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United States Department of Agriculture

Agricultural Research Service

Title: Mapping Expressed Sequence Tags (Ests) in Pigs Using Single Nucleotide Polymorphisms (Snps)

Authors
item Freking, Bradley
item Fahrenkrug, Scott
item Rohrer, Gary
item Smith, Timothy
item Keele, John

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: February 5, 2001
Publication Date: N/A

Technical Abstract: A high density type-I marker map allows rapid identification of segments of the human genome map orthologous to porcine segments harboring economically relevant loci. Existing swine genetic linkage maps have been used to scan the porcine genome for chromosomal regions that affect economically important traits, but these maps lack power for comparative mapping efforts stargeted to specific regions. Our objective is to directly integrate sequence variability associated with ESTs into the existing genetic map. Bovine and porcine ESTs obtained from clones derived from mixed-tissue normalized cDNA libraries were subjected to an automated primer design process to produce a product flanking a predicted intron region. Primers were designed if EST sequence matched a mapped human orthologous sequence with genomic sequence data to predict position of introns. Successful porcine genomic amplification products (n=264 unique loci) were sequenced and screened for SNPs in a total of 16 animals. Nine of these animals were parents of the MARC swine reference population. A total of 948 SNPs were identified. Sequencing revealed an average of 7.4 heterozygous animals per amplicon. Based on sequence data, an average of 74 informative meioses per amplicon are generated by genotyping the reference population for the available SNP. Genotyping assays were designed to utilize the MALDI-TOF detection coupled microsequencing approach. A total of 93 amplicons have assays designed for 167 individual porcine SNPs. Genotyping has been completed on the MARC swine reference population for 50 of these assays. Genotypic data from these SNP assays allows confirmation of segregation of the SNPs and provides map location of EST associated marker loci directly on the existing genetic map.

Last Modified: 7/12/2014