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Non-additive genetic variation in growth, carcass and fertility traits of beef cattle
- Source :
- Genetics Selection Evolution, Genetics Selection Evolution, 2015, 47 (1), pp.26. ⟨10.1186/s12711-015-0114-8⟩, Genetics, Selection, Evolution : GSE
- Publication Year :
- 2015
- Publisher :
- HAL CCSD, 2015.
-
Abstract
- International audience; AbstractBackgroundA better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of individuals. Genome-wide panels of single nucleotide polymorphisms (SNPs) have been mainly used to map additive effects for quantitative traits, but they can also be used to investigate non-additive effects. We estimated dominance and epistatic effects of SNPs on various traits in beef cattle and the variance explained by dominance, and quantified the increase in accuracy of phenotype prediction by including dominance deviations in its estimation.MethodsGenotype data (729 068 real or imputed SNPs) and phenotypes on up to 16 traits of 10 191 individuals from Bos taurus, Bos indicus and composite breeds were used. A genome-wide association study was performed by fitting the additive and dominance effects of single SNPs. The dominance variance was estimated by fitting a dominance relationship matrix constructed from the 729 068 SNPs. The accuracy of predicted phenotypic values was evaluated by best linear unbiased prediction using the additive and dominance relationship matrices. Epistatic interactions (additive × additive) were tested between each of the 28 SNPs that are known to have additive effects on multiple traits, and each of the other remaining 729 067 SNPs.ResultsThe number of significant dominance effects was greater than expected by chance and most of them were in the direction that is presumed to increase fitness and in the opposite direction to inbreeding depression. Estimates of dominance variance explained by SNPs varied widely between traits, but had large standard errors. The median dominance variance across the 16 traits was equal to 5% of the phenotypic variance. Including a dominance deviation in the prediction did not significantly increase its accuracy for any of the phenotypes. The number of additive × additive epistatic effects that were statistically significant was greater than expected by chance.ConclusionsSignificant dominance and epistatic effects occur for growth, carcass and fertility traits in beef cattle but they are difficult to estimate precisely and including them in phenotype prediction does not increase its accuracy.
- Subjects :
- Male
Meat
[SDV]Life Sciences [q-bio]
Best linear unbiased prediction
Quantitative trait locus
Biology
Beef cattle
Polymorphism, Single Nucleotide
03 medical and health sciences
Genetic variation
Inbreeding depression
Genetics
Animals
Genetics(clinical)
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Genes, Dominant
2. Zero hunger
0303 health sciences
Research
0402 animal and dairy science
Epistasis, Genetic
04 agricultural and veterinary sciences
General Medicine
Explained variation
040201 dairy & animal science
Fertility
Phenotype
Epistasis
Cattle
Female
Animal Science and Zoology
Residual feed intake
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 12979686
- Database :
- OpenAIRE
- Journal :
- Genetics Selection Evolution, Genetics Selection Evolution, 2015, 47 (1), pp.26. ⟨10.1186/s12711-015-0114-8⟩, Genetics, Selection, Evolution : GSE
- Accession number :
- edsair.doi.dedup.....7e924dd0ac01a8e6ccde70bc639e3bc3