Optimizing selection decisions in the Danish Dairy Shorthorn conservation program

The Danish Dairy Shorthorn is a small cattle population experiencing a rapid loss of genetic diversity, as demonstrated by both pedigree and genomic analyses.There is therefore an urgent need to manage inbreeding more effectively to safeguard the long-term viability of this endangered breed.The last initiative to address this critical situation was the use of two Northern Dairy Shorthorn bulls-a related Shorthorn line from the UK.In this research-based advisory report, we developed a data-analysis pipeline that uses available pedigree information to support breeders in making informed decisions about which animals to retain and how to design matings that minimize inbreeding increase in the next generation(s).The pipeline is built around Optimal Contribution Selection (OCS), a state-of-the-art method for controlling inbreeding in small populations.OCS analyses highlighted the need to broaden the set of bulls used for breeding, including gene bank bulls, and to distribute their contributions more evenly.We also integrated genomic data from the entire live population and from bulls with cryopreserved semen to evaluate the added value of genomics within the OCS framework.Overall, genomic and pedigree-based OCS yielded consistent recommendations.Genomic information revealed several deviations between expected and realized inbreeding and relationships.In such cases, genomic OCS placed greater emphasis on individuals that were less related to the population than expected from pedigree records.This is especially useful when selecting among closely related breeding candidates.Our analyses showed that strategic use of two gene bank bulls, Thy Texas and U. Ralf, could produce offspring little related to the population that would be valuable for the conservation program.Using this pipeline, the current inbreeding level of Danish Dairy Shorthorn could be reduced from 0.20 to 0.16 by implementing the pedigreebased mating plan, and even to 0.13 with genomic information.The OCS recommendations incorporating genomic data were not sensitive to the method used to build the genomic relationship matrix.Genomic data also helped identify Northern Dairy Shorthorn-sired bull calves with potential to enrich the gene bank.Among the five calves genotyped from the 2025 cohort, one exhibited low kinship both with living females and existing gene bank bulls, making it a strong candidate for inclusion.The remaining calves shared the same maternal grandsire-an individual with a very high contribution to the current population-reducing their usefulness for improving genetic diversity.Additional biological samples from recently born bull calves have been collected and are currently undergoing genotyping.Overall, these results demonstrate the substantial benefits of integrating genomic information into the management of genetic diversity in endangered livestock populations.The tools and workflow developed in this project can readily be adapted for other species within the national conservation program.