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https://hdl.handle.net/1959.11/31338
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DC Field | Value | Language |
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dc.contributor.author | Al Kalaldeh, Mohammad | en |
dc.contributor.author | Gibson, John | en |
dc.contributor.author | Duijvesteijn, Naomi | en |
dc.contributor.author | Daetwyler, Hans D | en |
dc.contributor.author | MacLeod, Iona | en |
dc.contributor.author | Moghaddar, Nasir | en |
dc.contributor.author | Hong Lee, Sang | en |
dc.contributor.author | van der Werf, Julius H J | en |
dc.date.accessioned | 2021-08-18T06:29:21Z | - |
dc.date.available | 2021-08-18T06:29:21Z | - |
dc.date.issued | 2019-06-26 | - |
dc.identifier.citation | Genetics Selection Evolution, v.51, p. 1-13 | en |
dc.identifier.issn | 1297-9686 | en |
dc.identifier.issn | 0999-193X | en |
dc.identifier.uri | https://hdl.handle.net/1959.11/31338 | - |
dc.description.abstract | <p><b>Background:</b> This study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide polymorphism (SNP) panels; (2) investigating whether the use of variants within quantitative trait loci (QTL) regions that were selected from regional heritability mapping (RHM) in an independent dataset improved the accuracy more than variants selected from genome-wide association studies (GWAS); and (3) comparing the prediction accuracies between variants selected from WGS data to variants selected from the HD SNP panel.</p> <p><b>Results:</b> The accuracy of genomic prediction improved marginally from 0.16 ± 0.02 and 0.18 ± 0.01 when using all the variants from 50k and HD genotypes, respectively, to 0.19 ± 0.01 when using all the variants from WGS data. Fitting a GRM from the selected variants alongside a GRM from the 50k SNP genotypes improved the prediction accuracy substantially compared to fitting the 50k SNP genotypes alone. The gain in prediction accuracy was slightly more pronounced when variants were selected from WGS data compared to when variants were selected from the HD panel. When sequence variants that passed the GWAS -<i>log<sub>10</sub></i>(<i>p value</i>) threshold of 3 across the entire genome were selected, the prediction accuracy improved by 5% (up to 0.21 ± 0.01), whereas when selection was limited to sequence variants that passed the same GWAS −<i>log<sub>10</sub></i>(<i>p value</i>) threshold of 3 in regions identified by RHM, the accuracy improved by 9% (up to 0.25 ± 0.01).</p> <p> <b>Conclusions:</b> Our results show that through careful selection of sequence variants from the QTL regions, the accuracy of genomic prediction for parasite resistance in sheep can be improved. These findings have important implications for genomic prediction in sheep.</p> | en |
dc.language | en | en |
dc.publisher | BioMed Central Ltd | en |
dc.relation.ispartof | Genetics Selection Evolution | en |
dc.rights | Attribution 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.title | Using imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheep | en |
dc.type | Journal Article | en |
dc.identifier.doi | 10.1186/s12711-019-0476-4 | en |
dc.identifier.pmid | 31242855 | en |
dcterms.accessRights | UNE Green | en |
local.contributor.firstname | Mohammad | en |
local.contributor.firstname | John | en |
local.contributor.firstname | Naomi | en |
local.contributor.firstname | Hans D | en |
local.contributor.firstname | Iona | en |
local.contributor.firstname | Nasir | en |
local.contributor.firstname | Sang | en |
local.contributor.firstname | Julius H J | en |
local.profile.school | School of Environmental and Rural Science | en |
local.profile.school | School of Environmental and Rural Science | en |
local.profile.school | School of Environmental and Rural Science | en |
local.profile.school | School of Environmental and Rural Science | en |
local.profile.school | School of Environmental and Rural Science | en |
local.profile.email | malkala2@une.edu.au | en |
local.profile.email | jgibson5@une.edu.au | en |
local.profile.email | nduijves@une.edu.au | en |
local.profile.email | nmoghad4@une.edu.au | en |
local.profile.email | jvanderw@une.edu.au | en |
local.output.category | C1 | en |
local.record.place | au | en |
local.record.institution | University of New England | en |
local.publisher.place | United Kingdom | en |
local.identifier.runningnumber | 32 | en |
local.format.startpage | 1 | en |
local.format.endpage | 13 | en |
local.identifier.scopusid | 85068925716 | en |
local.peerreviewed | Yes | en |
local.identifier.volume | 51 | en |
local.access.fulltext | Yes | en |
local.contributor.lastname | Al Kalaldeh | en |
local.contributor.lastname | Gibson | en |
local.contributor.lastname | Duijvesteijn | en |
local.contributor.lastname | Daetwyler | en |
local.contributor.lastname | MacLeod | en |
local.contributor.lastname | Moghaddar | en |
local.contributor.lastname | Hong Lee | en |
local.contributor.lastname | van der Werf | en |
dc.identifier.staff | une-id:malkala2 | en |
dc.identifier.staff | une-id:jgibson5 | en |
dc.identifier.staff | une-id:nduijves | en |
dc.identifier.staff | une-id:nmoghad4 | en |
dc.identifier.staff | une-id:jvanderw | en |
local.profile.orcid | 0000-0002-3206-6421 | en |
local.profile.orcid | 0000-0003-0371-2401 | en |
local.profile.orcid | 0000-0002-3600-7752 | en |
local.profile.orcid | 0000-0003-2512-1696 | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.identifier.unepublicationid | une:1959.11/31338 | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
local.title.maintitle | Using imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheep | en |
local.relation.fundingsourcenote | The authors acknowledge and thank the Cooperative Research Centre for Sheep Industry Innovation for providing data and funding the project. | en |
local.output.categorydescription | C1 Refereed Article in a Scholarly Journal | en |
local.search.author | Al Kalaldeh, Mohammad | en |
local.search.author | Gibson, John | en |
local.search.author | Duijvesteijn, Naomi | en |
local.search.author | Daetwyler, Hans D | en |
local.search.author | MacLeod, Iona | en |
local.search.author | Moghaddar, Nasir | en |
local.search.author | Hong Lee, Sang | en |
local.search.author | van der Werf, Julius H J | en |
local.open.fileurl | https://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947 | en |
local.uneassociation | Yes | en |
local.atsiresearch | No | en |
local.sensitive.cultural | No | en |
local.identifier.wosid | 000473045600002 | en |
local.year.published | 2019 | en |
local.fileurl.open | https://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947 | en |
local.fileurl.openpublished | https://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947 | en |
local.subject.for2020 | 300305 Animal reproduction and breeding | en |
local.subject.seo2020 | 100412 Sheep for meat | en |
dc.notification.token | 072757ef-d2fe-4ea1-a9c0-b3d84c688f5f | en |
Appears in Collections: | Journal Article School of Environmental and Rural Science |
Files in This Item:
File | Description | Size | Format | |
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openpublished/UsingImputedAlKalaldehGibsonDuijvesteijnMoghaddarVanDerWerf2019JournalArticle.pdf | Published version | 2.7 MB | Adobe PDF Download Adobe | View/Open |
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