IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION
Title: Confirmation and discovery of maternal grandsires and great grandsires in dairy cattle
Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 22, 2012
Publication Date: March 1, 2013
Citation: Van Raden, P.M., Cooper, T.A., Wiggans, G.R., O'Connell, J.R., Bacheller, L.R. 2013. Confirmation and discovery of maternal grandsires and great grandsires in dairy cattle. Journal of Dairy Science. 96(3):1874-1879.
Interpretive Summary: Pedigree information that is unknown or incorrect can now be discovered or corrected using new genotyping tools. Breeders previously could identify parents and confirm those relationships using a few markers, or discover only the parents if they were genotyped with thousands of markers. Three methods to discover more remote ancestors were developed and compared. The most accurate method discovered >90% of the correct maternal grandsires and great grandsires from a list of >10,000 potential ancestor bulls. Suggested maternal grandsires are now provided to breeders routinely.
Genetic improvement and selection of dairy animals has required accurate pedigree information. Genomic tools allow paternal ancestors to be easily confirmed or discovered because most sires are genotyped for many markers, but maternal ancestors are more difficult to discover because most female ancestors are not genotyped. Three methods to discover the most likely maternal grandsire (MGS) were developed and compared. Conflicts were counted 1 single nucleotide polymorphism (SNP) at a time between genotypes of the animal and potential MGS (DUO method) or also using sire’s genotype (TRIO method). Alternatively, haplotypes of a potential MGS were matched to the animal’s maternal haplotype, obtained using linkage across loci (HAP method). The DUO and TRIO methods can be performed as soon as a genotype is received because no imputation is required. The HAP method was expected to have greater accuracy because genotypes with 2,683 (3K) SNP were imputed to the 45,187 (50K) SNP used for genomic evaluation, and additional animals contribute information. To test the HAP method, modified pedigrees were created with 5% of true MGS replaced by a random genotyped bull from the same birth year and 5% of MGS set to missing for 4,134 Holsteins, 552 Jerseys, and 142 Brown Swiss that had confirmed, genotyped sires. Those same animals were used to test the DUO and TRIO methods, except some animals had multiple genotypes and imputed dams were excluded. Accuracies of discovering the true MGS from among 12,152 genotyped Holstein, 2,265 Jersey, and 1,605 Brown Swiss potential MGS were 61, 60, and 65%, respectively, with the DUO method; 95, 91, and 94% with the TRIO method; and 97, 95, and 97% with the HAP method. Accuracy of the DUO method was poor (only 52% for animals genotyped with 3K and 65% with 50K) because it does not use additional information from the paternal genotype that the TRIO and HAP methods use. Accuracy of the TRIO method was 78% with 3K and much less than 97% with 50K because the missing SNP were not imputed. Accuracy of the HAP method was 94% with 3K genotypes, 98% with 50K, and 92% with non-genotyped, imputed dams. When the HAP method was extended to great grandsires, accuracy of maternal great-grandsire discovery was 92% for 652 Holsteins, 95% for 33 Jerseys, and 85% for 20 Brown Swiss. Accuracy was even higher using simulated genotypes. Because most dairy bulls over several generations have been genotyped, percentages of haplotypes shared with candidate males can accurately confirm, correct, or discover the sires, MGS, and even more distant ancestors of most animals.