Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Zeng, Jian; Toosi, Ali; Fernando, Rohan L.; Dekkers, Jack C. M.; Garrick, Dorian J.

doi:10.1186/1297-9686-45-11

Cited by 82 publications

(87 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the current study, we also observed similar results, and dominance variation accounted for a small proportion of the total genetic variation (4 to 10%). The lack of change in predictive ability also indicated the difficulty of distinguishing dominance genetic effects from additive genetic effects [9], but it confirmed a previous simulation study that concluded that the use of a dominance model did not negatively affect genomic evaluation even if the trait was purely additive [18]. …”

Section: Discussionsupporting

confidence: 68%

“…However, our results showed that inclusion of dominance deviations did not increase the predictive ability for crossbreds. This result was in line with conclusions in [9, 12, 20], but was opposite to those in [18, 19, 48, 49]. Theoretically, estimating dominance genetic effects should be useful because ignoring them will result in less accurate estimates of allele substitution effects and consequently less accurate estimated breeding values in genomic prediction [11].…”

Section: Discussionsupporting

confidence: 65%

“…However, these studies generally ignore the dominance effects. A number of studies have been carried out on genomic evaluation including dominance effects using either simulated [18] or real purebred data [9, 12]. …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs

et al. 2016

View full text Add to dashboard Cite

BackgroundImproved performance of crossbred animals is partly due to heterosis. One of the major genetic bases of heterosis is dominance, but it is seldom used in pedigree-based genetic evaluation of livestock. Recently, a trivariate genomic best linear unbiased prediction (GBLUP) model including dominance was developed, which can distinguish purebreds from crossbred animals explicitly. The objectives of this study were: (1) methodological, to show that inclusion of marker-based inbreeding accounts for directional dominance and inbreeding depression in purebred and crossbred animals, to revisit variance components of additive and dominance genetic effects using this model, and to develop marker-based estimators of genetic correlations between purebred and crossbred animals and of correlations of allele substitution effects between breeds; (2) to evaluate the impact of accounting for dominance effects and inbreeding depression on predictive ability for total number of piglets born (TNB) in a pig dataset composed of two purebred populations and their crossbreds. We also developed an equivalent model that makes the estimation of variance components tractable.ResultsFor TNB in Danish Landrace and Yorkshire populations and their reciprocal crosses, the estimated proportions of dominance genetic variance to additive genetic variance ranged from 5 to 11%. Genetic correlations between breeding values for purebred and crossbred performances for TNB ranged from 0.79 to 0.95 for Landrace and from 0.43 to 0.54 for Yorkshire across models. The estimated correlation of allele substitution effects between Landrace and Yorkshire was low for purebred performances, but high for crossbred performances. Predictive ability for crossbred animals was similar with or without dominance. The inbreeding depression effect increased predictive ability and the estimated inbreeding depression parameter was more negative for Landrace than for Yorkshire animals and was in between for crossbred animals.ConclusionsMethodological developments led to closed-form estimators of inbreeding depression, variance components and correlations that can be easily interpreted in a quantitative genetics context. Our results confirm that genetic correlations of breeding values between purebred and crossbred performances within breed are positive and moderate. Inclusion of dominance in the GBLUP model does not improve predictive ability for crossbred animals, whereas inclusion of inbreeding depression does.

show abstract

Section: Discussionsupporting

confidence: 68%

Section: Discussionsupporting

confidence: 65%

See 1 more Smart Citation

Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Further, GS with a dominance model was superior for the selection of purebreds for cross‐bred performance (Zeng et al . ). However, few studies have assessed the effect of dominance effects on the accuracy of GEBV in poultry.…”

Section: Introductionmentioning

confidence: 97%

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers

Heidaritabar

Wolc

Arango

et al. 2016

J Animal Breeding Genetics

View full text Add to dashboard Cite

Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population.

show abstract

“…Hybrids are then transferred to commercial operations where the final product, usually a three-way cross, is produced by more than one million commercial sows. For such systems, the breeding goal in purebred populations should be optimizing the performance of crossbred progeny [16]. Another important parameter to be evaluated is the genetic diversity of a population, as this is relevant to the sustainable use of genetic resources and continued long-term genetic improvement [17].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

et al. 2017

View full text Add to dashboard Cite

BackgroundKnowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers).ResultsThe overall LD (r 2) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire.ConclusionsAn overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0473-y) contains supplementary material, which is available to authorized users.

show abstract

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Cited by 82 publications

References 22 publications

Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs

Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

Contact Info

Product

Resources

About