Fine-scale recombination rate differences between sexes, populations and individuals

Recombination maps reveal differences between the sexes High-resolution recombination maps serve many purposes in genetic research. The currently available maps, which use linkage disequilibrium patterns of high-density SNP (single nucleotide polymorphism) data from the HapMap project, have proved to be very useful. But they have some limitations; for instance, they do not provide information on differences in recombination characteristics between and within the sexes. A team at biopharmaceutical firm deCODE genetics in Reykjavik has used genome-wide SNP data from more than 15,000 parent–offspring pairs to construct the first recombination maps based on directly observed recombination events, providing resolution down to 10 kilobases. Their data reveal interesting recombination differences between the sexes. In males, for example, recombination tends to shuffle exons, whereas in females it generates new combinations of nearby genes. Comparisons of these maps with those based on linkage disequilibrium reveal previously unrecognized differences between populations in Europe, Africa and the United States. Here, human genome-wide single-nucleotide polymorphism (SNP) data from more than 15,000 parent–offspring pairs have been used to construct the first recombination maps that are based on directly observed recombination events. The data reveal interesting differences between the sexes: for instance, in males recombination tends to shuffle exons, whereas in females it generates new combinations of nearby genes. Comparison of these maps with others also reveals population differences. Meiotic recombinations contribute to genetic diversity by yielding new combinations of alleles. Recently, high-resolution recombination maps were inferred from high-density single-nucleotide polymorphism (SNP) data using linkage disequilibrium (LD) patterns that capture historical recombination events 1 , 2 . The use of these maps has been demonstrated by the identification of recombination hotspots 2 and associated motifs 3 , and the discovery that the PRDM9 gene affects the proportion of recombinations occurring at hotspots 4 , 5 , 6 . However, these maps provide no information about individual or sex differences. Moreover, locus-specific demographic factors like natural selection 7 can bias LD-based estimates of recombination rate. Existing genetic maps based on family data avoid these shortcomings 8 , but their resolution is limited by relatively few meioses and a low density o