Recombination and selection at Brassica self-incompatibility loci

In Brassica species, self-incompatibility is controlled genetically by hapl otypes involving two known genes, SLG and SRK, and possibly an as yet unkno wn gene controlling pollen incompatibility types. Alleles at the incompatib ility loci are maintained by frequency-dependent selection, and diversity a t SLG and SRK appears to be very ancient, with high diversity at silent and replacement sites, particularly in certain "hypervariable" portions of the genes; It is important to test whether recombination occurs in these genes before inferences about function of different parts of the genes can be ma de from patterns of diversity within their sequences. In addition, it has b een suggested that, to maintain the relationship between alleles within a g iven S-haplotype, recombination is suppressed in the S-locus region. The hi gh diversity makes many population genetic measures of recombination inappl icable. We have analyzed linkage disequilibrium within the SLG gene of two Brassica species, using published coding sequences. The results suggest tha t intragenic recombination has occurred in the evolutionary history of thes e alleles. This is supported by patterns of synonymous nucleotide diversity within both the SLG and SRK genes, and between domains of the SRK gene. Fi nally, clusters of linkage disequilibrium within the SLG gene suggest that hypervariable regions are under balancing selection, and are not merely reg ions of relaxed selective constraint.