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 an...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2012-08-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00140/full |
| _version_ | 1818494093665239040 |
|---|---|
| author | Matthew eMcclure Tad Stewart Sonstegard George eWiggans Curtis P Van Tassell |
| author_facet | Matthew eMcclure Tad Stewart Sonstegard George eWiggans Curtis P Van Tassell |
| author_sort | Matthew eMcclure |
| collection | DOAJ |
| 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 4 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 (ISAG) 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. |
| first_indexed | 2024-12-10T18:02:10Z |
| format | Article |
| id | doaj.art-65a6f2863de54affb22a9aa9ce1474c1 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T18:02:10Z |
| publishDate | 2012-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-65a6f2863de54affb22a9aa9ce1474c12022-12-22T01:38:44ZengFrontiers Media S.A.Frontiers in Genetics1664-80212012-08-01310.3389/fgene.2012.0014030779Imputation of microsatellite alleles from dense SNP genotypes for parental verificationMatthew eMcclure0Tad Stewart Sonstegard1George eWiggans2Curtis P Van Tassell3United States Department of AgricultureUnited States Department of AgricultureUnited States Department of AgricultureUnited States Department of AgricultureMicrosatellite (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 4 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 (ISAG) 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.http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00140/fullParentage verificationMicrosatellite imputationSNP haplotypeISAGAcross breed imputation |
| spellingShingle | Matthew eMcclure Tad Stewart Sonstegard George eWiggans Curtis P Van Tassell Imputation of microsatellite alleles from dense SNP genotypes for parental verification Frontiers in Genetics Parentage verification Microsatellite imputation SNP haplotype ISAG Across breed imputation |
| 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 | Parentage verification Microsatellite imputation SNP haplotype ISAG Across breed imputation |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00140/full |
| work_keys_str_mv | AT matthewemcclure imputationofmicrosatelliteallelesfromdensesnpgenotypesforparentalverification AT tadstewartsonstegard imputationofmicrosatelliteallelesfromdensesnpgenotypesforparentalverification AT georgeewiggans imputationofmicrosatelliteallelesfromdensesnpgenotypesforparentalverification AT curtispvantassell imputationofmicrosatelliteallelesfromdensesnpgenotypesforparentalverification |