Evolution of the genomic relationship between a local breed and its mainstream sister breed

In Benelux countries, there is a genomic continuum of red-pied cattle breeds. Some of them are still rather common, like the Meuse-Rhine-Yssel (MRY), from the Netherlands, while others have the endangered European status like the Red-Pied of Ösling (RPO), from Luxembourg. Survival of a small population like RPO is based on finding a good balance between keeping genetic specificities and collaborating with their sister breeds. We therefore tried to estimate the historical evolution of the genomic relationship between RPO and MRY. For this purpose, we divided the MRY samples into four cohorts depending on the birthdate of animals: before 1990 (cohort 1), between 1990 and 1999 (cohort 2), between 2000 and 2009 (cohort 3) and after 2009 (cohort 4). Results from principal component analysis, Fst values and the genomic relationship matrix showed that current RPO animals were on average slightly more related to MRY animals from cohorts 1 and 4 (born before 1990 or after 2009) than to MRY animals from cohorts 2 and 3 (born between 1990 and 2009). These results confirmed the known history of RPO. Breeders in Luxembourg imported MRY animals or semen on a large scale before 1990. After 1990, breeding in Luxembourg was more focused on collaboration with Germany and German dual-purpose red-pied (RDN) cattle were not collaborating a lot with MRY at that time. This changed during the last 20 years and many recent RDN sires have MRY ancestors which could explain increasing relationships with RPO too. Even if this study did not contain RDN animals, it shows the evolution of the complex relationships between some of these sister breeds. Genome assisted mating advice should be used to help breeders in their choice of an appropriate MRY (or other related breed) animal for mating. These animals should be genomically close to the current RPO population which will strengthen the collaboration of these breeds and, finally, support the further across-breed genomic evaluations.