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

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.

Systematic profiling of short tandem repeats in the cattle genome

“…Although earlier studies based on a limited number of then known STRs suggested they are effectively tagged by SNPs (McClure et al. 2012, 2013), to fully explore the potential tagging relationship between STRs and SNPs, we investigated linkage disequilibrium (LD) pattern using SNPs around identified STRs, which is a simple method to understand their potential relationship without phasing STRs. We performed LD block estimation for each autosome using the 44 Holstein Bovine HD SNP array data retrieved from the Bovine HapMap panel.…”

“…Although previous studies have reported that most STRs can be tagged by SNPs (McClure et al. 2012, 2013), these conclusions were mainly based on a rather limited number of known microsatellites. Because it has been impossible to produce genome-wide profiles of STR variations, the majority of STRs in the cattle genome remain undetected and unexplored.…”

Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

“…Microsatellite genotyping is a PCR-based method that has been extensively used in parentage qualification (Tian et al 2008;Carolino et al 2009;Radko and Slota 2009); it requires a dedicated platform and skilled interpretation for accuracy (McClure et al 2013;Berry et al 2014). The polymorphic nature of microsatellite markers facilitates parentage qualification for moderately sized populations; however, larger populations require proportionally larger marker sets.…”

0309 Systematic profiling of short tandem repeats in the cattle genome

“…Furthermore, the exploration of the relationship between STRs with nearby SNPs can further help explain the results from SNP-based genome wide association studies (Brahmachary et al 2014). Although previous studies have reported that most STRs can be tagged by SNPs (McClure et al 2012(McClure et al , 2013, these conclusions were mainly based on a rather limited number of known microsatellites. Because it has been impossible to produce genome-wide profiles of STR variations, the majority of STRs in the cattle genome remain undetected and unexplored.…”