Genomic prediction in a numerically small breed population using prioritized genetic markers from whole‐genome sequence data

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 poly...

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Bibliographic Details
Published in:Journal of animal breeding and genetics (1986) 2022-01, Vol.139 (1), p.71-83
Main Authors: Moghaddar, Nasir, Brown, Daniel J, Swan, Andrew A, Gurman, Phillip M, Li, Li, Werf, Julius H
Format: Article
Language:English
Subjects:
Accuracy
Animal populations
Animals
Body weight
Breeding
Eating quality
Gene frequency
Gene polymorphism
Gene sequencing
Genetic Association Studies - veterinary
Genetic diversity
Genetic Markers
Genetic variance
Genome
Genomes
genomic prediction
Genomics
Genotype
Genotypes
Heritability
Markers
Models, Genetic
Nucleotide sequence
Nucleotides
numerically small sheep population
Phenotype
Phenotypes
Polymorphism
Polymorphism, Single Nucleotide
Population density
Population genetics
Predictions
Sheep
Sheep - genetics
Single-nucleotide polymorphism
whole‐genome sequence data
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Summary: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.
ISSN:0931-2668
1439-0388
DOI:10.1111/jbg.12638