Balancing genetic gain and diversity in dairy cattle breeding schemes in the genomics era

Managing the trade-off between genetic gain and genetic diversity is a central challenge in modern dairy cattle breeding. Genomic selection (GS) has accelerated genetic progress by improving selection accuracy, particularly for young animals, and shortening generation intervals. However, this has also led to increased inbreeding and reduced genetic variation in many populations, raising concerns about long-term sustainability. This study focuses on the Nordic Holstein and Jersey breeds, which differ in population size and breeding structure, offering a comparative perspective on diversity management under GS. <br/>The research consists of four studies combining empirical data analysis and stochastic simulation. The first study examines long-term trends in pedigree-based inbreeding and coancestry in Nordic Holstein, revealing stable trends and an increase in effective population size despite the adoption of GS. The second study compares pedigree- and genomic-based inbreeding and coancestry in Holstein and Jersey, showing that while pedigree inbreeding remained controlled, genomic inbreeding increased, highlighting the limitations of relying solely on pedigree information. The third study explores the effects of inbreeding on dairy cow survival. Results show that recent inbreeding, identified through long runs of homozygosity, is more detrimental to longevity than historical inbreeding. These findings underscore the importance of distinguishing between recent and distant coancestry in breeding decisions. The fourth study uses simulation to evaluate the application of multi-stage optimal contribution selection (OCS). When applied during both the selection of calves for genotyping and the selection of calves for being AI bulls, OCS reduced genomic inbreeding and increased effective population size. Findings demonstrate that the consequences of GS for genetic diversity depend not only on the technology itself, but also on how it is implemented within the breeding program. Early and structured use of genomic tools, including multi-stage OCS, can effectively support sustainable genetic progress. <br/>Overall, this thesis demonstrates that securing long-term genetic sustainability in dairy cattle breeding programs under genomic selection requires the early implementation of genomic diversity management strategies, adaptation to breed-specific characteristics, and continuous monitoring of genetic diversity.<br/>