Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle |
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Authors: | Mirjam Frischknecht Theodorus H.E. Meuwissen Beat Bapst Franz R. Seefried Christine Flury Dorian Garrick Heidi Signer-Hasler Christian Stricker Anna Bieber Ruedi Fries Ingolf Russ Johann Sölkner Alessandro Bagnato Birgit Gredler-Grandl |
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Affiliation: | 2. School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen 3052, Switzerland;3. Department of Animal and Aquacultural Sciences, Norwegian University of Life Science, Ås 1432, Norway;4. Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North 4442, New Zealand;6. Interbull Center, Uppsala 75007, Sweden;5. Department of Animal Sciences, Research Institute of Organic Agriculture (FiBL), Frick 5070, Switzerland;11. Tierzuchtforschung e.V., Poing-Grub 85586, Germany;12. Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Wien 1180, Austria;8. Department of Veterinary Sciences and Technologies for Food Safety, University of Milan, Milano 20133, Italy |
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Abstract: | The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods. |
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Keywords: | genomic prediction Brown Swiss whole-genome sequence data |
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