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Patterns of Genomic Variation and Whole Genome Association Studies of Economically Important Traits in Cattle Open Access


Other title
Economically Important Traits
Whole Genome Association Studies
Type of item
Degree grantor
University of Alberta
Author or creator
Li, Honghao
Supervisor and department
Wang, Zhiquan (Department of Agricultural, Food and Nutritional Science)
Stothard, Paul (Department of Agricultural, Food and Nutritional Science)
Examining committee member and department
Zhang, Peng (Mathematical and Statistical Sciences)
Li, Changxi (Department of Agricultural, Food and Nutritional Science)
Moore, Stephen (Queensland Alliance for Agriculture & Food Innovation, University of Queensland)
Miglior, Filippo (Agriculture Agri-Food Canada)
Department of Agricultural, Food, and Nutritional Science
Animal Science
Date accepted
Graduation date
Doctor of Philosophy
Degree level
Functionally important genetic variations in cattle have great potential as tools to increase agricultural production once they are identified through association studies of phenotype and genotype. The objectives of this thesis were: 1) to characterize the genome-wide patterns of linkage disequilibrium (LD) and haplotype blocks using the genotyping data obtained from the BovineSNP50 BeadChip (50K) assay; 2) to map functionally important genomic regions and genes via genome-wide association studies for economically important traits in dairy and beef cattle; and 3) to investigate the genetic contribution of epistatic QTL to quantitative traits in cattle. First, genome-wide LD and haplotype block maps were constructed for both dairy and hybrid beef populations, and different genome-wide and regional patterns of haplotype blocks between dairy and beef cattle were compared. Next, whole-genome association studies for several economically important traits were performed. Two approaches, single marker regression and Bayesian regression, were used to detect and fine map QTL for five milk production traits and eight beef carcass traits. Both methods revealed QTL regions and functional candidate genes and their networks in dairy and beef cattle. In addition to the novel QTL regions identified, many of the large effect QTL regions overlap with QTL reported in previous studies, and there were many concordances between the single-marker and Bayesian approaches. Following the one-dimensional genome scan for QTL, genome-wide pair-wise epistatic QTL analyses were carried out for dairy traits by using an empirical Bayes method. We ii identified strong additive-by-additive (A × A) epistasis with considerable contribution to the phenotypic variation of analyzed traits. We also observed that epistasis plays different roles in the genetic architectures of different types of traits. The identified A × A epistatic QTL may need to be considered in future breeding programs after further validation studies. Overall, this study will contribute to a better understanding of the genetic basis of phenotypic variation of economically important traits in cattle and identifies markers and genes which may be useful for genetic improvement programs.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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