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Pimentel, E. C. G.; Reichenbach, H.-D.; Edel, C.; Emmerling, R.; Jung, S.; Fries, R.; Wolf, E.; Grupp, T.; Reichenbach, M.; Götz, K.-U. (2017): Genomische Zuchtwertschätzung von Rinderembryonen beim Fleckvieh. In: Zuchtungskunde, Vol. 89, No. 5: pp. 333-344
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Abstract

The study aimed at assessing the quality of SNP-Chip genotyping of embryos, and of the genomic breeding values predicted from them. Genotypes (Illumina Bovine SNP50 Bead-Chip) of 55 Fleckvieh embryo-calf pairs were used in this investigation. Call-rates and heterozygosity levels were calculated and genomic breeding values for 49 traits were predicted. For the embryo genotypes with low call-rates (e.g. below 0.90) also the genotypes that were successfully 'called' had a poor agreement with the genotypes of the corresponding calf. The average proportion of equal genotypes between embryo and calf was 0.93 +/- 0.03 for embryos with call-rate < 0.90 and 0.99 +/- 0.01 for the embryos with call-rate > 0.90. The correlation between this proportion and the call-rate of the embryo was 0.92. Most inconsistencies between the genotypes of embryos and calves were due to wrongly assigned homozygote genotypes of embryos. Correlations between genomic breeding values of embryos and of their corresponding calves ranged from 0.978 to 0.999 depending on the trait and averaged 0.989 +/- 0.005. The concordance between predicted breeding values of embryos and calves was also influenced by the call-rate of the embryo. When the embryos with call-rate below 0.90 were excluded the average correlation was 0.996 +/- 0.002. These results show that the genomic evaluation of embryos can be successfully done. For a routine implementation it seems reasonable to set an embryo call-rate of at least 0.90 as a threshold requirement for the quality of embryo genotypes.