Main content

Effects of Sample Size and Single- vs. Multiple-Breed Analyses on Characterizing Runs of Homozygosity in Dairy Cattle

Show full item record

Title: Effects of Sample Size and Single- vs. Multiple-Breed Analyses on Characterizing Runs of Homozygosity in Dairy Cattle
Author: Vogelzang, Calista
Department: Department of Animal Biosciences
Program: Animal and Poultry Science
Advisor: Baes, Christine
Abstract: The understanding and management of inbreeding is an ongoing challenge in the dairy industry. Runs of homozygosity (ROH) can provide more accurate estimates of the realized proportion of the genome shared between individuals. The objective of this thesis was to characterize ROH in dairy cattle breeds using different ROH detection methods. Data was prepared using PLINK and R, and BCFtools was the used to detect ROH. The R packages detectRUNS and pedigree were then used to characterize ROH and to calculate pedigree-based inbreeding respectively. SNP inclusion in single- and multiple-breed analyses impacted the degree of breed differences observed. Sample size was shown to affect the accuracy of ROH characterization. The results from this study indicate ROH could potentially be used manage inbreeding levels. Future research will aim to develop a method to minimize breed bias in multiple-breed analyses and to understand breed differences.
URI: http://hdl.handle.net/10214/14262
Date: 2018-08
Rights: Attribution 2.5 Canada


Files in this item

Files Size Format View
Vogelzang_Calista_201808_Msc.pdf 1.030Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record

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