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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #200776
Title: Single Nucleotide Polymorphisms for Pig Identification and Parentage Exclusion

Author
item Rohrer, Gary
item Freking, Bradley - Brad
item Nonneman, Danny - Dan

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/6/2007
Publication Date: 5/10/2007
Citation: Rohrer, G.A., Freking, B.A., Nonneman, D.J. 2007. Single nucleotide polymorphisms for pig identification and parentage exclusion. Animal Genetics. 38:253-258.

Interpretive Summary: Demand for genetic markers that are able to discriminate between lines of animals and potentially identify each animal has increased dramatically in recent years. Genetic identification of individual livestock animals is critical to determining farm of origin of animals that were diagnosed with important contagious diseases or to insure the integrity of "branded" products with specific eating qualities. To fill this need, DNA markers (SNP) were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Sixty SNP marker were selected for the final panel. Theoretically, this panel is able to discriminate between every pig in the world. In addition, this panel can be used to determine parentage. Parentage exclusion probability when DNA from only one parent is available was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam's genotype is known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. This panel of SNP markers is theoretically sufficient for individual identification or for most parentage scenarios and is available for use by the swine industry.

Technical Abstract: Single nucleotide polymorphisms have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, a large number of highly informative public SNP markers tested in commercial pig populations have not been available to genotyping laboratories. To fill this need, SNP markers previously mapped in the USMARC swine reference population were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Multiplex assay groups of 5-7 SNP assays/group were designed and genotypes were determined using Sequenom’s MassARRAY® system. Eighty SNP were evaluated. Sixty SNP assays, with minor allele frequencies greater than 0.15, were selected for the final panel of markers. For some SNP, reliable assay systems could not be designed; other SNP were not informative enough (minor allele frequency < 0.15) for use within breeds included. Overall identity power across breeds was 4.6E-23 but within breeds ranged from 4.3E-14 (Hampshire) to 2.6E-22 (Yorkshire). Parentage exclusion probability when only one parent is sampled was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam’s genotype is known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. Power of exclusion was compared between the 60 SNP with 10 microsatellite markers. The parental exclusion probabilities for SNP and microsatellite marker panels were similar, but the SNP panel was much more sensitive for individual identification. This panel of SNP markers is theoretically sufficient for individual identification of any pig in the world and is available for use by the swine industry.