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Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/3/2006
Publication Date: 8/10/2006
Citation: Ernst, C.W., Rilington, V.D., Raney, N.E., Venta, P.J., Housley, D.J., Rohrer, G.A., Choi, I., Thorn, S.R. 2006. Identification of single nucleotide polymorphisms in pig sequence tagged-sites. (Abstract) Animal Genetics International Conference Proceedings. p. 59. Abstract #B503.
Technical Abstract: The objective of this study was to identify single-nucleotide polymorphisms (SNPs) in pig sequence tagged-sites (STS) generated from Type I (gene) amplicons. For SNP identification, we use a pool-and-sequence strategy in which a pool of DNA samples from different breeds is PCR-amplified and sequenced. SNPs are identified as ambiguous bands occurring at identical positions in a sequencing gel. For this study, we have screened 327 oligonucleotide primer pairs, developed 127 pig STS, placed 87 STS on a pig radiation hybrid (RH) map using the INRA-University of Minnesota porcine 7,000 rad RH panel, and identified 210 SNPs in 78 STS (1-6 SNPs per STS). PCR primers were designed using heterologous sequences and the identity of each STS was confirmed by DNA sequencing. Two-point analysis of RH data showed significant linkage of STS with markers on 12 different pig chromosomes. Genetic linkage analysis was performed using SNP genotypes in the USDA-ARS MARC reference families placing 19 STS onto eight different pig chromosomes. Genetic linkage analysis was also performed using SNP genotypes for nine additional STS in the PiGMaP reference families placing markers on five different pig chromosomes. Three of these STS (IGFBP2, PAX3 and PSMD1) are significantly linked to microsatellite markers at the distal end of SSC 15 in the order PAX3-(10 cM)-SW936-(11.2 cM)-IGFBP2-(14.2 cM)-SW1119-(17.5 cM)-PSMD1. SNPs identified in this study contribute to the growing SNP collection for pigs and will aid in identifying genes responsible for genetic variation in economically important traits.