A genomic-based approach to redefine herd book information in two local cattle breeds.

Reggiana and Modenese are autochthonous cattle breeds of the North of Italy. Their milk is mainly used to produce breed branded Protected Designation of Origin Parmigiano-Reggiano cheeses. As in most local breeds, pedigree records in Reggiana and Modenese herd books are not always complete. In this study, we applied a few approaches to verify and complete pedigree information: opposing homozygotes (OH) that identifies parentage inconsistencies in candidate parent offspring pairs; methods that apply Identity by Descent (IBD). Pedigree information was evaluated on a total of 3400 Reggiana and 630 Modenese cattle (which represent about 3/4th and 2/3rd of the respective breed populations), using genotyping data obtained from the GGP Bovine 150k single nucleotide polymorphism array. PLINK, and KING software and ad hoc scripts provided pairwise comparisons of the genotyped cattle. By comparing OH and IBD approaches and estimating the genotyping error rate, a threshold of inconsistent OH SNPs to correct a record and to infer up to 2nd or 3rd relationship degree was defined. These methods made it possible to correct and complete Herd Book information in the two breeds. These approaches will improve conservation strategies in Reggiana and Modenese breeds.Acknowledgements: Funded by the Programma di Sviluppo Rurale Nazionale (PSRN) Dual Breeding 2, co-funded by the European Agricultural Fund for Rural Development of the European Union and by the MASAF.