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We propose a novel approach that quantifies the degree of linkage disequilibrium (LD) between the candidate SNP and the putative disease locus through joint modeling of linkage and association.
Although this design allows for the simultaneous modeling of linkage and association, we limit the analysis to the association, but note that linkage information (i.e., IBD sharing estimation) could be included in exact data simulation scripts.
In a commercial cattle population for which pedigree information is absent, such as in this study, it is likely that unknown pedigree relationships will bias the accuracies upward through the modeling of linkage information.
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In HaploMax, there was no probabilistic modelling of linkage disequilibrium evolution.
There are advantages and disadvantages to automated models of linkage service delivery.
It combines family information with probabilistic modelling of linkage disequilibrium evolution (LDL stands for Linkage and Linkage Disequilibrium).
For each of these scenarios, we investigated the improvement produced by probabilistic modelling of linkage disequilibrium evolution.
Our results indicated that the improvement produced by probabilistic modelling of linkage disequilibrium evolution was not significant.
Parametric linkage analyses were performed under dominant and recessive models of linkage assuming a disease frequency of 35% (as described in the Robinson Crusoe population) and full penetrance.
When dealing with populations with large effective sizes or with very old mutations, combining linkage with probabilistic modelling of linkage disequilibrium evolution should produce the greatest accuracy.
Our objective was to determine whether modelling of linkage disequilibrium evolution improved the mapping accuracy of a quantitative trait locus of agricultural interest in these populations.
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