Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/18194
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dc.contributor.authorAl-Mamun, Hawlader Abdullahen
dc.contributor.authorClark, Sam Aen
dc.contributor.authorKwan, Paul Hen
dc.contributor.authorGondro, Cedricen
dc.date.accessioned2015-11-26T14:53:00Z-
dc.date.issued2015-
dc.identifier.citationGenetics Selection Evolution, v.47, p. 1-14en
dc.identifier.issn1297-9686en
dc.identifier.issn0999-193Xen
dc.identifier.urihttps://hdl.handle.net/1959.11/18194-
dc.description.abstract'Background': Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size ('N'ₑ), heterozygosity, fixation index ('F'ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. 'Methods': In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r² and D¹), Ne, heterozygosity, FST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). 'Results': Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller Nₑthan MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest 'F'ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. 'Conclusions': This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofGenetics Selection Evolutionen
dc.titleGenome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheepen
dc.typeJournal Articleen
dc.identifier.doi10.1186/s12711-015-0169-6en
dcterms.accessRightsGolden
dc.subject.keywordsGene Expression (incl. Microarray and other genome-wide approaches)en
dc.subject.keywordsAnimal Breedingen
dc.subject.keywordsBioinformatics Softwareen
local.contributor.firstnameHawlader Abdullahen
local.contributor.firstnameSam Aen
local.contributor.firstnamePaul Hen
local.contributor.firstnameCedricen
local.subject.for2008070201 Animal Breedingen
local.subject.for2008080301 Bioinformatics Softwareen
local.subject.for2008060405 Gene Expression (incl. Microarray and other genome-wide approaches)en
local.subject.seo2008890201 Application Software Packages (excl. Computer Games)en
local.subject.seo2008830310 Sheep - Meaten
local.subject.seo2008830311 Sheep - Woolen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Science and Technologyen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailahawlade@une.edu.auen
local.profile.emailsclark37@une.edu.auen
local.profile.emailwkwan2@une.edu.auen
local.profile.emailcgondro2@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20151125-093814en
local.publisher.placeUnited Kingdomen
local.identifier.runningnumber90en
local.format.startpage1en
local.format.endpage14en
local.identifier.scopusid84948394755en
local.peerreviewedYesen
local.identifier.volume47en
local.access.fulltextYesen
local.contributor.lastnameAl-Mamunen
local.contributor.lastnameClarken
local.contributor.lastnameKwanen
local.contributor.lastnameGondroen
dc.identifier.staffune-id:ahawladeen
dc.identifier.staffune-id:sclark37en
dc.identifier.staffune-id:wkwan2en
dc.identifier.staffune-id:cgondro2en
local.profile.orcid0000-0001-8605-1738en
local.profile.orcid0000-0003-0666-656Xen
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:18399en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleGenome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheepen
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.relation.grantdescriptionARC/DP130100542en
local.search.authorAl-Mamun, Hawlader Abdullahen
local.search.authorClark, Sam Aen
local.search.authorKwan, Paul Hen
local.search.authorGondro, Cedricen
local.uneassociationUnknownen
local.identifier.wosid000365338400001en
local.year.published2015en
local.subject.for2020300109 Non-genetically modified uses of biotechnologyen
local.subject.for2020460103 Applications in life sciencesen
local.subject.for2020310505 Gene expression (incl. microarray and other genome-wide approaches)en
local.subject.seo2020220401 Application software packagesen
local.subject.seo2020100412 Sheep for meaten
local.subject.seo2020100413 Sheep for woolen
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