Marker-assisted selection in an outbred poultry breeding nucleus

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Abstract
The value of using a marker for a quantitative trait locus (QTL) affecting a sex-limited trait in an outbred poultry breeding nucleus was studied. Marker and QTL were in linkage equilibrium in the base population. The recombination rate between marker and QTL was 0-05. A closed nucleus with 9000 chickens per generation was deterministically simulated. The genetic model contained polygenes and a QTL linked to a marker. Genetic effects explained proportionately 0·3 of the phenotypic variance before selection. Under selection, polygenic variance reached an equilibrium and QTL variance decreased continuously over time. Cocks were selected in two steps. First the best cocks of each full-sib family were selected (within-family selection) while final selection took place after information on fiill-sibs was available. Hens were selected after they had completed production. The effect of using marker information in estimating breeding values was studied in an ongoing breeding programme. Transmission of marker alleles was always traceable. Cumulative response over five generations increased proportionately by 0·06 to 0·13 if a marker linked to a QTL that explained 0·2 of the genetic variance was used. Cumulative response increased up to 0·28 if the QTL explained 0-8 of the genetic variance. Additional response due to the use of a marker increased with increasing intensity of within-family selection of cocks, increased with increasing variance explained by the QTL and was higher if within-family selection of cocks was carried out after rather than before their sibs had complete records.