Parent-of-origin effects cause genetic variation in pig performance traits

Neugebauer, N.; Luther, Henning; Reinsch, Norbert

doi:10.1017/s1751731109991625

Cited by 41 publications

(70 citation statements)

References 28 publications

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“…In general, the reliability of genetic estimates depends mainly on the availability of data such as individual records and kinship information (Mrode, 2014). The amount of kinship information depends mainly on the number of progeny.…”

Section: Resultsmentioning

confidence: 99%

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

Blunk

Mayer

Hamann³

et al. 2017

Animal

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Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial). Imprinting effects (or more generally: parent-of-origin effects (POE)) are determined by taking the difference between the two genetic effects in each animal. However, the computation of their prediction error variance (PEV) is laborious; thus, we propose a new model that is equivalent to the aforementioned imprinting model, which facilitates the direct estimation of imprinting effects instead of taking the differences and the PEV is readily obtained. We applied the new model to slaughterhouse data for Brown Swiss cattle, among which imprinting has never been investigated previously. Data were available for up to 173 051 fattening bulls, where the pedigrees contained up to 428 710 animals representing the entire Brown Swiss population of Austria and Germany. The traits analysed comprised the net BW gain, fat score, EUROP class and killing out percentage. The analysis demonstrated that the net BW gain, fat score and EUROP class were influenced significantly by POE. After estimating the POE, the new model yielded estimates with reliabilities ranging between 0.4 and 0.9. On average, the imprinting variances accounted for 9.6% of the total genetic variance, where the maternal gamete was the main contributor. Moreover, our results agreed well with those obtained using linear models when the EUROP class and fat score were treated as categorical traits by applying a GLMM with a logit link function.

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Section: Resultsmentioning

confidence: 99%

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

Blunk

Mayer

Hamann³

et al. 2017

Animal

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“…Analysis of an advanced intercross in mice has shown that body weight is controlled in a parent-of-origin-specific manner throughout life and that about half of the variance at imprinted quantitative trait loci (iQTLs) is attributable to these effects (Wolf et al., 2008). Similarly, large pedigrees of farm animals have been used to demonstrate significant maternal and paternal influences on growth (e.g., Neugebauer et al., 2010), although in the absence of genotype data.…”

Section: Introductionmentioning

confidence: 99%

The Architecture of Parent-of-Origin Effects in Mice

Mott

Wei

Kaisaki

et al. 2014

Cell

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SummaryThe number of imprinted genes in the mammalian genome is predicted to be small, yet we show here, in a survey of 97 traits measured in outbred mice, that most phenotypes display parent-of-origin effects that are partially confounded with family structure. To address this contradiction, using reciprocal F1 crosses, we investigated the effects of knocking out two nonimprinted candidate genes, Man1a2 and H2-ab1, that reside at nonimprinted loci but that show parent-of-origin effects. We show that expression of multiple genes becomes dysregulated in a sex-, tissue-, and parent-of-origin-dependent manner. We provide evidence that nonimprinted genes can generate parent-of-origin effects by interaction with imprinted loci and deduce that the importance of the number of imprinted genes is secondary to their interactions. We propose that this gene network effect may account for some of the missing heritability seen when comparing sibling-based to population-based studies of the phenotypic effects of genetic variants.

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“…Apart from genetic factors that follow Mendelian rules of inheritance, prenatal muscle development and postnatal muscle phenotype may be affected by genetic and epigenetic factors with Non-Mendelian modes of inheritance. This includes effects of mitochondrial genome [22], X- and Y-chromosomes [23], [24], non-random X-inactivation [25], microRNA (miRNA) interference [26] and genomic imprinting [24], [27]–[29]. Genomic imprinting, i.e., parent-of-origin dependent allele-specific gene expression [30], has been described for genes with pivotal roles in myogenesis, including IGF2 and its receptor IGF2R [31], [32].…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the ovine Carwell locus, which exerts paternal effects on weight of M. longissimus dorsi and a shift from type IIA to type IIX myofibres, was mapped to the same chromosome region as the CLPG mutation [41]–[43]. More recently, statistical modelling revealed significant parent-of-origin effects attributed to genomic imprinting on postnatal absolute and relative weights of specific muscles in porcine [27] and bovine [28].…”

Section: Introductionmentioning

confidence: 99%

Maternal and Paternal Genomes Differentially Affect Myofibre Characteristics and Muscle Weights of Bovine Fetuses at Midgestation

et al. 2013

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Postnatal myofibre characteristics and muscle mass are largely determined during fetal development and may be significantly affected by epigenetic parent-of-origin effects. However, data on such effects in prenatal muscle development that could help understand unexplained variation in postnatal muscle traits are lacking. In a bovine model we studied effects of distinct maternal and paternal genomes, fetal sex, and non-genetic maternal effects on fetal myofibre characteristics and muscle mass. Data from 73 fetuses (Day153, 54% term) of four genetic groups with purebred and reciprocal cross Angus and Brahman genetics were analyzed using general linear models. Parental genomes explained the greatest proportion of variation in myofibre size of Musculus semitendinosus (80–96%) and in absolute and relative weights of M. supraspinatus, M. longissimus dorsi, M. quadriceps femoris and M. semimembranosus (82–89% and 56–93%, respectively). Paternal genome in interaction with maternal genome (P<0.05) explained most genetic variation in cross sectional area (CSA) of fast myotubes (68%), while maternal genome alone explained most genetic variation in CSA of fast myofibres (93%, P<0.01). Furthermore, maternal genome independently (M. semimembranosus, 88%, P<0.0001) or in combination (M. supraspinatus, 82%; M. longissimus dorsi, 93%; M. quadriceps femoris, 86%) with nested maternal weight effect (5–6%, P<0.05), was the predominant source of variation for absolute muscle weights. Effects of paternal genome on muscle mass decreased from thoracic to pelvic limb and accounted for all (M. supraspinatus, 97%, P<0.0001) or most (M. longissimus dorsi, 69%, P<0.0001; M. quadriceps femoris, 54%, P<0.001) genetic variation in relative weights. An interaction between maternal and paternal genomes (P<0.01) and effects of maternal weight (P<0.05) on expression of H19, a master regulator of an imprinted gene network, and negative correlations between H19 expression and fetal muscle mass (P<0.001), suggested imprinted genes and miRNA interference as mechanisms for differential effects of maternal and paternal genomes on fetal muscle.

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Parent-of-origin effects cause genetic variation in pig performance traits

Cited by 41 publications

References 28 publications

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

The Architecture of Parent-of-Origin Effects in Mice

Maternal and Paternal Genomes Differentially Affect Myofibre Characteristics and Muscle Weights of Bovine Fetuses at Midgestation

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