Abstract
A simulation study was conducted to evaluate the effect of reciprocal cross on the detection and characterization of parent-of-origin (POE) QTL in F 2 QTL 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, totaling 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 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 F 1 parents.
Highlights
Genetic improvement schemes and quantitative trait loci (QTL) mapping experiments in livestock usually assume Mendelian inheritance, in which parents contribute to progeny
Most QTL were detected when alternate QTL alleles were fixed in parental breeds across all QTL types, sizes and mating designs
The overall detection powers were similar in the two mating designs across all QTL types, sizes, and allele frequency difference (FD) (Table 2)
Summary
Genetic improvement schemes and quantitative trait loci (QTL) mapping experiments in livestock usually assume Mendelian inheritance, in which parents contribute to progeny. A non-Mendelian effect where only one of the two parental copies of a gene is expressed, has been an interesting research area in mammalian genetics due to its unique expression and inheritance mechanisms, and its important role in growth, development, and behavior (Tycko and Morison, 2002; Wilkens and Haig, 2003). Genomic regions with imprinting or parent-of-origin (POE) effects can be detected using QTL interval mapping in F2 crosses between lines or breeds that segregate for marker alleles because of the. The one-way mating design can generate progeny with phenotypic differences due to breed-specific maternal environmental effects, mitochondrial inheritance, genomic imprinting, or sex chromosome-linked effects (Thallman et al, 1992). Reciprocal cross designs have been used for QTL detection in swine, in which individuals of two breeds were used as both grand-sires and grand-dams (Rohrer et al, 2006). Characterization of imprinting QTL due to the reciprocal cross is unknown in F2 outbred populations
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