The impact of Linkage Disequilibrium on estimable genetic effects at markers in the presence of dominance

Abstract Text:

Genomewide association studies are widely being used for making inference about the genetic architecture of quantitative traits. In a deterministic approach the impact of dominance and LD between one marker and one QTL has been investigated. If there is incomplete LD and dominance present at the QTL, estimates for genetic parameters are biased by that interaction. This is caused by unequal haplotype frequencies due to differing conditional probabilities of QTL-genotypes at marker genotypes. The additive effect observable at the marker is not only influenced by the additive effect of the QTL but also by the dominance deviation. Even in the absence of an additive effect almost all genetic variance at the marker is additive at weak LD and partitioning of genetic effects into additive and interaction components becomes difficult.

Keywords:

linkage disequilibrium
quantitative trait loci
dominance