Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/31406
Title: Genomic prediction in a numerically small breed population using prioritized genetic markers from whole-genome sequence data
Contributor(s): Moghaddar, Nasir  (author)orcid ; Brown, Daniel J  (author)orcid ; Swan, Andrew A  (author)orcid ; Gurman, Phillip M  (author)orcid ; Li, Li  (author)orcid ; Van Der Werf, Julius H  (author)orcid 
Publication Date: 2022-01
Early Online Version: 2021-08-10
DOI: 10.1111/jbg.12638
Handle Link: https://hdl.handle.net/1959.11/31406
Abstract: The objective of this study was to investigate the accuracy of genomic prediction of body weight and eating quality traits in a numerically small sheep population (Dorper sheep). Prediction was based on a large multi-breed/admixed reference population and using (a) 50k or 500k single nucleotide polymorphism (SNP) genotypes, (b) imputed whole-genome sequencing data (~31 million), (c) selected SNPs from whole genome sequence data and (d) 50k SNP genotypes plus selected SNPs from whole-genome sequence data. Furthermore, the impact of using a breed-adjusted genomic relationship matrix on accuracy of genomic breeding value was assessed. The selection of genetic variants was based on an association study performed on imputed whole-genome sequence data in an independent population, which was chosen either randomly from the base population or according to higher genetic proximity to the target population. Genomic prediction was based on genomic best linear unbiased prediction (GBLUP), and the accuracy of genomic prediction was assessed according to the correlation between genomic breeding value and corrected phenotypes divided by the square root of trait heritability. The accuracy of genomic prediction was between 0.20 and 0.30 across different traits based on common 50k SNP genotypes, which improved on average by 0.06 (absolute value) on average based on using prioritized genetic markers from whole-genome sequence data. Using prioritized genetic markers from a genetically more related GWAS population resulted in slightly higher prediction accuracy (0.02 absolute value) compared to genetic markers derived from a random GWAS population. Using high-density SNP genotypes or imputed whole-genome sequence data in GBLUP showed almost no improvement in genomic prediction accuracy however, accounting for different marker allele frequencies in reference population according to a breed-adjusted GRM resulted to on average 0.024 (absolute value) increase in accuracy of genomic prediction.
Publication Type: Journal Article
Source of Publication: Journal of Animal Breeding and Genetics, 139(1), p. 71-83
Publisher: Wiley-Blackwell Verlag GmbH
Place of Publication: Germany
ISSN: 1439-0388
0931-2668
Fields of Research (FoR) 2020: 300305 Animal reproduction and breeding
Socio-Economic Objective (SEO) 2020: 100412 Sheep for meat
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Journal Article
School of Environmental and Rural Science

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