A unique outbred by inbred F1 resource population was established. Thepopulation structure facilitated the unique opportunity of examining gene bygenetic background interaction through crossing two modern broiler sires withdams from two unrelated inbred lines, with no selection for growth rate, toproduce about 600 F1 chicks. Pools of DNA were generated from the phenotypicextremes (20% high and low) for 8-week body weight for each of the fourcombinations of sire and dam line. For one sire family, pools were alsoseparately generated for each sex. The pools were genoyped with 25 informative(segregating) microsatellites. This unique F1 cross between outbred and inbredpopulations allowed use of the inbred alleles as an 'internal control' forpolymerase chain reaction amplification quality in DNA pools. Tenmicrosatellites showed marked differences (P < 0.05) in allele frequenciesbetween high and low pools, suggesting an association between marker andquantitative trait loci (QTL). These differences were verified using selectivegenotyping. For many markers, differences in allele frequencies between the highand the low pools, or marker effect, varied between the two dam lines and thetwo sexes, suggesting an interaction between some genes and the geneticbackground as represented by different dam lines or sexes. The suggestivemarker-QTL associations identified in this F1 population demonstrate theefficiency of this population design while different QTL effects in differentgenetic line crosses and sexes highlight the importance of gene by geneticbackground interaction in QTL detection.