Submitted to: Animal Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/27/2001
Publication Date: 5/26/2002
Citation: Fahrenkrug, S.C., Freking, B.A., Smith, T.P., Rohrer, G.A., Keele, J.W. 2002. Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Animal Genetics. 33:186-195. Interpretive Summary: A critical objective of swine genomic research is the development of rapid, accurate, and automated genotyping systems for sequence variation influencing economically important traits. Single nucleotide polymorphisms (SNPs) represent the most abundant form of genetic variation available. Markers based on SNPs are suitable for use in high throughput genotyping systems and can be targeted within expressed porcine genes to integrate the porcine/human comparative map. In this manuscript we describe the approaches used in discovery of 1,650 SNPs within 403 targeted porcine gene sequences. This information directly supports development of a comprehensive gene map of swine. Discovered variation is being used to construct genotyping assays for a swine reference population which will provide chromosomal position of each gene. Application of the discovered variation to pertinent commercial populations of swine will depend on genome position and frequency of the alternative alleles. These data provide the first large-scale assessment of frequency and distribution of porcine SNPs.
Technical Abstract: High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes to develop the porcine/human comparative map. Locus Specific Amplification (LSA) and comparative sequencing were used to generate diploid PCR products and allelic information from parents of a swine reference family. Discovery of 1,650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs.