Frontiers in Genetics (Sep 2013)

Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parentage Verification Across Multiple Bos taurus and Bos indicus breeds

  • Matthew Charles Mcclure,
  • Matthew Charles Mcclure,
  • Tad Stewart Sonstegard,
  • George R Wiggans,
  • Alison Louise Van Eenennaam,
  • Kristina L Weber,
  • M. Cecilia Torres Penedo,
  • Donagh eBerry,
  • John eFlynn,
  • Jose Fernando eGarcia,
  • Adriana Santana Carmo,
  • Luciana C.A. Regitano,
  • Milla eAlbuquerque,
  • Marcos V.G.B Silva,
  • Marco Antonio Machado,
  • Mike eCoffey,
  • Kirsty eMoore,
  • Marie-Yvonne eBoscher,
  • Lucie eGenestout,
  • Raffaele eMazza,
  • Jeremy Francis Taylor,
  • Robert D Schnabel,
  • Barry eSimpson,
  • Elisa eMarques,
  • John eMcEwan,
  • Andrew eCromie,
  • Luiz Lehmann Coutinho,
  • Larry eKuehn,
  • John eKeele,
  • Emily ePiper,
  • Jim eCook,
  • Robert eWilliams,
  • Curtis eVan Tassell

DOI
https://doi.org/10.3389/fgene.2013.00176
Journal volume & issue
Vol. 4

Abstract

Read online

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 8,000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9,410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles for 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.

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