We measured linkage disequilibrium in mostly noncoding regions of Cryptomeria japonica, a conifer belonging to Cupressaceae. Linkage disequilibrium was extensive and did not decay even at a distance of 100 kb. The average estimate of the population recombination rate per base pair was 1.55×10 -5 and was <1/70 of that in the coding regions. We discuss the impact of low recombination rates in a large part of the genome on association studies.
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