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

Authors
item Mcclure, Matthew -
item Sonstegard, Tad
item Wiggans, George
item Van Eenennaam, Alison -
item Weber, Kristina -
item Penedo, M. Cecilia -
item Berry, Donagh -
item Flynn, John -
item Garcia, Jose Fernando -
item Santana Do Carmo, Adriana -
item Regitano, Luciana C.A. -
item Albuquerque, Milla -
item Silva, Marcos -
item Machado, Marco -
item Coffey, Mike -
item Moore, Kristy -
item Boscher, Marie-Yvonne -
item Genestout, Lucie -
item Mazza, Raffaele -
item Taylor, Jeremy -
item Schnabel, Robert -
item Simpson, Barry -
item Marques, Elisa -
item Mc Ewan, John -
item Cromie, Andrew -
item Lehmann Coutinho, Luiz -
item Kuehn, Larry
item Keele, John
item Piper, Emily Kate -
item Cook, Jim -
item Williams, Robert -
item Hap Map Consortium, Bovine -
item Van Tassell, Curtis

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 22, 2013
Publication Date: September 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.

Last Modified: 11/28/2014
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