Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds

Abstract

Currently, enhancing the collaboration between related breeds is of main importance to increase the competitivity and the sustainability of local breeds. One type of collaboration is the development of an across-breed reference population that will allow a better management of local breeds. For this purpose, the genomic relatedness between the local target breed and possible breeds to be included in the reference population should be estimated. In Europe, there are several local red-pied cattle breeds that would benefit from this kind of collaboration. However, how different red-pied cattle breeds from the Benelux are related to each other and can collaborate is still unclear. The objectives of this study were therefore: (1) to estimate the level of inbreeding of the East Belgian Red and White (EBRW), the Red-Pied of the Ösling (RPO) and Dutch red-pied cattle breeds; (2) to determine the genomic relatedness of several red-pied cattle breeds, with a special focus on two endangered breeds: the EBRW and the RPO, and (3) based on the second objective, to detect animals from other breeds that were genomically close enough to be considered as advantageous in the creation of an across-breed reference population of EBRW or RPO. The estimated inbreeding levels based on runs of homozygosity were relatively low for almost all the studied breeds and especially for the EBRW and RPO. This would imply that inbreeding is currently not an issue in these two endangered breeds and that their sustainability is not threatened by their level of inbreeding. The results from the principal component analysis, the phylogenetic tree and the clustering all highlighted that the EBRW and RPO breeds were included in the genomic continuum of the studied red-pied cattle breeds and can be therefore considered as genomically close to Dutch red-pied cattle breeds, highlighting the possibility of a collaboration between these breeds. Especially, EBRW animals were closely related to Deep Red and Improved Red animals while, to a lesser extent, the RPO animals were closely related to the Meuse-Rhine-Yssel breed. Based on these results, we could use distance measures, based either on the principal component analysis or clustering, to detect animals from Dutch breeds that were genomically closest to the EBRW or RPO breeds. This will finally allow the building of an across-breed reference population for EBRW or RPO for further genomic evaluations, considering these genomically closest animals from other breeds.