Submitted to: Animal Genomics Symposium North Carolina State University Raleigh
Publication Type: Proceedings
Publication Acceptance Date: September 15, 2003
Publication Date: October 9, 2003
Citation: FREKING, B.A. DEVELOPMENT OF AN EST-DERIVED SNP-BASED LINKAGE MAP IN PIGS. 3rd ANIMAL GENOMICS SYMPOSIUM NORTH CAROLINA STATE UNIVERSITY RALEIGH. 2003. P. 19. Technical Abstract: Quantitative trait evaluation and gene discovery efforts in the pig are hindered by a low- density comparative map to identify potential candidate genes within a genetic region of interest. In the absence of a whole genome sequence for the pig (the ultimate comparative map), a high density gene-based map is an intermediate goal. 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. Generation of a porcine gene index containing over 56,000 unique expressed gene sequences has provided a valuable resource to direct mapping efforts in regions homologous to the human genome, thus creating comparative markers on the porcine genetic map. We developed an approach to generate a comprehensive comparative genetic map from these resources. An automated process targeted design of PCR primers flanking exon-intron boundary regions with predicted intron length of 700 to 1000 bp. Over 2,270 primer pairs generated successful genomic sequence in our SNP discovery panel (n=8 pigs). The panel represented the parent generation of the MARC reference families used to construct the microsatellite-based linkage map. Approximately 1.4 Mb / animal of high quality genomic sequence was generated. Seventy percent of the amplicons contained an SNP in this panel. On average, 4.8 SNPs per amplicon (1 SNP / 183 bp) were tagged in the sequence chromatograms by manual interaction with Consed software. Transition polymorphisms (67%) were the most prevalent SNP, followed by transversions (26%), and insertion/deletion events (6%). We validated segregation of more than 1650 of these SNP by genotyping the MARC reference families. MALDI-TOF mass spec genotyping assays provided the necessary genotypic information to position these loci on the genetic map. 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 as well as establishing a higher resolution comparative map. This comparative map will also be helpful in assembly of early draft genomic sequence data.