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Application of High-throughput Genomic Data in the Genetic Analysis of Pigs Open Access

Descriptions

Other title
Subject/Keyword
genomic data
pigs
genetic analysis
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Yang, Tianfu
Supervisor and department
Wang, Zhiquan (Department of Agricultural, Food and Nutritional Science)
Plastow, Graham (Department of Agricultural, Food and Nutritional Science)
Examining committee member and department
Plastow, Graham (Department of Agricultural, Food and Nutritional Science)
Stothard, Paul (Department of Agricultural, Food and Nutritional Science)
Wang, Zhiquan (Department of Agricultural, Food and Nutritional Science)
Coltman, David (Department of Biological Sciences)
De Koning, Dirk-Jan (Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences)
Department
Department of Agricultural, Food, and Nutritional Science
Specialization
Animal Science
Date accepted
2017-06-09T09:14:51Z
Graduation date
2017-11:Fall 2017
Degree
Doctor of Philosophy
Degree level
Doctoral
Abstract
The emergence of high-throughput genomic data provides new opportunities for genetic analysis. Especially, in terms of genetic improvement of animals, genomic tools provide new tools for animal selection, while still suffering from some statistical issues due to the high-dimension of the genomic data. In my thesis work, I aimed to better interpret available genomic data by integrating information from various sources (e.g. different types of data) and knowledge in different areas (e.g. genomics, statistics and animal science), and attempted to make better use of high-throughput genomic data in the genetic analysis of pigs, especially in the context of genetic improvement. More specifically, the objective of the thesis work is twofold: 1) to improve the detection power and precision in two genome-wide association studies (GWAS), one for meat colour of pork and one for fetal response to PRRSV challenge in pigs; and 2) to explore a new strategy for constructing linkage maps. I worked toward this goal in four studies. For the studies about GWAS (Chapter 2-4), I discussed the issue about detection power and precision due to the high dimension of genomic data. In the study about the adaptive LASSO (Chapter 2), I assessed its performance and discussed how it may help to increase the detection power in GWAS. In the GWAS of fetal response to type 2 PRRSV challenge (Chapter 3), I made use of permutation to improve the precision of the results, and used transcriptomic data to further scan for candidate genes. In the TDT study (Chapter 4), I improved the precision of GWAS by integrating raw genotyping data (fluorescence intensity data) into the analysis. In the study about multiple sperm typing (Chapter 5), I proposed a new model for the allele dosage data of haploids, in order to improve the efficiency of linkage map construction. In the thesis work. Twenty candidate genomic regions were found to be associated with meat colour of pork (Chapter 2), and 21 candidate regions were found for fetal response to PRRSV challenge in pigs (Chapter 3). These candidate regions may lead to new genetic markers for marker-assisted selection in the future. Some results implied better performance of the methods used in the GWAS, in terms of higher detection power and/or higher precision, which provides valuable experience in the analysis of high-dimensional genomic data. In addition, a new strategy was proposed to construct linkage maps using allele dosage data of sperm cells, which showed good accuracy in simulation studies (Chapter 5). The good performance in the simulation studies implied its application in animal genomics. Especially, its potential ability to genotype chromosome structural variations (CSVs) and estimate recombination rate on an individual level may provide additional materials for genetic improvement.
Language
English
DOI
doi:10.7939/R3C824T9J
Rights
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. 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.
Citation for previous publication
Tianfu Yang, Zhiquan Wang, Younes Miar, Heather Bruce, Chunyan Zhang, and Graham Plastow, “A Genome-wide Association Study of Meat Colour in Commercial Crossbred Pigs.” Accepted by Canadian Journal of Animal ScienceTianfu Yang, James Wilkinson, Zhiquan Wang, Andrea Ladinig, John Harding, and Graham Plastow. 2016. “A Genome-Wide Association Study of Fetal Response to Type 2 Porcine Reproductive and Respiratory Syndrome Virus Challenge.” Scientific Reports, 6 (February): 20305.Tianfu Yang, Zhiquan Wang, Zhiqiu Hu and Graham Plastow, 2014. A New Method to Estimate Recombination Rate Based on SNP Allelic Dosage Data. in Proceedings of 10th World Congress of Genetics Applied to Livestock Production. Asas.

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