The effect of linkage disequilibrium on the estimates of Single Nucleotide Polymorphic effects

Abstract

The identification and exploitation of single nucleotide polymorphisms (SNP) associated with production traits present new opportunities for livestock genetic improvement. Often the identified SNP is not the causative mutation but rather is in some degree of linkage disequilibrium (LD). LD markers within 5cM can be considered as direct markers for the causative mutation because they are located close to the causative mutation (Dekkers, 2004). In a dairy herd, Farnir et al., (2000) estimated that the average LD, measured as D' was 0.5 for loci pairs positioned within 5cM. Goddard et al., (2006) estimated that LD measured as r² decreased rapidly as the physical distance between loci increased; at a separating distance of 0.5 Mb the LD (r²) was only approximately 0.2. The aim of this work was to use stochastic simulation to investigate the effect that the distance between the SNP and causative mutation had on the accuracy of estimating additive and dominance effects of the causative mutation.