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Accelerating the shift to SNP-based parentage verification through microsatellite imputation in Ireland
As the livestock industry moves into the genomic era a major financial hindrances is the transition from microsatellite- to single nucleotide polymorphisms (SNP)-based parentage verification. To address this, the custom International Beef and Dairy (IDB) SNP chip was designed to include SNP for imputation of microsatellite (MS) alleles. MS were imputed using a publically available reference database of 7,130 animals from 33 Bos taurus breeds plus 1,128 additional Irish animals who have both MS and SNP genotypes. Since March, 2013 >10,000 Irish bovines whose pedigree could not be SNP verified had MS imputed. Any animal with >1 MS concordance error with its listed pedigree were MS genotyped to maintain stringent verification quality levels. With a >98% success rate of MS imputation this process saved Irish farmers >€200,000 in 2013 that would have been spent to MS genotype their animal for parentage verification.
Keywords:
Microsatellite, Imputation, Parentage verification
