Investigation of three strategies for an international genetic evaluation of beef cattle weaning weight

Phocas, Florence; Donoghue, K. A.; Graser, H. U.

doi:10.1186/1297-9686-37-5-361

Cited by 8 publications

(12 citation statements)

References 16 publications

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“…In beef cattle, Phocas et al (2005) estimated genetic parameters and compared different strategies for an international genetic evaluation on Limousin breed. Venot et al (2007) implemented a genetic evaluation for weaning weight on the same breed among France, Ireland and United Kingdom.…”

Section: Introductionmentioning

confidence: 99%

Genotype × country interaction for weaning weight in the Angus populations of Brazil and Uruguay

et al. 2011

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-It was analyzed the existence of genotype × environment interaction for weaning weight in populations of Angus from Brazil and Uruguay by using records of 73,205 animals (10,257 from Uruguay and 62,948 from Brazil) belonging to 33 and 161 farms and 13 and 34 regions in Uruguay and Brazil, respectively. It was used the one-and two-trait animal model analyses considering weight at weaning of each country as different characters. Coefficients of direct and maternal additivegenetic correlation estimated by two statistical models (including or not bull × country effect) Models included the fixed effects of contemporary group (herd-year and month of birth), sex of the calf, the covariates age of dam at calving (years) and age of calf at weaning (days), and the random effects genetic-additive maternal and direct, maternal permanent environment and residual. Herdabilidades (of direct effect) were similar in both countries and with moderate magnitude (0.35 and 0.15, respectively). Coeficients of correlation among maternal and direct genetic effects between Brazil and Uruguay were 0.77 and 0.13, respectively, and comparison among models (with and without bull × country effect) showed significant differences.

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Section: Introductionmentioning

confidence: 99%

Genotype × country interaction for weaning weight in the Angus populations of Brazil and Uruguay

et al. 2011

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“…41 did not allow the deregression of two genetic effects simultaneously, which would, however, be appropriate using models that consider imprinting by including two genetic effects. In an article on the international genetic evaluation of beef cattle weaning weight 63 , the separate deregression of direct genetic effects and maternal genetic effects was described. A correction was presented, in which the contributions of the second correlated effect to the variance of the first are eliminated, when the first genetic effect is deregressed.…”

Section: Discussionmentioning

confidence: 99%

“…A correction was presented, in which the contributions of the second correlated effect to the variance of the first are eliminated, when the first genetic effect is deregressed. With the help of a λ-value, corrected heritability was computed both for the direct and maternal effect, which can be interpreted as equivalent heritability under a single trait model 63 . The same principle could be applied to the reduced imprinting model (for details see the Supplementary Material).…”

Section: Discussionmentioning

confidence: 99%

Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny

Blunk

Mayer

Hamann³

et al. 2019

Sci Rep

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Depending on their parental origin, alleles at imprinted loci are fully or partially inactivated through epigenetic mechanisms. Their effects contribute to the broader class of parent-of-origin effects. Standard methodology for mapping imprinted quantitative trait loci in association studies requires phenotypes and parental origin of marker alleles (ordered genotypes) to be simultaneously known for each individual. As such, many phenotypes are known from un-genotyped offspring in ongoing breeding programmes (e.g. meat animals), while their parents have known genotypes but no phenotypes. By theoretical considerations and simulations, we showed that the limitations of standard methodology can be overcome in such situations. This is achieved by first estimating parent-of-origin effects, which then serve as dependent variables in association analyses, in which only imprinted loci give a signal. As a theoretical foundation, the regression of parent-of-origin effects on the number of B-alleles at a biallelic locus — representing the un-ordered genotype — equals the imprinting effect. The applicability to real data was demonstrated for about 1800 genotyped Brown Swiss bulls and their un-genotyped fattening progeny. Thus, this approach unlocks vast data resources in various species for imprinting analyses and offers valuable clues as to what extent imprinted loci contribute to genetic variability.

