Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/23153
Title: Accounting for population structure in genomic prediction of Australian merino sheep
Contributor(s): Moghaddar, Nasir  (author); Brown, Daniel  (author); Swan, Andrew  (author)orcid ; Van Der Werf, Julius H  (author)orcid 
Publication Date: 2017
Open Access: Yes
Handle Link: https://hdl.handle.net/1959.11/23153
Open Access Link: http://agbu.une.edu.au/AAABG%202017/139Moghaddar22593.pdfOpen Access Link
Abstract: The aim of this study was to compare different ways of accounting for population structure for genomic prediction of three economic traits in an Australian Merino sheep population. Population structure was accounted for either by fitting genetic groups (GG) derived from pedigree, or fitting principal components (PCs) calculated from the genomic relationship matrix based on 50k density SNP marker genotypes. Genomic breeding values (GBV) were calculated using genomic best linear unbiased prediction (GBLUP) and the GBV accuracy was evaluated based on 5 fold cross-validation across half-sib families. Best linear unbiased estimation (BLUE) of GG or PC effects were added to the GBV. Results showed that accounting for population structure either by fitting GG or PCs improved the accuracy of genomic prediction. Furthermore, fitting the first two PCs gave a similar accuracy to fitting GG derived from pedigree. The improvement in GBV accuracy after accounting for population structure in studied traits was not high (3.8% when averaged across traits) which may be because the genomic relationship matrix will implicitly account for some of the population structure effect when the GG or PCs are not fitted in analysis. In the case of missing or incomplete pedigrees, PCs can be used to account for population structure and to improve the prediction accuracies.
Publication Type: Conference Publication
Conference Name: 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics, Townsville, Australia, 2nd - 5th July, 2017
Conference Details: 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics, Townsville, Australia, 2nd - 5th July, 2017
Source of Publication: Proceedings of the Twenty-second (22nd) Conference of the Association for the Advancement of Animal Breeding and Genetics, v.22, p. 593-596
Publisher: AAABG: Association for the Advancement of Animal Breeding and Genetics
Place of Publication: Fitzroy, Australia
Field of Research (FOR): 070201 Animal Breeding
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Other Links: http://www.aaabg.org/aaabghome/
Series Name: Proceedings of the AAABG ... Conference
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication
School of Environmental and Rural Science

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