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dc.contributor.authorvan den Berg, I
dc.contributor.authorBoichard, D
dc.contributor.authorLund, MS
dc.date.accessioned2021-02-04T00:19:35Z
dc.date.available2021-02-04T00:19:35Z
dc.date.issued2016-11-04
dc.identifierpii: 10.1186/s12711-016-0259-0
dc.identifier.citationvan den Berg, I., Boichard, D. & Lund, M. S. (2016). Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle. GENETICS SELECTION EVOLUTION, 48 (1), https://doi.org/10.1186/s12711-016-0259-0.
dc.identifier.issn0999-193X
dc.identifier.urihttp://hdl.handle.net/11343/259084
dc.description.abstractBACKGROUND: Sequence data can potentially increase the reliability of genomic predictions, because such data include causative mutations instead of relying on linkage disequilibrium (LD) between causative mutations and prediction variants. However, the location of the causative mutations is not known, and the presence of many variants that are in low LD with the causative mutations may reduce prediction reliability. Our objective was to investigate whether the use of variants at quantitative trait loci (QTL) that are identified in a multi-breed genome-wide association study (GWAS) for milk, fat and protein yield would increase the reliability of within- and multi-breed genomic predictions in Holstein, Jersey and Danish Red cattle. A wide range of scenarios that test different strategies to select prediction markers, for both within-breed and multi-breed prediction, were compared. RESULTS: For all breeds and traits, the use of variants selected from a multi-breed GWAS resulted in substantial increases in prediction reliabilities compared to within-breed prediction using a 50 K SNP array. Reliabilities depended highly on the choice of the prediction markers, and the scenario that led to the highest reliability varied between breeds and traits. While genomic correlations across breeds were low for genome-wide sequence variants, the effects of the QTL variants that yielded the highest reliabilities were highly correlated across breeds. CONCLUSIONS: Our results show that the use of sequence variants, which are located near peaks of QTL that are detected in a multi-breed GWAS, can increase reliability of genomic predictions.
dc.languageEnglish
dc.publisherBIOMED CENTRAL LTD
dc.titleSequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle
dc.typeJournal Article
dc.identifier.doi10.1186/s12711-016-0259-0
melbourne.affiliation.departmentAgriculture and Food Systems
melbourne.affiliation.facultyVeterinary and Agricultural Sciences
melbourne.source.titleGenetics Selection Evolution
melbourne.source.volume48
melbourne.source.issue1
dc.rights.licenseCC BY
melbourne.elementsid1203732
melbourne.contributor.authorvan den Berg, Irene
dc.identifier.eissn1297-9686
melbourne.accessrightsOpen Access


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