Main content

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

Show full item record

Title: Investigating the role of non-additive genetic effects on the genetic architecture and control of fertility and reproduction traits in Holsteins
Author: Alves, Kristen
Department: Department of Animal Biosciences
Program: Animal and Poultry Science
Advisor: Schenkel, Flavio
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.
URI: http://hdl.handle.net/10214/12990
Date: 2018-04
Rights: Attribution-NonCommercial-NoDerivs 2.5 Canada
Terms of Use: All items in the Atrium are protected by copyright with all rights reserved unless otherwise indicated.


Files in this item

Files Size Format View
Alves_Kristen_201804_PhD.pdf 6.121Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record

Attribution-NonCommercial-NoDerivs 2.5 Canada Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivs 2.5 Canada