Evaluation of Reciprocal Cross Design on Detection and Characterization of Mendelian QTL in Outbred Populations

A simulation study was conducted to evaluate the effect of reciprocal cross on the detection and characterization of Mendelian QTL in $F_2$ QTL swine populations. Data were simulated under two different mating designs. In the one-way cross design, six $F_0$ grand sires of one breed and 30 $F_0$ grand dams of another breed generated 10 $F_1$ offspring per dam. Sixteen $F_1$ sires and 64 $F_1$ dams were randomly chosen to produce a total of 640 $F_2$ offspring. In the reciprocal design, three $F_0$ grand sires of A breed and 15 $F_0$ grand dams of B breed were mated to generate 10 $F_1$ offspring per dam. Eight $F_1$ sires and 32 $F_1$ dams were randomly chosen to produce 10 $F_2$ offspring per $F_1$ dam, for a total of 320 $F_2$ offspring. Another mating set comprised three $F_0$ grand sires of B breed and 15 $F_0$ grand dams of A breed to produce the same number of $F_1$ and $F_2$ offspring. A chromosome of 100 cM was simulated with large, medium or small QTL with fixed, similar, or different allele frequencies in parental breeds. Tests between Mendelian models allowed QTL to be characterized as fixed (LC QTL), or segregating at similar (HS QTL) or different (CB QTL) frequencies in parental breeds. When alternate breed alleles segregated in parental breeds, a greater proportion of QTL were classified as CB QTL and estimates of QTL effects for the CB QTL were more unbiased and precise in the reciprocal cross than in the one-way cross. This result suggests that reciprocal cross design allows better characterization of Mendelian QTL in terms of allele frequencies in parental breeds.