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Again, we overcome this difficulty by calculating a probability value for each predicted loci pair using the empirical fragment length distribution and reporting the one with highest probability.
We include all six loci in our analysis because we did not uncover linkage disequilibrium for any loci pair in any population and observed heterozygosity deviated from expected heterozygosity in only one locus in few populations [ 34].
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Moderate linkage disequilibrium (LD) indicates the usefulness of loci pairs for whole genome selection.
For linkage disequilibrium (LD), the mean r2 value for all polymorphism loci pairs was 0.48, and LD did not decay over 748 bp.
The loci OarFCB304 (9 pairs out of the 25 significant pairs) and BM757 (6 pairs out of 25) seemed to occur the most frequently in linkage disequilibrium of loci pairs.
Four loci pairs displayed linkage disequilibrium.
No loci pairs demonstrated significant LD.
There was no evidence of LD for any loci pairs.
The 95% quantile of r2 for unlinked loci pairs was used as significance threshold for the linked loci pairs.
Among all loci pairs, only 39.4% were in significant LD in the whole panel.
Among all loci pairs (1,807,882), only 11.8% were in significant LD in the whole panel.
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