Consequences of Splitting Sequencing Effort over Multiple Breeds on Imputation Accuracy

Imputation from a high-density SNP panel (777k) to whole-genome sequence with a reference population of 20 Holstein resulted in an average imputation accuracy of 0.70, and increased to 0.83 when the reference population was increased by including 3 other dairy breeds with 20 animals each. When the same amount of animals from the Holstein breed were added the accuracy improved to 0.88. Imputation of variants with very low minor allele frequency in Holstein that were also segregating in the mixed breed reference population benefitted from the inclusion of other breeds in the reference population, whereas Holstein specific variants benefitted from the large Holstein reference population. This study shows that splitting sequencing effort over multiple breeds is a good strategy for imputation from high-density SNP panels towards whole-genome sequence when reference populations are small