Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #294637

Title: Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

item MCCLURE, MATTHEW - Collaborator
item Sonstegard, Tad
item Wiggans, George
item VAN EENENNAAM, ALISON - University Of California
item WEBER, KRISTINA - University Of California
item PENEDO, M. CECILIA - University Of California
item FLYNN, JOHN - Weatherbys
item GARCIA, JOSE FERNANDO - Sao Paulo State University (UNESP)
item SANTANA DO CARMO, ADRIANA - Deoxy Biotechnolgoy
item REGITANO, LUCIANA C.A. - Embrapa
item ALBUQUERQUE, MILLA - Universidad De Sao Paulo
item SILVA, MARCOS - Embrapa
item MACHADO, MARCO - Embrapa
item COFFEY, MIKE - Sruc-Scotland'S Rural College
item MOORE, KRISTY - 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 - Laboratoire D'Analyses Genetiques Pour Les Especes Animales(LABOGENA)
item TAYLOR, JEREMY - University Of Missouri
item SCHNABEL, ROBERT - University Of Missouri
item SIMPSON, BARRY - Geneseek Inc, A Neogen Company
item MARQUES, ELISA - Geneseek Inc, A Neogen Company
item MC EWAN, JOHN - Agresearch
item CROMIE, ANDREW - Irish Cattle Breeder Federation (ICBF)
item LEHMANN COUTINHO, LUIZ - Luiz De Queiroz College Of Agriculture (ESALQ)
item Kuehn, Larry
item Keele, John
item PIPER, EMILY KATE - University Of Queensland
item COOK, JIM - University Of Queensland
item WILLIAMS, ROBERT - American-International Charolais Association
item HAP MAP CONSORTIUM, BOVINE - Collaborator
item Van Tassell, Curtis - Curt

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2013
Publication Date: 9/18/2013
Citation: McClure, M.C., Sonstegard, T.S., Wiggans, G.R., Van Eenennaam, A., Weber, K., Penedo, M., Berry, D.P., Flynn, J., Garcia, J., Santana Do Carmo, A., Regitano, L., Albuquerque, M., Silva, M.V., Machado, M.A., Coffey, M., Moore, K., Boscher, M., Genestout, L., Mazza, R., Taylor, J.F., Schnabel, R., Simpson, B., Marques, E., Mc Ewan, J., Cromie, A., Lehmann Coutinho, L., Kuehn, L.A., Keele, J.W., Piper, E., Cook, J., Williams, R., Hap Map Consortium, B., Van Tassell, C.P. 2013. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Frontiers in Genetics. 4:176. DOI.10.3389/fgene.2013.00176.

Interpretive Summary: Microsatellites are the current international molecular marker standard for genomically verifying parentage in livestock species. There is industry interest in using Single Nucleotide Polymorphism (SNP) markers instead of microsatellites as they are easier to automate for genotyping, have a lower error rate, and can have a lower producer cost. Currently there is no economically feasible way to move from a microsatellite- to a SNP-based marker panel for parental verification without fully genotyping one generation of individuals using both panels. Expanding from our previous research, we assembled a reference panel of >8,000 animals from 39 cattle breeds to develop a minimal SNP set for microsatellite imputation in all Bos taurus breeds. Implementation of this SNP panel and reference population will allow both beef and dairy producers in the US and worldwide to quickly transition from microsatellite- to SNP-based panels for parentage verification.

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 cattle breeds. This method was verified with a limited SNP data set representing 4 dairy breeds (N=479) to be >98% accurate for imputing alleles for the 12 MS markers of the International Society of Animal Genetics’ (ISAG) parental verification panels. Some MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds, implying that some combinations were present before modern breed formations and remain in high linkage disequilibrium. To expand the utility of this imputation across breeds, MS and SNP data from more than 8,000 animals representing 39 breeds (Bos taurus and indicus) were used to identify 9,410 haplotypes, average size of 73 SNP, that can be accurately imputed to MS genotypes. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N=2 to 36). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small decrease in accuracy. Our findings suggest these imputation methods can be integrated into any species that desires to move from MS- to SNP- based parental verification.