LINKAGE MAPPING ESTS IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS): SNP DISCOVERY

Authors: Fahrenkrug, Scott; Freking, Bradley - Brad; Rohrer, Gary; Smith, Timothy - Tim; Grosse, William; Keele, John

Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 3/14/2000
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Comparative mapping between human and swine genomes requires the localization of conserved genes in both species. Our objective is to improve the resolution of the human/swine comparative map by mapping markers within expressed pig genes. SNPs associated with porcine expressed sequence tags (ESTs) orthologous to genes with known human map positions will be mapped by linkage analysis. Single-pass porcine EST sequence derived from two normalized libraries is subjected to automated PCR primer design aimed at developing primer-pairs that span intron/exon junctions. The results of PCR amplification from porcine, bovine, and ovine DNAs are entered into a relational database (MARCDB). Successful primer-pairs are used to generate amplicons from nine parents of the MARC porcine reference population, and seven animals likely to harbor breed-specific alleles present in mapping animals. Amplicons are purified and subject to fluorescent di-deoxy sequencing. Chromatograms are imported into MARCDB, assembled into contigs, and assessed for SNPs using Polyphred. Potential polymorphisms are interactively evaluated and tagged using Consed. Validated SNPs are exported to MARCDB for automated genotyping assay design. Preliminary assessment of our strategy for SNP-discovery reveals it to be quite efficient. Up to 85% of the amplicons sequenced harbor SNPs. To date polymorphisms have been detected in over 100 porcine genes.