The inbreeding in the region around a QTL under selection was investigated. A segment of the genome was simulated on which a QTL, contributing to the additive genetic effect of a trait under selection, was located. The trait was also under the control of an unlinked polygenic effect. Neutral markers were simulated to calculate the true inbreeding coefficient at positions along the genome. Optimised selection was undertaken, aimed at maximising genetic gain while constraining coancestry using either the pedigree relationship matrix (Ap) or an identity by descent matrix (Am) calculated at a specific position of the genome utilising information from microsatellite markers. Inbreeding increased in the region around a QTL under selection when using Ap and this increase in inbreeding could be avoided by restricting coancestry at a position close to the QTL using Am, at the cost of an increase in overall inbreeding.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 30.07, 2006
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