Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/14397
Full metadata record
DC FieldValueLanguage
dc.contributor.authorBolormaa, Sunduimijiden
dc.contributor.authorPryce, Jennie Een
dc.contributor.authorKemper, Kathryn Een
dc.contributor.authorHayes, Ben Jen
dc.contributor.authorZhang, Yuandanen
dc.contributor.authorTier, Bruceen
dc.contributor.authorBarendse, Williamen
dc.contributor.authorReverter, Antonioen
dc.contributor.authorGoddard, Mike Een
dc.date.accessioned2014-03-28T10:47:00Z-
dc.date.issued2013-
dc.identifier.citationGenetics Selection Evolution, v.45, p. 1-12en
dc.identifier.issn1297-9686en
dc.identifier.issn0999-193Xen
dc.identifier.urihttps://hdl.handle.net/1959.11/14397-
dc.description.abstractBackground: The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between 'Bos indicus' and 'Bos taurus' because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a 'Bos taurus' or 'Bos indicus' ancestor. Methods: Phenotype data on one or more traits and SNP genotype data for 10 181 cattle from 'Bos taurus', 'Bos indicus' and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. 'indicus' or B. 'taurus' on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin. Results: Fitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies. Conclusions: The results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. 'indicus' and B. 'taurus' cattle. Thus, the QTL that segregate in current populations likely resulted from mutations that occurred in one of the subspecies and can have both positive and negative effects on the traits. There was no evidence that selection has increased the frequency of alleles that increase body weight.en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofGenetics Selection Evolutionen
dc.titleDetection of quantitative trait loci in 'Bos indicus' and 'Bos taurus' cattle using genome-wide association studiesen
dc.typeJournal Articleen
dc.identifier.doi10.1186/1297-9686-45-43en
dcterms.accessRightsGolden
dc.subject.keywordsAnimal Breedingen
dc.subject.keywordsGenomicsen
local.contributor.firstnameSunduimijiden
local.contributor.firstnameJennie Een
local.contributor.firstnameKathryn Een
local.contributor.firstnameBen Jen
local.contributor.firstnameYuandanen
local.contributor.firstnameBruceen
local.contributor.firstnameWilliamen
local.contributor.firstnameAntonioen
local.contributor.firstnameMike Een
local.subject.for2008070201 Animal Breedingen
local.subject.for2008060408 Genomicsen
local.subject.seo2008830301 Beef Cattleen
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.emailbolormaa.sunduimijid@depi.vic.gov.auen
local.profile.emailjennie.pryce@dpi.vic.gov.auen
local.profile.emailkathryn.kemper@dpi.vic.gov.auen
local.profile.emailyzhang4@une.edu.auen
local.profile.emailbtier@une.edu.auen
local.profile.emailBill.Barendse@csiro.auen
local.profile.emailToni.Reverter-Gomez@csiro.auen
local.profile.emailmeg@unimelb.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20140311-14062en
local.publisher.placeUnited Kingdomen
local.identifier.runningnumber43en
local.format.startpage1en
local.format.endpage12en
local.identifier.scopusid84886436618en
local.peerreviewedYesen
local.identifier.volume45en
local.access.fulltextYesen
local.contributor.lastnameBolormaaen
local.contributor.lastnamePryceen
local.contributor.lastnameKemperen
local.contributor.lastnameHayesen
local.contributor.lastnameZhangen
local.contributor.lastnameTieren
local.contributor.lastnameBarendseen
local.contributor.lastnameReverteren
local.contributor.lastnameGoddarden
dc.identifier.staffune-id:yzhang4en
dc.identifier.staffune-id:btieren
local.profile.orcid0000-0002-1998-3313en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:14612en
local.identifier.handlehttps://hdl.handle.net/1959.11/14397en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleDetection of quantitative trait loci in 'Bos indicus' and 'Bos taurus' cattle using genome-wide association studiesen
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.relation.urlhttp://www.gsejournal.org/content/45/1/43en
local.search.authorBolormaa, Sunduimijiden
local.search.authorPryce, Jennie Een
local.search.authorKemper, Kathryn Een
local.search.authorHayes, Ben Jen
local.search.authorZhang, Yuandanen
local.search.authorTier, Bruceen
local.search.authorBarendse, Williamen
local.search.authorReverter, Antonioen
local.search.authorGoddard, Mike Een
local.uneassociationUnknownen
local.year.published2013en
local.subject.for2020300305 Animal reproduction and breedingen
local.subject.for2020310509 Genomicsen
local.subject.seo2020100401 Beef cattleen
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Journal Article
Files in This Item:
2 files
File Description SizeFormat 
Show simple item record

SCOPUSTM   
Citations

43
checked on Sep 14, 2024

Page view(s)

2,220
checked on Jul 23, 2023
Google Media

Google ScholarTM

Check

Altmetric


Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.