Relation between LD Levels in Inbred Strains and Recombination Rates in HS and RIs on Chromosome 7

<p>The top figure is the recombination rate (cM/Mb) for the HS and RIs in 1-Mb non-overlapping windows across a 25-Mb region in Chromosome 7. Below, the six boxes represent the location of four recombination jungles (in red) and two deserts (in blue) of 1 Mb each. The bottom figure is the LD structure of the same region based on the SNP genotypes of 55 inbred strains. Each dot represents the pairwise LD level between two different SNPs. Regions of high LD measured by <i>r²</i> are in blue, whereas regions of linkage equilibrium are in red. As can be seen in this example, deserts tend to overlap with large blocks of LD, and jungles are typically located on the border of the blocks. The overlap proportion of the four recombination jungles with haplotype blocks is 0.00, 0.58, 0.55, and 0.35 for regions 1, 2, 5, and 6. The two deserts (3 and 4) overlap completely with haplotype blocks.