Unravelling the Genetic Structure of Local and Mainstream Red‐Pied Cattle Breeds Using Genomics and Extended Pedigree Analysis

During the last decade, there has been a growing interest for local and endangered breeds as they are often seen as more resilient and healthier than mainstream breeds. They can also provide high added-value products like meat or dairy products. To better preserve these breeds, it is of main importance to characterize their genetic diversity and have an insight of historical gene flow with more mainstream breeds. In this study, we focused on the genetic relationships of five red-pied cattle breeds: the east Belgian red and white (EBRW); the red-pied of the Ösling (RPO), from Luxembourg; the deep red (DR) and the Meuse-Rhine-Yssel (MRY), both from the Netherlands; and the German red and white dual purpose (RDN). The EBRW, RPO and DR breeds have an official European endangered status. We first investigated the pedigree completeness of available genotyped animals as well as their complex historical relationships through the analysis of common ancestors. We also compared pedigree and SNP-based inbreeding coefficients, defined as the sum of homozygosity-by-descent segments (HBD). We then dived into genomic relationships through a classical multi-dimensional scaling (MDS) of genotyped animals and their admixture. The pedigree analyses showed the complex gene flow between all breeds and that the RPO breed was the most connected to other breeds. Results also showed that the level of inbreeding was so far not an issue in all five breeds even if some animals, for example, in EBRW and MRY breeds, showed higher inbreeding levels than the average of their breeds. Finally, the MDS and admixture analysis also highlighted complex gene flow between the studied breeds and that they may be considered as a genetic continuum. This genomic proximity has the potential to improve genetic evaluations of local breeds by the inclusion of information from more mainstream breeds like MRY and RDN.