Improving the Herd Management Using Genomic Information Improving within-herd selection

Genomic selection (GS) as theoretically introduced by Meuwissen et al. (2001) has been successfully implemented worldwide in dairy cattle breeding programs reflecting large populations, i.e., Holsteins, Fleckvieh, Jersey, and Brown Swiss, and has revolutionized conventional breeding schemes. Revolution of dairy cattle breeding programs via GS was the logical consequence due to the obvious possibilities in shortening generation intervals combined with highly accurate genomic breeding values, increased selection intensities, and prevention of preferential treatment of bull dams. Improvement of those breeding program characteristics simultaneously contributed to increased economic gain (König et al., 2009; König and Swalve, 2009). Prerequisite for highly accurate genomic breeding values is the implementation of large sire calibration groups including bulls with highly reliable conventional breeding values, as established within the EuroGenomics consortium (Lund et al., 2010). Typically, calibration group sires are genotyped with high-density SNP-chip panels, and estimated additive-genetic values for SNP or haplotype effects are transmitted to male selection candidates (young bulls) from the broad population. Further GS applications focus on genotyping females with the objectives i) to improve within-herd selection strategies using low-density 10K SNP-chip panels and ii) to predict phenotypes and to explain causal mutations using high-density or even whole-genome sequence data. Objective i addresses the evaluation of on-farm selection strategies combined with the utilization of reproduction technologies while still using “SNP-equations” from a bull calibration group. Objective ii implies relating genotypes directly to phenotypes, along with an evaluation of statistical methodology for phenotype prediction, with genome-wide association studies and with studies on genotype by environment (farm) interactions. As outlined, a major focus is placed on dairy cattle, but at specific points, applications to other species will be discussed as well.