GENOMICS OF EFFICIENCY, RESILIENCE AND BIODIVERSITY IN HOLSTEIN AND LOCAL CATTLE BREEDS

This thesis explores the genomics of biodiversity, resilience, and efficiency in Holstein (a cosmopolitan population) and local cattle breeds, focusing on their genetic diversity, adaptation to environmental challenges and the application of genomic tools in breeding programs. The research primarily investigates genetic diversity among autochthonous cattle breeds in the Aosta Valley, particularly the Aosta Red Pied, Aosta Black Pied-Chestnut, and their subgroup Aosta Chestnut-Hérens, alongside the highly selected Holstein Friesian breed. The study leveraged genomic information such as Single Nucleotide Polymorphism (SNP) markers to assess genetic variation across breeds and conduct genome-wide association studies. Emphasis was placed on exploring the impact of genomic variations on traits linked to disease resistance (e.g., mastitis and bovine respiratory disease) and milk production efficiency. The Holstein breed, a specialised cosmopolitan population known for its high milk production and intensive farming system, served as a reference. In contrast, local breeds like Aosta were studied for their resilience and production efficiency in harsh environmental conditions, such as alpine mountain pastures. Key findings include the identification of Runs of Homozygosity (ROH), used to estimate inbreeding and genomic diversity and to map genomic regions under selection. The ROH analysis showed that local breeds possess unique adaptations, exhibiting lower inbreeding coefficients than the Holstein, which has faced a loss of genetic variation due to the intense selection that occurred for milk production traits in the early past. This thesis also mapped genomic regions associated with mastitis resistance in Holstein, contributing to better breeding strategies aimed at improving animal health and welfare. Additionally, this work highlights the critical role of local breeds in maintaining biodiversity. These breeds offer a source of genetic variation essential for sustainable cattle farming and their resilience could help in facing future environmental changes. The genetic makeup of local breeds also supports cultural and economic activities in the Aosta Valley, such as the production of Fontina cheese, a Product of Designated Origin (PDO), and the Bataille de Reines. Finally, this thesis proposes that coupling genomic data with phenotypic variability enhances the understanding of resilience traits in cattle. It suggests that local breeds, despite their small population size, are valuable resources in the face of global challenges such as climate change and the increasing demand for sustainable livestock systems.