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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #289071

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 - University Of California
item WEBER, KRISTINA - University Of California
item PENEDO, CECILIA - University Of California
item FLYNN, JOHN - Weatherbys
item FERNANDO GARCIA, JOSE - Universidade Estadual Paulista (UNESP)
item SANTA, ADRIANA - Deoxi Biotecnologia
item REGITANO, LUCIANA - Embrapa
item ALBUQUERQUE, MILLA - Luiz De Queiroz College Of Agriculture (ESALQ)
item SILVA, MARCOS - Embrapa
item COFFEY, MIKE - Sruc-Scotland'S Rural College
item MOORE, KIRSTY - Sruc-Scotland'S Rural College
item BOSCHER, MARIE-YVONNE - Laboratoire D'Analyses Genetiques Pour Les Especes Animales(LABOGENA)
item GENESTOUT, LUCIE - Laboratoire D'Analyses Genetiques Pour Les Especes Animales(LABOGENA)
item MAZZA, RAFFAELE - Laboratorio Di Genetica E Servizi (LGS)
item TAYLOR, JERRY - University Of Missouri
item SCHNABEL, ROBERT - University Of Missouri
item MACHADO, MARCO - Embrapa
item SIMPSON, BARRY - Geneseek Inc, A Neogen Company
item MCEWAN, JOHN - Agresearch
item CROMIE, ANDREW - Irish Cattle Breeder Federation (ICBF)
item COUNTINHO, LUIZ - Luiz De Queiroz College Of Agriculture (ESALQ)
item Kuehn, Larry
item Keele, John
item PIPER, EMILY - University Of Queensland
item COOK, JIM - University Of Queensland
item MARQUES, ELISA - Geneseek Inc, A Neogen Company

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.