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

dc.contributor.advisorBaes, Christine
dc.contributor.authorVogelzang, Calista
dc.date.accessioned2018-09-05T20:21:31Z
dc.date.available2018-09-05T20:21:31Z
dc.date.copyright2018-08
dc.date.created2018-08-15
dc.date.issued2018-09-05
dc.degree.departmentDepartment of Animal Biosciencesen_US
dc.degree.grantorUniversity of Guelphen_US
dc.degree.nameMaster of Scienceen_US
dc.degree.programmeAnimal and Poultry Scienceen_US
dc.description.abstractThe 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.en_US
dc.description.sponsorshipCanadian Dairy Network
dc.description.sponsorshipNatural Sciences and Engineering Research Council of Canada
dc.identifier.urihttp://hdl.handle.net/10214/14262
dc.language.isoenen_US
dc.publisherUniversity of Guelphen_US
dc.rightsAttribution 2.5 Canada*
dc.rights.urihttp://creativecommons.org/licenses/by/2.5/ca/*
dc.subjectruns of homozygosityen_US
dc.subjectinbreedingen_US
dc.subjectdairy cattleen_US
dc.titleEffects of Sample Size and Single- vs. Multiple-Breed Analyses on Characterizing Runs of Homozygosity in Dairy Cattleen_US
dc.typeThesisen_US

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