CRUMBLER: A tool for the Prediction of Ancestry in Cattle

Background: In many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation. Results: We tested an approach to estimate the global ancestry of individuals using ADMIXTURE and SNPweights. ADMIXTURE estimates ancestry using a model-based approach applied to large single nucleotide polymorphism (SNP) genotype datasets. Individuals are assumed to be unrelated and a supervised analysis can be performed using reference animals sampled to represent ancestral populations. SNPweights infers ancestry using weights estimated by principal component analysis for genome-wide SNP panels that have been genotyped in the reference panel animals. We constructed analysis pipelines to determine the ancestry of individuals with potentially complex ancestries using both methods and a specified reference population SNP dataset. The reference population was constructed using breed association pedigree information and an iterative analysis to identify sets of purebred individuals representative of each breed. Conclusion: The finally adopted CRUMBLER pipeline extracts a subset of genotypes that are common to all current commercially available genotyping platforms and processes these into the file formats required for the analysis software and predicts admixture proportions using the reference population dataset.