Screening for highly heterozygous chickens in outbred commercial broiler lines to increase detection power for mapping quantitative trait loci.

Two commercial broiler lines were used in an experiment to map quantitative trait loci (QTL) affecting disease resistance. Chickens from these lines were genotyped with 27 microsatellite markers to estimate heterozygosity and polymorphism information content (PIC), the probability that one parent is heterozygous at a marker locus and the other has a different genotype. Heterozygosity estimated from allelic frequencies was 0.52 for the two lines; however, heterozygosity calculated from actual counts of heterozygous loci was much lower (0.36) than the estimated heterozygosity. The PIC was 0.45 in these lines, and average allele number per marker locus was about 3.5. Twenty-five males produced from a cross between these two lines were screened with the DNA markers to select birds with high heterozygosity at marker loci. Mating simulation showed that uninformative matings could be reduced by about 5% if 12 pairs of males and females with the highest heterozygosity at marker loci were selected, which was about a 25% reduction in total uninformative matings. This experiment demonstrated that the heterozygosity and PIC in commercial broiler lines were low and selection for the birds with high heterozygosity at marker loci could increase informative content in chickens used in the experiments of QTL mapping, thus increasing detection power for QTL mapping.