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Evaluation of Reciprocal Cross Design on Detection and Characterization of Non-Mendelian QTL in Outbred Populations: I. Parent-of-origin Effect
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 Title & Authors
Evaluation of Reciprocal Cross Design on Detection and Characterization of Non-Mendelian QTL in Outbred Populations: I. Parent-of-origin Effect
Lee, Yun-Mi; Lee, Ji-Hong; Kim, Jong-Joo;
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A simulation study was conducted to evaluate the effect of reciprocal cross on the detection and characterization of parent-of-origin (POE) QTL in QTL populations. Data were simulated under two different mating designs. In the one-way cross design, six grand sires of one breed and 30 grand dams of another breed generated 10 offspring per dam. Sixteen sires and 64 dams were randomly chosen to produce a total of 640 offspring. In the reciprocal design, three grand sires of A breed and 15 grand dams of B breed were mated to generate 10 offspring per dam. Eight sires and 32 dams were randomly chosen to produce 10 offspring per dam, totaling 320 offspring. Another mating set comprised three grand sires of B breed and 15 grand dams of A breed to produce the same number of and offspring. A chromosome of 100 cM was simulated with large, medium or small QTL with fixed or different allele frequencies in parental breeds. A series of tests between Mendelian and POE models were applied to characterize QTL as Mendelian, paternal, maternal or partial expression QTL. The overall detection powers were similar between the two mating designs. However, the proportions of paternally expressed QTL that were declared as paternal QTL type were greater in the reciprocal cross design than in the one-way cross, and vice versa for Mendelian QTL. When QTL alleles were segregating in parental breeds, a significant proportion of Mendelian QTL were spuriously declared POE QTL, suggesting that care must be taken to characterize imprinting QTL in a QTL mapping population with a small number of parents.
Quantitative Trait Loci Swine;Detection Power;Imprinting;Simulation;
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