Imputation in Swiss cattle breeds

  • B Gredler
  • F R Seefried
  • U Schuler
  • B Bapst
  • U Schnyder
  • J M Hickey

Abstract

Imputation from Illumina 3k to 54k was carried out using AlphaImpute and Findhap V2 for Swiss cattle breeds. Genotypes of Original Braunvieh and Brown Swiss were combined on the one hand, and on the other hand Simmental, Swiss Fleckvieh and Holstein (mixture data set). Accuracy of imputation was slightly better for the Brown Swiss data set than for the mixture data set. AlphaImpute outperformed Findhap V2 when close relatives of imputation candidates were 54k-genotyped. Findhap V2 resulted in higher imputation accuracy when candidates were less related to 54k reference animals.