Fig. 3

Linkage disequilibrium based approach to delineate a physical window around each SNP, exemplified with chromosome 3. Linkage disequilibrium (LD) windows were defined for each SNP based on physical LD extent in low recombinogenic regions (left part) and based on genetic LD extent in high recombinogenic regions (right part). These LD windows were used (i) to group significant SNPs into QTLs when they overlapped, (ii) to estimate genome coverage region covered by LD windows around SNPs, and (iii) identify putative genes underlying QTLs involved in trait variations