Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/3141
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dc.contributor.authorMoore, Kirsty Leeen
dc.contributor.authorJohnston, Daviden
dc.contributor.authorGibson, Johnen
dc.date.accessioned2009-11-18T09:52:00Z-
dc.date.created2008en
dc.date.issued2009-
dc.identifier.urihttps://hdl.handle.net/1959.11/3141-
dc.description.abstractGenetic markers provide the Australian beef industry with the opportunity to increase rates of genetic gains. However, accurate estimates of the gene frequencies and the marker size of effects are first required. Stochastic simulation was used to examine the methods and models required to estimate SNP effects. Results showed for a single SNP explaining 2% of the phenotypic variation, 1,500 animals were required to estimate the SNP effects when the favourable allele frequency (p) was 0.5. However, increasing the additive SNP effects decreased the number of animals required. SNP effect estimates were inflated when the power to detect genotype effects was low. In addition, when the allele frequency was rare (p=0.1), biased dominance effects were estimated. For SNPs that were in linkage disequilibrium with the causative SNP, the SNP effects were accurately estimated when linkage disequilibrium was greater than D'=0.9. This thesis found that when there was linkage disequilibrium between the two direct SNPs (explaining 8% of the phenotypic variation, collectively), and one SNP was ignored in the model, estimates of the SNP effects were biased upwards. Ignoring epistatic effects (1% of the phenotypic variance) also increased the estimates of the SNP effects. To estimate accurate SNP and epistatic effects 3,000 animals were required. If SNPs were excluded in the model, the SNP and epistatic variance was partitioned as polygenic and residual variances, respectively. The inclusion of SNPs was shown to increase the accuracy of the estimated breeding value (EBV); the more phenotypic variation explained by the SNPs the higher the increase in EBV accuracy (or estimated genetic merit when non-additive (i.e. epistasis) effects were included). This thesis shows that the population size, allele frequency, statistical power to detect genotype effects, statistical models and the data structure all affect the ability to accurately estimate the size of SNP effects.en
dc.languageenen
dc.titleMethods and Models for the Accurate Estimation of the Effects of Single Nucleotide Polymorphisms (SNP) in Beef Cattleen
dc.typeThesis Doctoralen
dcterms.accessRightsUNE Greenen
dc.subject.keywordsAnimal Breedingen
local.contributor.firstnameKirsty Leeen
local.contributor.firstnameDaviden
local.contributor.firstnameJohnen
local.subject.for2008070201 Animal Breedingen
local.subject.seo630103 Beef cattleen
dcterms.RightsStatementCopyright 2008 - Kirsty Lee Mooreen
dc.date.conferred2009en
local.thesis.degreelevelDoctoralen
local.thesis.degreenameDoctor of Philosophyen
local.contributor.grantorUniversity of New Englanden
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailkmoore7@une.edu.auen
local.profile.emaildjohnsto@une.edu.auen
local.profile.emailjgibson5@une.edu.auen
local.output.categoryT2en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune_thesis-20091023-152444en
local.access.fulltextYesen
local.contributor.lastnameMooreen
local.contributor.lastnameJohnstonen
local.contributor.lastnameGibsonen
dc.identifier.staffune-id:kmoore7en
dc.identifier.staffune-id:djohnstoen
dc.identifier.staffune-id:jgibson5en
local.profile.orcid0000-0001-6779-0148en
local.profile.orcid0000-0002-4995-8311en
local.profile.orcid0000-0003-0371-2401en
local.profile.roleauthoren
local.profile.rolesupervisoren
local.profile.rolesupervisoren
local.identifier.unepublicationidune:3224en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleMethods and Models for the Accurate Estimation of the Effects of Single Nucleotide Polymorphisms (SNP) in Beef Cattleen
local.output.categorydescriptionT2 Thesis - Doctorate by Researchen
local.thesis.borndigitalyesen
local.search.authorMoore, Kirsty Leeen
local.search.supervisorJohnston, Daviden
local.search.supervisorGibson, Johnen
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/529f2318-db80-4e2a-86ca-3bc7ec17e001en
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/eb4e6231-d4fb-4352-93ec-8db2f537ad29en
local.uneassociationYesen
local.year.conferred2009en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/eb4e6231-d4fb-4352-93ec-8db2f537ad29en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/529f2318-db80-4e2a-86ca-3bc7ec17e001en
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Thesis Doctoral
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