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Reliability of genomic prediction for German Holsteins using imputed genotypes from low-density chips
1Vereinigte Informationssysteme Tierhaltung w.v. (VIT), Heideweg 1, 27283 Verden, Germany; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098 Kiel, Germany.
Journal of Dairy Science
|August 25, 2012
Summary
Cheaper low-density chips offer accurate genomic evaluation in dairy cattle. The BovineLD 6K chip provides higher imputation accuracy and genomic prediction reliability than the 3K chip, making it suitable for large-scale genotyping.
Area of Science:
- Animal Genetics
- Genomic Evaluation
- Dairy Cattle Breeding
Background:
- Single nucleotide polymorphism (SNP) marker chips like the Illumina BovineSNP50 BeadChip (50K) are used for genomic evaluation in dairy cattle.
- The high cost of 50K chips limits widespread adoption among dairy producers.
- Lower-density chips are being explored as a cost-effective alternative.
Purpose of the Study:
- To assess the accuracy of cheaper low-density chips (Bovine3K and BovineLD 6K) for genomic evaluation in dairy cattle.
- To compare the imputation accuracy and genomic prediction reliability of different low-density chips and imputation programs.
- To determine the feasibility of using low-density chips for large-scale genotyping in dairy breeding programs.
Main Methods:
- Simulated genotypes for 3K and 6K chips based on original marker maps.
- Imputed missing 50K genotypes using Beagle and Findhap programs.
- Compared imputed genotypes with original ones to calculate allele error rate across three datasets.
- Conducted genomic evaluation using imputed genotypes to assess prediction accuracy and reliability.
Main Results:
- The BovineLD 6K chip demonstrated significantly higher imputation accuracy and genomic prediction reliability compared to the 3K chip.
- Beagle imputation program showed approximately twice the accuracy of Findhap across datasets.
- The reduction in genomic prediction reliability using imputed genotypes was lowest for Beagle on the 6K chip (1%) compared to Findhap on the 3K chip (5.3%).
- Differences in genome-enhanced breeding values were minimized when using Beagle on the 6K chip.
Conclusions:
- The BovineLD 6K chip offers a cost-effective solution for genomic evaluation in dairy cattle with minimal loss in prediction accuracy.
- The Beagle imputation program is recommended for its superior performance with low-density chips.
- The 6K chip is a viable option for large-scale genotyping, provided the costs are acceptable to breeders.
