Across-Breed Imputation with Whole Genome Sequence Data in Dairy Cattle

In dairy cattle populations, medium and high-density genotype array information is available for most male and some female breeding animals. This data can be used to fine-map genomic regions related to economically important traits (genome-wide association studies, GWAS).

Because sequence data includes variant information in its entirety, whole genome sequence data will likely provide more concise information for GWAS than that available using SNP arrays. GWAS with sequence data requires large sample sizes to ensure suitable statistical power – a prerequisite that may not be easily met due to financial limitations. Since only few ancestors account for most of the variation in dairy cattle populations, sequence information of key ancestors can be used to impute available array-based genotypes, providing a cost-effective alternative to sequencing all animals.

Using single and multi-breed scenarios, sequence information of over 1200 animals was used to impute the autosomal sequence of 12,000 genotyped Brown Swiss and 2,000 genotyped Simmental / dual-purpose Fleckvieh animals. The accuracy of imputation from medium and high-density arrays to sequence genotypes was evaluated. Accuracy of imputation when the reference population was solely comprised of the breed to be imputed was compared with results obtained when the reference population was comprised of multiple breeds.

Financial support from the ASR and the KTI is gratefully acknowledged. Array genotypes were provided by Intergenomics. Sequence information was provided by the 1000 Bull’s Genome Project and the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no 289592 – Gene2Farm.