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“…In the context of international evaluations, international EBVs (IEBVs) are computed across different environments (i.e., countries) for a series of traits ( Durr and Philipsson, 2012 ; Crook et al, 2019 ). Some of the traits evaluated in beef international evaluations are influenced by maternal effects, e.g., birth weight, weaning weight, and calving ease ( Phocas et al, 2005 ; Venot et al, 2006 ; Venot et al, 2007 ; Venot et al, 2008 ; Pabiou et al, 2014 ; Crook et al, 2019 ; Vesela et al, 2019 ). Due to the presence of genotype by environment interaction (i.e., genotype by country interaction), and differences in trait and model definition, genetic correlations ( r g ) for direct genetic effects, maternal genetic effects, and r dm can differ between countries ( De Mattos et al, 2000 ; Mark et al, 2005 ; Pabiou et al, 2014 ; Bonifazi et al, 2020b ).…”

Section: Introductionmentioning

confidence: 99%

“…International genetic evaluations require estimates of across-country r g ( Phocas et al, 2005 ). However, the estimation process can be challenging ( Mark et al, 2005 ; Venot et al, 2007 ), especially in beef cattle due to the low number of existing genetic connections between countries ( Berry et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

The impact of direct-maternal genetic correlations on international beef cattle evaluations for Limousin weaning weight

Bonifazi

Vandenplas

Napel

et al. 2021

Journal of Animal Science

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In beef cattle maternally influenced traits, estimates of direct-maternal genetic correlations (rdm) are usually reported to be negative. In international evaluations, rdm can differ both within countries (rdm_WC) and between countries (rdm_BC). The rdm_BC are difficult to estimate and are assumed to be zero in the current model for international beef cattle evaluations (Interbeef). Our objective was to investigate re-ranking of international EBV (IEBV) in international beef cattle evaluations between models that either used estimated values for rdm or assumed them to be 0. Age-adjusted weaning weights and pedigree data were available for Limousin beef cattle from ten European countries. International EBV were obtained using a multi-trait animal model with countries modelled as different traits. We compared IEBV from a model that uses estimated rdm_BC (ranging between -0.14 and +0.14) and rdm_WC (between -0.33 and +0.40) with IEBV obtained either from the current model that assumes rdm_BC to be 0, or from an alternative model that assumes both rdm_BC and rdm_WC to be 0. Direct and maternal IEBV were compared across those three scenarios for different groups of animals. The ratio of population accuracies from the Linear Regression method was used to further investigate the impact of rdm on international evaluations, for both the whole set of animals in the evaluation and the domestic ones. Ignoring rdm_BC, i.e. replacing estimated values with 0, resulted in no (rank correlations > 0.99) or limited (between 0.98 and 0.99) re-ranking for direct and maternal IEBV, respectively. Both rdm_BC and rdm_WC had less impact on direct IEBV than on maternal IEBV. Re-ranking of maternal IEBV decreased with increasing reliability. Ignoring rdm_BC resulted in no re-ranking for sires with IEBV that might be exchanged across countries, and limited re-ranking for the top 100 sires. Using estimated rdm_BC values instead of considering them to be to 0, resulted in null to limited increases in population accuracy. Ignoring both rdm_BC and rdm_WC resulted in considerable re-ranking of animals’ IEBV in all groups of animals evaluated. This study showed the limited impact of the current practice of ignoring rdm_BC in international evaluations for Limousin weaning weight, most likely because the estimated rdm_BC were close to 0. We expect that these conclusions can be extended to other traits that have reported rdm values in the range of rdm_WC values for weaning weight in Limousin.

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Investigation of three strategies for an international genetic evaluation of beef cattle weaning weight

Cited by 8 publications

References 16 publications

Genotype × country interaction for weaning weight in the Angus populations of Brazil and Uruguay

Genotype × country interaction for weaning weight in the Angus populations of Brazil and Uruguay

Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny

The impact of direct-maternal genetic correlations on international beef cattle evaluations for Limousin weaning weight

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