Estimation of variance components due to imprinting effects with DFREML and VCE: results of a simulation study

Essl, A.; Voith, K.

doi:10.1046/j.1439-0388.2002.00314.x

Cited by 10 publications

(6 citation statements)

References 14 publications

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“…More recently, Blunk, Mayer, Hamann, and Reinsch (2017b) reported genomic imprinting effects for beef cattle performance by calculating variance components obtained from parsimonious, sire–maternal grandsire (MGS) models by reducing the number of equations. Various imprinting models have been used to evaluate the effects of imprinting on the quantitative traits in beef cattle (Blunk, Mayer, Hamann, & Reinsch, 2017a; Blunk et al., 2017b; Engellandt & Tier, 2002; Neugebauer, Rader, et al, 2010; Tier & Meyer, 2012), dairy cattle (Essl & Voith, 2002) and pigs (De Vries et al., 1994; Neugebauer, Luther, et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Inoue

Nishio

Shoji³

et al. 2020

J Animal Breeding Genetics

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Genomic imprinting should be considered in animal breeding systems to avoid lead in bias in genetic parameter estimation. The objective of this study was to clarify the effects of pedigree information on imprinting variances for carcass traits and fatty acid composition in Japanese Black cattle. Carcass records [carcass weight, rib eye area, rib thickness (RT), subcutaneous fat thickness and beef marbling score (BMS)] and fatty acid composition were obtained for 11,855 Japanese Black feedlot cattle. To estimate and compare the imprinting variances for the traits, two imprinting models with different pedigree information [the sire–dam gametic relationship matrix (Model 1) and the sire–maternal grandsire (MGS) numerator relationship matrix (Model 2)] were fitted. The ratio of the imprinting variance to the total additive genetic variance for RT (6.33%) and BMS (19.00%) was significant in Model 1, but only that for BMS (21.09%) was significant in Model 2. This study revealed that fitting the sire–MGS model could be useful in estimating imprinting variance under certain conditions, such as when restricted pedigree information is available. Furthermore, the present result suggested that the maternal gametic effects on BMS should be included in breeding programmes for Japanese Black cattle to avoid selection bias caused by imprinting effects.

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Section: Introductionmentioning

confidence: 99%

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Inoue

Nishio

Shoji³

et al. 2020

J Animal Breeding Genetics

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“…To model imprinting effects with statistical methods, de Vries, Kerr, Tier, Long, and Meuwissen () first fitted an animal model with an additional paternal or maternal gametic effect. Subsequently, Engellandt and Tier () estimated the effects of paternally expressed (maternally imprinted) genes on carcass traits of beef cattle, and Essl and Voith () estimated variance components caused by genomic imprinting for dairy‐ and fitness‐related traits of dairy cows. In a recent report, Neugebauer, Luther, and Reinsch (); Neugebauer, Räder, Schild, Zimme, and Reinsch () fitted a model with correlated sire and dam gametes to simultaneously estimate for both sexes the imprinting variance of growth and carcass traits in pigs and beef cattle.…”

Section: Introductionmentioning

confidence: 99%

Parent‐of‐origin effects on carcass traits in Japanese Black cattle

Okamoto

Oishi

Nakamura

et al. 2019

J Animal Breeding Genetics

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Variances caused by the differential expression of paternally and maternally imprinted genes controlling carcass traits in Japanese Black cattle were estimated in this study. Data on marbling score (BMS), carcass weight, rib thickness, rib-eye area (REA) and subcutaneous fat thickness (SFT) were collected from a total of 13,115 feedlot steers and heifers in a commercial population. A sire-maternal grandsire model was used to analyse the data, and then, imprinting parameters were derived by replacing the genetic effect of the dam with the effect of the maternal grandsire in the imprinting model to calculate the genetic parameter estimates. The proportions of the total genetic variance attributable to imprinted genes ranged from 8.7% (SFT) to 35.2% (BMS). The remarkably large imprinting variance of BMS was mainly contributed by maternally expressed inheritance because the maternal contribution of the trait was much larger than that of the paternal trait. The parent-of-origin effect originating from maternal gene expression was also observed for REA. The results suggested the existence of genomic imprinting effects on the traits of the Japanese Black cattle. Hence, the parent-of-origin effect should be considered for the genetic evaluation of Japanese Black cattle in breeding programmes. K E Y W O R D S genetic parameter, imprinted genes, imprinting model, Japanese Black, maternal grandsire model, parent-of-origin effect, sire 2 sire =

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“…This approach has been applied to swine (De Vries et al, 1994) and beef cattle (Engellandt and Tier, 2002). Essl and Voith (2002a) proposed a third test based on the difference between variances of maternal and paternal gametic effects obtained from dam and sire models, respectively. Essl and Voith (2002a) applied both of these latter two methods to data from dairy cattle.…”

Section: Introductionmentioning

confidence: 99%

Estimation of variances for gametic effects on litter size in Yorkshire and Landrace swine

Stella

Stalder

Saxton

et al. 2003

Journal of Animal Science

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The objective of this study was to test for effects of gametic imprinting on litter size in swine by estimating variances for parent-specific gametic effects. Data were 64,047 and 137,009 multiparous records of number born alive for the U.S. Landrace and Yorkshire breeds, respectively. The statistical model included fixed effects of parity number and herd, and random effects of herd-year-season, mate, permanent environment, animal (additive genetic), and either maternal or paternal gametes. A Bayesian approach that used Gibbs sampling to obtain posterior distributions was employed. To aid in the interpretation of results, the Landrace data structure was used to simulate data with and without effects of imprinting. Analyses of the simulated records indicated that the model applied was capable of detecting effects of imprinting when such effects were present. Small, but non-zero, estimates of gametic variances were obtained when no imprinting was simulated. Estimates of the proportion of total variance accounted for by paternally transmitted gametes were 0.8 and 0.9% for Landrace and Yorkshires, respectively. These estimates were different from zero, but were similar to the results observed for data simulated without an imprinting effect. Corresponding results for maternally transmitted gametes were 1.6% for Landrace and 0.8% for Yorkshires. The estimate for Landrace was significantly greater than that observed for Yorkshires and for the simulations without a true effect and suggested the presence of a non-Mendelian genetic influence on litter size. Paternally imprinted genes are a plausible reason for the observed results. Assuming that the effect observed was due to paternal imprinting at a single biallelic locus, the substitution effect of the superior allele could be greater than 0.7 piglets per litter. Identification of a genetic marker for such an allele would be useful in marker-assisted selection of females. Other possible explanations exist for the increased gametic variance in the Landrace breed, but these explanations (such as maternal or cytoplasmic effects) may be less likely than paternal imprinting.

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Estimation of variance components due to imprinting effects with DFREML and VCE: results of a simulation study

Cited by 10 publications

References 14 publications

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Parent‐of‐origin effects on carcass traits in Japanese Black cattle

Estimation of variances for gametic effects on litter size in Yorkshire and Landrace swine

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