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Application of selection index calculations to determine selection strategies in genomic breeding programs

S. König^*,1 and H. H. Swalve

^* Institute of Animal Breeding and Genetics, University of Göttingen, 37075 Göttingen, Germany
Institute of Agricultural and Nutritional Sciences, University of Halle, 06099 Halle, Germany

¹ Corresponding author: skoenig2{at}gwdg.de

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r_TI), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r_TI strongly depends on the accuracy of GEBV (r_mg) and the heritability of the trait. For a desired r_TI of 0.8, h² = 0.10, and r_mg = 0.5, at least 57 additional daughters have to be included in the genetic evaluation. Daughter records of genotyped sires are not necessary for optimal scenarios where r_mg is greater than or equal to r_TI. There still is a substantial need for phenotypic daughter records, especially for low-heritability functional traits and r_mg < 0.7. Phenotypic records from genotyped potential bull dams have no relevance for increasing r_TI, even with a low value for r_mg of 0.5. Hence, genomic breeding programs should focus on recording functional traits within progeny groups, preferably in cooperator herds. For low-heritability traits and with r_mg > 0.7, the RSR of conventional breeding programs was only 10% of RSR from genomic breeding strategies. As shown in scenarios including 2 traits in the index as well as in the aggregate genotype, the availability of highly accurate GEBV for production traits and low-accuracy GEBV for functional traits increased the risk of widening the gap between selection responses in production and functionality. Counteractions are possible, such as via higher economic weights for low-heritability functional traits. Finally, an alternative selection strategy considering only 2 pathways of selection for genotyped male calves and for cow dams was evaluated. This strategy is competitive with a 4-pathway genomic breeding program if the fraction of selected male calves for the artificial insemination program is below 1% and if selection is focused on functionality, thus pointing to substantial insufficiencies caused by low reliabilities of breeding values for cows for such traits in conventional bull dam selection schemes.

Key Words: genomic selection • breeding program • selection index