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dc.contributor.advisorØdegård, Jørgen
dc.contributor.advisorMeuwissen, Theo
dc.contributor.authorGrashei, Kim Erik
dc.coverage.spatialNorway, Åsen_US
dc.description.abstractThe use of high-density single nucleotide polymorphism (SNP) genotypes enables us to perform highly accurate parentage assignment. However, dependence between loci often results in using a subset of the data to obtain independent loci (likelihood- based parentage assignment), or just a fraction of the genotypes may be informative (exclusion-based parentage assignment). In this thesis, a novel method is suggested to perform parentage assignment using, at its core, genomic relationships which are estimated without the assumption of independence between the loci. Thus, all information from the SNP genotypes is used. In Paper 1, we show that the suggested method, called genomic relationship likelihood (GRL), obtains high accuracies when applied to high-density genotypes. The accuracy obtained by GRL is similar to the one obtained by the exclusion-based method we used for comparison, however with some differences as noted in Paper 1. Genotyping triploid individuals who inherit two chromatids from the mother and a single chromatid from the father may be useful for species where escapees are an issue, such as in aquaculture. Genotyping triploids may also be useful for breeding programs where triploids are part of the product portfolio because genetic traits may differ between triploids and diploids. In Paper 2, we suggest a novel way of calling genotypes for triploids, and we use the called genotypes to assign the parents of triploid offspring. Due to the special inheritance pattern between mother and triploid offspring, direct assignment of mothers is shown to be both possible and useful. In addition, this inheritance pattern allowed us to map maternal crossovers which have occurred during meiosis. In some situations, genotyping may be restricted to one category of a binary trait (cases), for example when there is a disease outbreak in a commercial population. In Paper 3, we show that it is possible to estimate heritability and to predict genomic breeding values even when using case-only genotypes in combination with their parental genotypes. The proposed method, called transmission disequilibrium genomic prediction (TDGP), is essentially a genome-wide generalization of the transmission disequilibrium test (TDT), with many of the same pros and cons.en_US
dc.publisherNorwegian University of Life Sciences, Åsen_US
dc.relation.ispartofseriesPhd Thesis;2021:7
dc.rightsNavngivelse 4.0 Internasjonal*
dc.subjectParentage assignmenten_US
dc.subjectGenotype callingen_US
dc.subjectMixture modelsen_US
dc.subjectQuantitative geneticsen_US
dc.titleGenomic methods in breeding programs: Parental assignment, triploid genomics and case-parental control modellingen_US
dc.title.alternativeGenomiske metoder i avlsprogrammer: Foreldretilordning, triploid genomikk og kasus-foreldrekontroll-modelleringen_US
dc.typeDoctoral thesisen_US
dc.subject.nsiVDP::Mathematics and natural science: 400en_US
dc.subject.nsiVDP::Mathematics and natural science: 400::Basic biosciences: 470::Bioinformatics: 475en_US
dc.subject.nsiVDP::Mathematics and natural science: 400::Mathematics: 410::Statistics: 412en_US
dc.relation.projectNorges Forskningsråd 251664en_US
dc.relation.projectNorges Forskningsråd 245519en_US

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Navngivelse 4.0 Internasjonal
Except where otherwise noted, this item's license is described as Navngivelse 4.0 Internasjonal