Imprinting in Genome Analysis: Modeling Parent‐Of‐Origin Effects in QTL Studies

Rowe, Suzanne; Bishop, Stephen; Koning, Dirk-Jan de

doi:10.1002/9781119949930.ch7

Cited by 3 publications

(4 citation statements)

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“…The problems caused by PofO on genome-wide association (GWA) analyses has been discussed in detail by Rowe et al (2012) and it is obvious that this remains challenging, as the recent standard approach for fine mapping using dense SNPs may not work well. Typically, GWA studies regress the phenotype on the number of (minor) alleles present at the locus, however, with polar overdominance and an allele frequency approaching 0.5, the regression of a trait showing polar overdominance on allele count will be close to zero (see Rowe et al, 2012). Hence standard GWA analyses miss the effect.…”

Section: Discussionmentioning

confidence: 99%

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Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs

Macfarlane

Lambe

Matika

et al. 2014

animal

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TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n = 34) in addition to homozygote non-carriers (+ / + ; n = 40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/ + ; n = 53) or their dam (+ /TM; n = 17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from + 0.54 to + 2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/ + than + / + lambs (+2.9% to + 7.9%; P < 0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant ( P < 0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly ( P < 0.05) heavier than + / + (+11.1% and + 7.3%, respectively) and + /TM animals (+11.9% and + 11.7%, respectively), with TM/ + intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/ TM than + / + lambs ( P < 0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/ + than + / + lambs ( P < 0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/ + than + / + lambs (−11.2%; P < 0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).

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Section: Discussionmentioning

confidence: 99%

“…Hence standard GWA analyses miss the effect. To overcome this problem, one would need phased haplotypes, that is knowledge of the PofO, and specifically fit phased-haplotype-derived genotype class in the analysis, as suggested earlier (Rowe et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs

Macfarlane

Lambe

Matika

et al. 2014

animal

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“…Here we show this decomposition can be written in a mathematically equivalent way that makes its biological interpretation clearer. Earlier work on partitioning kinship matrices into maternal and paternal components is described in ( Rowe et al 2009 , 2011 ).…”

Section: Methodsmentioning

confidence: 99%

Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

Mont

Hernandez-Pliego

Cañete

et al. 2018

G3 Genes|Genomes|Genetics

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In this study we investigate the effects of parent of origin on complex traits in the laboratory rat, with a focus on coping style behavior in stressful situations. We develop theory, based on earlier work, to partition heritability into a component due to a combination of parent of origin, maternal, paternal and shared environment, and another component that estimates classical additive genetic variance. We use this theory to investigate the effects on heritability of the parental origin of alleles in 798 outbred heterogeneous stock rats across 199 complex traits. Parent-of-origin-like heritability was on average 2.7fold larger than classical additive heritability. Among the phenotypes with the most enhanced parent-of-origin heritability were 10 coping style behaviors, with average 3.2 fold heritability enrichment. To confirm these findings on coping behavior, and to eliminate the possibility that the parent of origin effects are due to confounding with shared environment, we performed a reciprocal F1 cross between the behaviorally divergent RHA and RLA rat strains. We observed parent-of-origin effects on F1 rat anxiety/coping-related behavior in the Elevated Zero Maze test. Our study is the first to assess genetic parent-of-origin effects in rats, and confirm earlier findings in mice that such effects influence coping and impulsive behavior, and suggest these effects might be significant in other mammals, including humans.

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“…The formulae are given in 7 and are not repeated here (the decomposition for SNPs given here is new). Earlier work on partitioning kinship matrices into maternal and paternal components is described in 11,47 . The important point is that matrices , can be constructed, representing maternal and paternal genotype or haplotype contributions as required.…”

Section: Parent-of-origin Heritability In the Hs Ratsmentioning

confidence: 99%

Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

Mont

Piliego

Cañete

et al. 2018

Preprint

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We develop theory, based on earlier work, to partition heritability into a component due to a combination of parent of origin, maternal, paternal and shared environment, and another component that estimates classical additive genetic variance. We then investigate the effects on heritability of the parental origin of alleles in outbred heterogeneous stock rats across 199 complex traits. Parent-of-origin-like heritability was on average 2.7-fold larger than classical additive heritability. Among the phenotypes with the most enhanced parent-of-origin heritability were 10 coping style behaviors, with average 3.2-fold heritability enrichment. To confirm these findings on coping behaviour, and to eliminate the possibility that the parent of origin effects are due to confounding with shared environment, we performed a reciprocal F1 cross between the behaviourally divergent RHA and RLA rat strains. We observed parentof-origin effects on F1 rat anxiety/coping-related behavior in the Elevated Zero Maze test. Our results are the first to assess genetic parent-of-origin effects in rats, and confirm earlier findings in mice that such effects influence mammalian coping and impulsive behavior. Parent of Origin Effects in the Rat

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Imprinting in Genome Analysis: Modeling Parent‐Of‐Origin Effects in QTL Studies

Cited by 3 publications

References 50 publications

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs

Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

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