Distribution of intra-chromosomal linkage disequilibrium (r2) as a function of physical and genetic distance between all marker pairs for the 12 linkage groups of the maritime pine composite linkage map (see Additional File
, for each LG independently). SNPs from the same contig were placed at 0 cM. r2 was determined by the Rogers and Huff  approximation for loci with unknown phase, based on the polymorphic data for 186 unrelated trees of the Aquitaine population. In yellow: r2 values below a cutoff value of 0.1. In red: r2 values above this cutoff.