Previous work has demonstrated differences in the magnitude of linkage disequilibrium, as measured at a megabase scale, among genes associated with different functions3,40. Using the fine-scale genetic map estimated from the Phase II HapMap data we can quantify local increases in recombination rate associated with genes of different function using the Panther gene ontology annotation41. Average recombination rates vary more than sixfold among such gene classes (Fig. 5b), with defence and immunity genes showing the highest rates (1.9 cM Mb−1) and chaperones showing the lowest rates (0.3 cM Mb−1). Gene functions associated with cell surfaces and external functions tend to show higher recombination rates (immunity, cell adhesion, extracellular matrix, ion channels, signalling) whereas those with lower recombination rates are typically internal to cells (chaperones, ligase, isomerase, synthase). Controlling for systematic differences between gene classes in base composition and gene clustering, the differences between groups remain significant. We also find that the density of hotspot-associated DNA motifs varies systematically among gene classes and that variation in motif density explains over 50% of the variance in recombination rate among gene functions (Supplementary Fig. 7).
