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United States Department of Agriculture

Agricultural Research Service

Title: Single Nucleotide Polymorphisms for Pig Identification and Parentage Exclusion

Authors
item Rohrer, Gary
item Freking, Bradley
item Nonneman, Danny

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2004
Publication Date: January 15, 2005
Citation: Rohrer, G.A., Freking, B.A., Nonneman, D.J. 2005. Single nucleotide polymorphisms for pig identification and parentage exclusion. Proc., Plant & Animal Genome XIII, San Diego, CA. P203. p. 125.

Technical Abstract: Single nucleotide polymorphisms (SNP) are abundant in mammalian genomes and amenable for automated genotyping systems. Therefore, SNP markers are the preferred marker type for individual animal identification, traceback and parentage exclusion if economically feasible. The SNP mapping project at MARC has mapped over 1,500 SNP markers in the swine reference population. SNP markers for identification were selected based on their informativeness in occidental pig germplasm and location in the genome. A panel of 24 unrelated boars for each of the four main US breeds (Duroc, Hampshire, Landrace and Yorkshire) was developed by the National Swine Registry. Additional boars of these four breeds used in research projects at MARC were also included. Multiplex assay groups of 5-7 SNP/assay group were designed and genotypes were determined using Sequenom's Mass Array system. To date, 60 SNP have been evaluated and 34 have exceeded the selection criteria. In multiplexes, 9 assays failed, 6 assays were not robust and 10 SNP were not informative enough to be useful. Overall identity power across breeds was 1.8E-15 but within breeds ranged from 3.6E-8 (Hampshire) to 5.0E-14 (Landrace). Exclusion probability when only one parent is sampled was .982 across breeds and ranged from .872 (Hampshire) to .970 (Landrace) within breeds. Sire exclusion probability when the dam's genotype is known was .999 across breeds and ranged from .994 (Hampshire) to .999 (Yorkshire). Additional SNP are being tested to produce a panel of 40 SNP.

Last Modified: 7/23/2014