A transmission/disequilibrium test approach to screen for quantitative trait loci in two selected lines of Large White pigs

Pedigree and marker data from a multiple-generation pig selection experimen t have been analysed to screen for loci affecting quantitative traits (QTL) . Pigs from a base population were selected either for low backfat thicknes s at fixed live weight (L-line) or high live weight at fixed age (F-line). Selection was based on single-trait own performance and DNA was available o n selected individuals only. Genotypes for three marker loci with known pos itions on chromosome 4 were available. The transmission/disequilibrium test (TDT) was originally described in human genetics to test for linkage betwe en a genetic marker and a disease-susceptibility locus, in the presence of association. Here, we adapt the TDT to test for linkage between a marker an d QTL favoured by selection, and for linkage disequilibrium between them in the base population. The a priori unknown distribution of the test statist ic under the null hypothesis, no linkage, was obtained via Monte Carlo simu lation. Significant TDT statistics were found for markers AFABP and SW818 i n the F-line, indicating the presence of a closely linked QTL affecting gro wth performance. In the L-line, none of the markers studied showed signific ance. This study emphasizes the potential of the TDT as a quick and simple approach to screen for QTL in situations where marker genotypes are availab le on selected individuals. The results suggest that previously identified QTL in crosses of genetically diverse breeds may also segregate in commerci al selection lines.