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Title: Imputation of microsatellite allele from dense SNP genotypes for parentage verification

item McClure, Matthew
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Wiggans, George

Submitted to: Frontiers in Livestock Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2012
Publication Date: 8/14/2012
Citation: Mcclure, M.C., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R. 2012. Imputation of Microsatellite Allele from Dense SNP Genotypes for Parentage Verification. Frontiers in Livestock Genomics. 3:140.

Interpretive Summary: Microsatellites are the current international molecular marker standard for genomically determining parental verification in livestock species. There is industry interest in using Single Nucleotide Polymorphisms (SNP) 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 having to fully genotype one generation of individuals with both panels. Using data from USA dairy breeds, we have devised a simple and economical method to impute microsatellite alleles within a breed from phased SNP genotypes, using existing technology. Implementation of this method will allow dairy producers in the USA and worldwide to quickly transition from microsatellite to SNP based panels for parentage verification. Additionally the methods can be applied to any species with accurate microsatellite genotypes and sufficiently dense SNP genotypes.

Technical Abstract: Microsatellite (MS) markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international interest from producers and research communities, no viable means currently exist to verify parentage for an individual unless all familial connections were analyzed using the same DNA marker type (MS or SNP). A simple and cost-effective method was devised to impute MS alleles from SNP haplotypes within breeds. For some MS, imputation results may allow inference across breeds. This approach has been verified (>98% accurate) for imputing the International Society of Animal Genetics (ISAG) recommended panel of 12 MS for cattle parentage verification. A total of 347 dairy cattle representing 4 dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey) were used. Implementation of this method will allow producers and breed associations to transition to SNP-based parentage verification utilizing MS genotypes from historical data on parents where SNP genotypes are missing. This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP- based parental verification.