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

  • Author / Creator
    Li, Honghao
  • 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.

  • Subjects / Keywords
  • Graduation date
    2012-11
  • Type of Item
    Thesis
  • Degree
    Doctor of Philosophy
  • DOI
    https://doi.org/10.7939/R3T713
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Doctoral
  • Department
    • Department of Agricultural, Food, and Nutritional Science
  • Specialization
    • Animal Science
  • Supervisor / co-supervisor and their department(s)
    • Wang, Zhiquan (Department of Agricultural, Food and Nutritional Science)
    • Stothard, Paul (Department of Agricultural, Food and Nutritional Science)
  • Examining committee members and their departments
    • 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)