Beyond studying genetic diversity: how can pedigree and genomic data help us assigning individuals to breeds?

Determining to which breed an individual belongs is not always an unbiased choice. Definition of breeds is not always clear and takes some subjective elements into account (e.g. phenotypes or administrative rules). Moreover, insufficient pedigree deepness worsens this issue. This explains the need for development of breed assignment tools and their routine use. This kind of tools supposes a known "Reference population" containing maximum genetic diversity of the breed considered. Moreover, "Candidate individuals" have to be close enough to this "Reference population" to allow correct individual assignment. Tools based on classification methods allow breed assignment and subsequently subsidy payment schemes in Wallonia (Southern Belgium) and Luxembourg. Currently, a principal component analysis (PCA) based on genotypes is used as a routine to determine if individuals belong to two local dual-purpose cattle breeds (i.e. East Belgian Red and White, Belgium, and Ösling Red Pied, Luxembourg). This analysis relies on the position of individuals on the PCA compared to those of reference individuals from different breeds (East Belgian Red and White and Ösling Red Pied but also “sister breeds” and (Red-)Holstein). However, the continuum of Red-Pied breeds in Western Europe makes it difficult to choose to which breed the animal belongs. One example is the overlapping observed on the PCA between East Belgian Red and White and Ösling Red Pied. One solution is maybe to include these animals in both herdbooks. This would allow exchange program between so closely related breeds. Furthermore, the question arises to what extent peripherical individuals, but potentially phenotypically interesting, should be included, as they could provide more diversity to the current gene pool. In these cases, the study of different parameters that inform us about inbreeding (e.g. runs of homozygosity or effective population size) and admixture within breeds or differentiation levels (e.g. fixation index) between breeds, can help to assign individuals to breeds.