Parentage Analysis Services for Dairy Cattle in Canada

Abstract

Since the implementation of genomic evaluations in 2009, Canadian Dairy Network (CDN) has used SNP genotypes to verify the reported parents if genotyped and, when missing or incorrect, to discover the animal's sire and/or dam based on all existing SNP genotypes. To date, for breeds with official genomic evaluations in Canada, CDN has over 1.4M genotypes including 1.2M Holstein, 163,000 Jersey, 29,000 Brown Swiss, 6,000 Ayrshire and 3,000 Guernsey. These genotypes involve 23 different genotype panels, including low (3K-30K), medium (44K-140K) and high (over 600K) density. For parentage analysis, a list of 2,683 SNP in common from the 3K and 50K genotype panels are used as the basis for parentage verification, parentage discovery and for identifying families of genetically identical animals. Using the list of SNP proposed for inclusion in GenoEx-PSE for parentage verification (200) and parentage discovery (additional 675 or 354), it was concluded that the 200 SNP recommended by ISAG for parentage verification performed very well compared to the SNP routinely used  by CDN for dairy cattle breeds in Canada.  It was also concluded that parentage discovery using either set of additional 675 or 354 SNP also provided accurate results. To avoid a possible misuse of the additional SNP for parentage discovery, the reduced set of 354 SNP, selected from only 10 chromosome, are recommended for GenoEx-PSE due to the higher level of imputation error and lower accuracy of GEBV estimation compared to results based on the additional 675 SNP.