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

McClure, Matthew C., Sonstegard, Tad S., Wiggans, George R., Van Eenennaam, Alison L., Weber, Kristina L., Penedo, Cecilia T., Berry, Donagh P., Flynn, John, Garcia, Jose F., Carmo, Adriana S., Regitano, Luciana C. A., Albuquerque, Milla, Silva, Marcos V. G. B., Machado, Marco A., Coffey, Mike, Moore, Kirsty, Boscher, Marie-Yvonne, Genestout, Lucie, Mazza, Raffaele, Taylor, Jeremy F., Schnabel, Robert D., Simpson, Barry, Marques, Elisa, McEwan, John C., Cromie, Andrew, Coutinho, Luiz L., Kuehn, Larry A., Keele, John W., Piper, Emily K., Cook, Jim, Williams, Robert, Bovine HapMap Consortium and Van Tassell, Curtis 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 SEP: 176.1-176.11. doi:10.3389/fgene.2013.00176

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Author McClure, Matthew C.
Sonstegard, Tad S.
Wiggans, George R.
Van Eenennaam, Alison L.
Weber, Kristina L.
Penedo, Cecilia T.
Berry, Donagh P.
Flynn, John
Garcia, Jose F.
Carmo, Adriana S.
Regitano, Luciana C. A.
Albuquerque, Milla
Silva, Marcos V. G. B.
Machado, Marco A.
Coffey, Mike
Moore, Kirsty
Boscher, Marie-Yvonne
Genestout, Lucie
Mazza, Raffaele
Taylor, Jeremy F.
Schnabel, Robert D.
Simpson, Barry
Marques, Elisa
McEwan, John C.
Cromie, Andrew
Coutinho, Luiz L.
Kuehn, Larry A.
Keele, John W.
Piper, Emily K.
Cook, Jim
Williams, Robert
Bovine HapMap Consortium
Van Tassell, Curtis P.
Total Author Count Override 33
Title Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds
Formatted title
Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds
Journal name Frontiers in Genetics   Check publisher's open access policy
ISSN 1664-8021
Publication date 2013-08-23
Sub-type Article (original research)
DOI 10.3389/fgene.2013.00176
Open Access Status DOI
Volume 4
Issue SEP
Start page 176.1
End page 176.11
Total pages 11
Place of publication Lausanne, Switzerland
Publisher Frontiers Research Foundation
Collection year 2014
Language eng
Formatted abstract
To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
Keyword Microsatellite
STR
SNP
Imputation
Parentage verification
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Veterinary Science Publications
 
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Created: Fri, 30 Aug 2013, 03:22:28 EST by Dr Emily Piper on behalf of School of Veterinary Science