Abstract
A least squares regression interval mapping model was derived to detect quantitative trait loci (QTL) with a unique mode of genomic imprinting, polar overdominance (POD), under a breed cross design model in outbred mammals. Tests to differentiate POD QTL from Mendelian, paternal or maternal expression QTL were also developed. To evaluate the power of the POD models and to determine the ability to differentiate POD from non-POD QTL, phenotypic data, marker data and a biallelic QTL were simulated on 512 F2 offspring. When tests for Mendelian versus parent-of-origin expression were performed, most POD QTL were classified as partially imprinted QTL. The application of the series of POD tests showed that more than 90% and 80% of medium and small POD QTL were declared as POD type. However, when breed-origin alleles were segregating in the grand parental breeds, the proportion of declared POD QTL decreased, which was more pronounced in a mating design with a small number of parents (F0 and F1). Non-POD QTL, i.e. with Mendelian or parent-of-origin expression (complete imprinting) inheritance, were well classified (>90%) as non-POD QTL, except for QTL with small effects and paternal or maternal expression in the design with a small number of parents, for which spurious POD QTL were declared.
Highlights
Genomic imprinting, a non-Mendelian form of gene expression, has been one of the interesting research areas 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)
Polar overdominance quantitative trait loci (QTL) models Derivation of the model was based on the framework of the least-squares regression interval mapping method for detection of QTL in a breed-cross model, which detects differences in the average effects of alleles that originated from the two parental breeds (Haley et al, 1994)
To generate polar overdominance (POD) models, restrictions were put on the QTL genotype effects, such that in a type I POD model, genotype effects of 11, 21, and 22 are the same, such that = (-apat+amat+d) and (-apat+amat+d) = (-apat amat)
Summary
A non-Mendelian form of gene expression, has been one of the interesting research areas 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 imprinted effects can be detected using QTL interval mapping in F2 crosses between lines or breeds that segregate for marker alleles because of the ability to follow parental origin (Thomsen et al, 2004; Choi et al, 2011; Li et al, 2011). The first objective of this study was to derive a POD model for a genome-scan in a cross between outbred breeds or lines, so as to enable a systematic search of other regions or loci that exhibit POD across the genomes of outbred animals. The second was to validate the proposed POD models by performing simulation studies with different mapping designs and sample sizes, and different modes of inheritance, QTL effects, and allele frequencies in parental.
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