Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/12339
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dc.contributor.authorWeerasinghe, Shalaneeen
dc.contributor.authorGondro, Cedricen
dc.contributor.authorHenshall, John Men
dc.contributor.authorJeyaruban, M Gilberten
dc.contributor.authorGibson, Johnen
local.source.editorEditor(s): S Koonawootrittriron, T Suwanasopee, T Jaichansukkit, D Jattawa, K Boonyanuwat and P Skunmunen
dc.date.accessioned2013-03-26T16:33:00Z-
dc.date.issued2012-
dc.identifier.citationImproving Smallholder and Industrial Livestock Production for Enhancing Food Security, Environment and Human Welfare: Proceedings - Full Papers of the 15th AAAP Animal Science Congress, p. 1755-1758en
dc.identifier.urihttps://hdl.handle.net/1959.11/12339-
dc.description.abstractAccurate prediction of breed composition in livestock species is important for a range of decision making in breeding programs. High density data on single nucleotide polymorphism (SNP) markers should provide more reliable predictions of breed compositions than data from microsatellite makers, which cannot achieve such high information content across the whole genome. Sheep populations in Australia consist of pure breeds, relatively recently developed synthetic breeds and various structured crosses. The main objective of this study was to assess the utility of SNP data to analyse population structure and breed composition in Australian sheep. First filial generation (F1) progeny from the Sheep CRC Information Nucleus (INF) were used in the analysis along with relevant breeds selected from the international Sheep HapMap data. After quality quntrol (QC) filtering, 46,700 SNPs genotyped on the Illumina Ovine 50k SNP chip were included in the study. Principal component analysis (PCA) was conducted with selected Sheep HapMap animals to determine the genetic structure of the pure breeds. Based on the PCA results pure breed individuals were selected as a reference population to obtain estimates of the breed composition of F1 offspring using STRUCTURE. Five crossbred groups were subjected to separate analyses with STRUCTURE using different subsets of SNPs and estimates were compared to the F1 pedigree expectation of proportion Merino (= 0.5). While animals from well-defined pure breeds formed tight clusters in the PCA, animals from synthetic breeds exhibited higher variation forming less well defined clusters. The F1 from the pure breeds were tightly clustered mid-way between the parent breeds while greater dispersion was observed in the F1 with a synthetic parental breed. When using all 46,700 markers in the analysis, the standard deviations for the estimated Merino proportions in the F1animals were 0.016, 0.026, 0.016 and 0.017 for, respectively, Merino X Border Leicester, Merino X Texel, Merino X Coopworth and Merino X Suffolk. With a higher number of SNPs the estimation of breed composition is highly accurate and has a low bias. The biases of estimation of breed proportion are higher with genetically more diverse synthetic breeds such as Coopworth and Suffolk.en
dc.languageenen
dc.publisherAnimal Husbandry Association of Thailand (AHAT)en
dc.relation.ispartofImproving Smallholder and Industrial Livestock Production for Enhancing Food Security, Environment and Human Welfare: Proceedings - Full Papers of the 15th AAAP Animal Science Congressen
dc.titleUse of SNP Marker Data to Analyse Population Structure in Crossbred Sheepen
dc.typeConference Publicationen
dc.relation.conferenceAAAP 2012: 15th Asian-Australasian Association of Animal Production Societies Animal Science Congressen
dc.subject.keywordsLife Historiesen
local.contributor.firstnameShalaneeen
local.contributor.firstnameCedricen
local.contributor.firstnameJohn Men
local.contributor.firstnameM Gilberten
local.contributor.firstnameJohnen
local.subject.for2008060308 Life Historiesen
local.subject.seo2008830310 Sheep - Meaten
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailsweerasi@une.edu.auen
local.profile.emailcgondro2@une.edu.auen
local.profile.emailJohn.Henshall@csiro.auen
local.profile.emailgjeyarub@une.edu.auen
local.profile.emailjgibson5@une.edu.auen
local.output.categoryE1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20130324-181635en
local.date.conference26th - 30th November, 2012en
local.conference.placeBangkok, Thailanden
local.publisher.placeBangkok, Thailanden
local.identifier.runningnumberPaper Code: C36-OP-331en
local.format.startpage1755en
local.format.endpage1758en
local.peerreviewedYesen
local.contributor.lastnameWeerasingheen
local.contributor.lastnameGondroen
local.contributor.lastnameHenshallen
local.contributor.lastnameJeyarubanen
local.contributor.lastnameGibsonen
dc.identifier.staffune-id:sweerasien
dc.identifier.staffune-id:cgondro2en
dc.identifier.staffune-id:jhenshalen
dc.identifier.staffune-id:gjeyaruben
dc.identifier.staffune-id:jgibson5en
local.profile.orcid0000-0003-0666-656Xen
local.profile.orcid0000-0002-0231-0120en
local.profile.orcid0000-0003-0371-2401en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:12546en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleUse of SNP Marker Data to Analyse Population Structure in Crossbred Sheepen
local.output.categorydescriptionE1 Refereed Scholarly Conference Publicationen
local.conference.detailsAAAP 2012: 15th Asian-Australasian Association of Animal Production Societies Animal Science Congress, Bangkok, Thailand, 26th - 30th November, 2012en
local.search.authorWeerasinghe, Shalaneeen
local.search.authorGondro, Cedricen
local.search.authorHenshall, John Men
local.search.authorJeyaruban, M Gilberten
local.search.authorGibson, Johnen
local.uneassociationUnknownen
local.year.published2012en
local.subject.for2020310408 Life historiesen
local.subject.seo2020100412 Sheep for meaten
local.date.start2012-11-26-
local.date.end2012-11-30-
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
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