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Genomic selection using low density marker panels with application to a sire line in pigs
Robin Wellmann1, Siegfried Preuß, Ernst Tholen
1Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, D-70599 Stuttgart, Germany. r.wellmann@uni-hohenheim.de
Genetics, Selection, Evolution : GSE
|July 31, 2013
Summary
Genomic selection in pigs can be cost-effective using low-density SNP panels and imputation. A minimum panel size of 384 markers is recommended for accurate genomic breeding values when parents have high-density genotypes.
Area of Science:
- Animal Genetics
- Quantitative Genetics
- Bioinformatics
Background:
- Genomic selection is standard in dairy cattle but costly for other species.
- Reduced-density single nucleotide polymorphism (SNP) panels can lower genotyping costs.
- This study investigates SNP panel selection and genotype imputation for pigs.
Purpose of the Study:
- To develop and evaluate methods for genomic selection using low-density SNP panels in pigs.
- To assess the accuracy of genotype imputation and its impact on genomic breeding values.
- To determine optimal SNP panel sizes for cost-effective genomic selection.
Main Methods:
- Proposed methods for SNP position approximation and low-density panel selection.
- Developed a genotype imputation method using high-density genotyped sires and low-density genotyped candidates.
- Applied methods to a German Piétrain pig population (895 boars).
Main Results:
- Genotype imputation error rates decreased with larger panels (0.133 for 384, 0.079 for 768, 0.022 for 3000 markers).
- High-density genotypes of relatives reduced imputation errors.
- Accuracy of genomic breeding values decreased by 3% for the 384-marker panel, negligible for larger panels with high-density parentage.
Conclusions:
- Genomic selection with imputation from low-density panels is feasible and cost-effective for pigs.
- A 384-SNP panel is a viable lower bound for selection candidates if at least one parent has high-density genotypes.
