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Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification

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...

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Autores principales: McClure, Matthew, Sonstegard, Tad, Wiggans, George, Van Tassell, Curtis P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Research Foundation 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418578/
https://www.ncbi.nlm.nih.gov/pubmed/22912645
http://dx.doi.org/10.3389/fgene.2012.00140
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author McClure, Matthew
Sonstegard, Tad
Wiggans, George
Van Tassell, Curtis P
author_facet McClure, Matthew
Sonstegard, Tad
Wiggans, George
Van Tassell, Curtis P
author_sort McClure, Matthew
collection PubMed
description 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. A total of 347 dairy cattle representing four dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey) were used to generate reference haplotypes. This approach has been verified (>98% accurate) for imputing the International Society of Animal Genetics recommended panel of 12 MS for cattle parentage verification across a validation set of 1,307 dairy animals. 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.
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spelling pubmed-34185782012-08-21 Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification McClure, Matthew Sonstegard, Tad Wiggans, George Van Tassell, Curtis P Front Genet Genetics 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. A total of 347 dairy cattle representing four dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey) were used to generate reference haplotypes. This approach has been verified (>98% accurate) for imputing the International Society of Animal Genetics recommended panel of 12 MS for cattle parentage verification across a validation set of 1,307 dairy animals. 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. Frontiers Research Foundation 2012-08-14 /pmc/articles/PMC3418578/ /pubmed/22912645 http://dx.doi.org/10.3389/fgene.2012.00140 Text en Copyright © 2012 McClure, Sonstegard, Wiggans and Van Tassell. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
spellingShingle Genetics
McClure, Matthew
Sonstegard, Tad
Wiggans, George
Van Tassell, Curtis P
Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title_full Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title_fullStr Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title_full_unstemmed Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title_short Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
title_sort imputation of microsatellite alleles from dense snp genotypes for parental verification
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418578/
https://www.ncbi.nlm.nih.gov/pubmed/22912645
http://dx.doi.org/10.3389/fgene.2012.00140
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