, 2006
Accepted on 28 March 2006
We have studied diversity in Arabidopsis lyrata of sequences orthologous to the ARK3 gene of A. thaliana. Our main goal was to test for recombination in the S-locus region In A. thaliana, the single copy ARK3 gene is closely linked to the non-functional copies of the self-incompatibility loci, and the orthologue in A. lyrata (a self-incompatible species), is in the homologous genome region and is known as Aly8. It is thus of interest to test whether Aly8 sequence diversity is elevated due to close linkage to the highly polymorphic incompatibility locus, as is theoretically predicted. However, Aly8 is not a single-copy gene, and the presence of paralogues could also lead to the appearance of elevated diversity. We established a typing approach based on different lengths of Aly8 PCR products, and show that most A. lyrata haplotypes have a single copy, but some have two gene copies, both closely linked to the incompatibility locus, one being a pseudogene. We determined the phase of multiple haplotypes in families of plants from Icelandic and other populations. Different Aly8 sequence types are associated with different SRK alleles, while haplotypes with the same SRK sequences tend to have the same Aly8 sequence. There is evidence of some exchange of sequences between different Aly8 sequences, making it difficult to determine which ones are allelic, or to estimate the diversity. However, the homogeneity of the Aly8 sequences of each S-haplotype suggests that recombination between the loci has been very infrequent over the evolutionary history of these populations. Overall, the results suggest that recombination rarely occurs in the interval between the S-loci and Aly8, and that linkage to the S-loci can probably account for the observed high Aly8 diversity.
Key Words: balancing selection, haplotypes, recombination, self-incompatibility, sequence diversity
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