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Investigating the role of non-additive genetic effects on the genetic architecture and control of fertility and reproduction traits in Holsteins

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dc.contributor.advisor Schenkel, Flavio
dc.contributor.author Alves, Kristen
dc.date.accessioned 2018-05-07T19:25:30Z
dc.date.available 2019-05-08T05:00:24Z
dc.date.copyright 2018-04
dc.date.created 2018-04-27
dc.date.issued 2018-05-07
dc.identifier.uri http://hdl.handle.net/10214/12990
dc.description.abstract In animal breeding, it is assumed that majority of the variation in a phenotype can be captured by gene variants which combine their effects in an additive manner. In dairy cattle, this assumption works well for most traits. However, for low heritability and complex traits such as fertility and reproduction traits, additive genetic effects may not capture most of the variation. This thesis set out to explore whether it is possible to capture interactions between alleles at one loci (dominance) and between alleles at different loci (additive by additive epistasis) to improve our understanding of the genetic architecture and control of fertility and reproduction traits in Holstein cattle. Additive, dominance, and epistatic genetic variance components using pedigree and genomic relationship matrices were estimated. Dominance and epistasis contributed a larger proportion of the total phenotypic variance than the additive model currently used in practice. Three transformations to the Hadamard product for deriving the epistatic relationship matrix on the estimation of epistatic genetic variance components was investigated. While removing the interaction of a marker with itself decreased the confounding between additive and epistatic genetic effects, there was not a clear advantage as to which matrix was best. Genomic predictions were performed to assess the impact of including genomic information, epistasis, and the variants of the epistatic genomic relationship matrix on the reliability of and bias in model predictions. The results suggest fitting epistatic genetic effects in genomic evaluation models may yield an improvement in the prediction of breeding values and future phenotypes. Lastly, a genome-wide association study was performed to investigate the genetic architecture of the traits. The results suggest that significant epistatic genetic effects are probably due to many loci with a small effect rather than few loci with a large effect. Improving our understanding of the genetic architecture and control of fertility and reproduction traits will help in the proper estimation of breeding values and correct ranking of candidate parents for the next generation. This research emphasizes the need for a re-examination of our tools to help detect causal links between genetic and phenotypic variation. en_US
dc.language.iso en en_US
dc.rights Attribution-NonCommercial-NoDerivs 2.5 Canada *
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/2.5/ca/ *
dc.subject dairy cattle en_US
dc.subject non-additive genetic effect en_US
dc.subject epistatic effect en_US
dc.subject dominance effect en_US
dc.subject fertility en_US
dc.subject reproduction en_US
dc.subject genomic prediction en_US
dc.subject accuracy en_US
dc.subject genome-wide association study en_US
dc.title Investigating the role of non-additive genetic effects on the genetic architecture and control of fertility and reproduction traits in Holsteins en_US
dc.type Thesis en_US
dc.degree.programme Animal and Poultry Science en_US
dc.degree.name Doctor of Philosophy en_US
dc.degree.department Department of Animal Biosciences en_US
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Attribution-NonCommercial-NoDerivs 2.5 Canada Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivs 2.5 Canada