Accuracy of breeding values in small genotyped populations using different sources of external information-A simulation study.
Genetically linked small and large dairy cattle populations were simulated to test the effect of different sources of information from foreign populations on the accuracy of predicting breeding values for young animals in a small population. A large dairy cattle population (PL) with >20 generations was simulated, and a small subpopulation (PS) with 3 generations was formed as a related population, including phenotypes and genomic information. Predicted breeding values for young animals in the small population were calculated using BLUP and single-step genomic BLUP (ssGBLUP) in 4 different scenarios: (S1) 3,166 phenotypes, 22,855 pedigree animals, and 1,000 to 6,000 genotypes for PS; (S2) S1 plus genomic estimated breeding value (GEBV) for 4,475 sires from PLas external information; (S3) S1 plus 221,580 phenotypes, 402,829 pedigree animals, and 53,558 genotypes for PL; and (S4) single nucleotide polymorphism (SNP) effects calculated based on PLdata. The ability to predict true breeding value was assessed in the youngest third of the genotyped animals in the small population. When data only from the small population were used and 1,000 animals were genotyped, the accuracy of GEBV was only 1 point greater than the estimated breeding value accuracy (0.32 vs. 0.31). Adding external GEBV for sires from PLdid not considerably increase accuracy (0.33 vs. 0.32 in S1). Combining phenotypes, pedigree, and genotypes for PSand PLwas beneficial for predicting accuracy of GEBV in the small population, and the prediction accuracy of GEBV in this scenario was 0.38 compared with 0.31 from estimated breeding values. When SNP effects from PLwere used to predict GEBV for young genotyped animals from PS, accuracy was greatest (0.56). With 6,000 genotyped animal in PS, accuracy was greatest (0.61) with the combined populations. In a small population with few genotypes, the highest accuracy of evaluation may be obtained by using SNP effects derived from a related large population.
Faculty of Agricultural Sciences and Food, University of Ss. Cyril and Methodius, PO Box 297, 1000 Skopje, Macedonia. Electronic address: sreten_andonov@yahoo.com.
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Andonov
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Lourenco
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Fragomeni
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Masuda
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Pocrnic
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Tsuruta
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
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Misztal
D000818:Animals; D001947:Breeding; D016678:Genome; D023281:Genomics; D005838:Genotype; D008957:Models, Genetic; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide
dairy cattle; genomic breeding value; prediction accuracy; small population