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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds

Authors
item McClure, Matthew
item Sonstegard, Tad
item Van Tassell, Curtis
item Wiggans, George
item Van Eenennaam, Alison -
item Weber, Kristina -
item Penedo, Cecilia -
item Berry, Donagh -
item Flynn, John -
item Fernando Garcia, Jose -
item Santa, Adriana -
item Regitano, Luciana -
item Albuquerque, Milla -
item Silva, Marcos -
item Coffey, Mike -
item Moore, Kirsty -
item Boscher, Marie-Yvonne -
item Genestout, Lucie -
item Mazza, Raffaele -
item Taylor, Jerry -
item Schnabel, Robert -
item Machado, Marco -
item Simpson, Barry -
item Mcewan, John -
item Cromie, Andrew -
item Countinho, Luiz -
item Kuehn, Larry
item Keele, John
item Piper, Emily -
item Cook, Jim -
item Marques, Elisa -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 26, 2012
Publication Date: January 12, 2013
Citation: Mcclure, M.C., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R., Van Eenennaam, A., Weber, K., Penedo, C., Berry, D., Flynn, J., Fernando Garcia, J., Santa, A., Regitano, L., Albuquerque, M., Silva, M., Coffey, M., Moore, K., Boscher, M., Genestout, L., Mazza, R., Taylor, J., Schnabel, R., Machado, M.A., Simpson, B., Mcewan, J., Cromie, A., Countinho, L.L., Kuehn, L.A., Keele, J.W., Piper, E., Cook, J., Marques, E. 2013. Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds. Plant Animal Genome XXI, paper PO132, pp. 206.

Technical Abstract: Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international demands from the livestock and research communities, no viable means currently exist to verify parentage for any individual unless all familial connections were analyzed using the same DNA marker type (MS or SNP). We have previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes within and potentially across breeds. This method was verified at >98% accuraty for imputing the MS alleles for 12 markers of ISAG recommended parentage panel using SNP genotypes from 479 dairy animals across 4 dairy cattle breeds (Brown Swiss, Guernsey, Holstein, and Jersey). Some MS-haplotype association held true across these phylogeneticly diverse breeds, implying that some combinations were present before modern breed formations and have been preserved across breeds. To expand the utility of this imputation >8,000 animals with MS and SNP data a from 45 breeds (Bos taurus and indicus) were used in this study to identify haplotypes that can be used across bovine breeds to impute MS genotypes. While MS are currently the international standard for parentage verification of exported semen, this work represents a tool to quickly migrate towards SNP based verification in 1 generation for any domesticated bovine breed. Finally, these imputation methods can be integrated into any livestock species that desires to move from MS- to SNP- based parental verification.

Last Modified: 12/18/2014
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