2017, Connors, Natalie, Cook, Jim, Girard, Christian, Tier, Bruce, Gore, Klint, Johnston, David, Ferdosi, Mohammad

Single step genomic BLUP (SS-GBLUP) for BREEDPLAN beef cattle evaluations is currently being tested for implementation across a number of breeds. A genomic data pipeline has been developed to enable efficient analysis of the industry-recorded SNP genotypes for incorporation in SS-GBLUP analyses. Complex data collection, along with format and/or naming convention inconsistencies challenges efficient data processing. This pipeline includes quality control of variable formatted data, and imputation of genotypes, for building the genomic relationship matrix required for implementation into single step evaluation.

2013, McClure, M C, Sonstegard, Tad S, Regitano, Luciana C A, Albuquerque, Milla, Silva, Marcos V G B, Machado, Marco A, Coffey, Mike, Moore, Kirsty, Boscher, Marie-Yvonne, Genestout, Lucie, Mazza, Raffaele, Taylor, Jeremy F, Wiggans, George R, Schnabel, Robert D, Simpson, Barry, Marques, Elisa, McEwan, J C, Cromie, A, Coutinho, Luiz L, Kuehn, Larry A, Keele, J W, Piper, Emily K, Cook, Jim, Van Eenennaam, Alison L, Williams, Robert, Bovine HapMap Consortium,, Van Tassell, Curtis P, Weber, Kristina L, Penedo, Cecilia T, Berry, Donagh P, Flynn, John, Garcia, Jose F, Carmo, Adriana S

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set ('N' = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds ('Bos taurus' and 'B. indicus') were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds ('N' = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.