Establishing a genomic-driven conservation of a cattle genetic resource: the case of the Parmigiano-Reggiano cheese iconic breed

Cattle genetic resources, represented by autochthonous breeds, can be considered genetically vulnerable populations due to their small size. Effective management of breeding programs is key to maintaining the integrity of these genetic resources, reducing the risk associated with inbreeding, monitoring the segregation of deleterious alleles and planning mating programs. The Reggiana breed is a local cattle breed that served as the founding population of the famous Parmigiano-Reggiano cheese. This breed is primarily raised in the cheese production area, in the North of Italy. In this study, we utilized whole genome sequencing data from all active Reggiana sires and high-density single nucleotide polymorphism genotypes from approximately 4,000 cattle, comprising almost the entire population, to generate genomic data for establishing a genomic-driven management approach for this breed. Pedigree information of animals registered in the breed herd book was adjusted using genomic relationship matrices. We identified potential low-frequency deleterious haplotypes by combining population genetic data with whole genome sequencing information. Additionally, we identified deleterious alleles that had been introduced through occasional past crossbreeding with cosmopolitan cattle breeds. We monitored the genomic inbreeding trend for the entire population and at the farm level to design appropriate mating programs aimed at preventing potential negative effects. These measures support the long-term sustainability of the unique genetic heritage represented by the Reggiana cattle breed. Funded by the European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice PRIN 2022 PNRR (DD N. 1409 del 14/09/2022), proposal code P2022ALHF4 - CUP J53D23018270001.