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United States Department of Agriculture

Agricultural Research Service


Location: Animal Genomics and Improvement Laboratory

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

item Mcclure, Matthew
item Sonstegard, Tad
item Van tassell, Curtis - Curt
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: 12/26/2012
Publication Date: 1/12/2013
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.

Interpretive Summary:

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: 8/24/2016
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