Population genomics in Reggiana cattle to manage diversity within and across farms

Reggiana is an autochthonous cattle breed mainly raised in the Emilia-Romagna region, in the North of Italy. This breed is important for economic and traditional reasons due to production of mono-breed branded Parmigiano-Reggiano cheese, which provides essential economic incomes for the sustainable conservation of this valuable genetic resource. The breed population includes around 4,500 animals registered in the Herd Book. In this study, more than 4,000 animals have been genotyped with GGP Bovine 150k and GGP Bovine 777k SNP chips. The animals included in the dataset cover almost the entire breed, including 280 sires, and come from 50 different farms. Genomic data were used to refine pedigree information and trace back the individual history of specific animals. Genomic inbreeding was estimated using runs of homozygosity (ROH). Admixture and multi-dimensional scaling analyses were carried out to check population genomic structure and differences in farm clustering. Among the most relevant results indicating variability between farms, Fst had a wide range of values, with an average of 0.018 ± 0043 and a maximum of 0.65 for some specific regions. Inbreeding levels were compared between different farms and showed various inbreeding patterns indicating differences in the management of mating. Farm-specific data were collected to evaluate among farms genetic diversity, monitor breeding practices and guide choices in farm management. These findings will support mating plans and conservation strategies for the Reggiana cattle breed, allowing tailored decisions to be made and contributing to the sustainability of this animal genetic resource. Research 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