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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #201385

Title: An updated USMARC genetic map for the pig integrated with the pig physical map

item Rohrer, Gary
item Snelling, Warren
item Freking, Bradley - Brad
item Nonneman, Danny - Dan
item Harhay, Gregory
item Keele, John

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/3/2006
Publication Date: 1/2/2007
Citation: Rohrer, G.A., Snelling, W.M., Freking, B.A., Nonneman, D.J., Harhay, G.P., Keele, J.W. 2007. An updated USMARC genetic map for the pig integrated with the pig physical map [abstract]. Plant and Animal Genome XV Conference. Poster No. W421.

Interpretive Summary:

Technical Abstract: Ten years ago, we published our last comprehensive genetic map for the pig. This map contained 1,042 markers (mostly microsatellites) and spanned 2,286 cM of the autosomal genome, ~98% estimated coverage based on information available at the time. Since that time, USMARC has continued to add genetic markers to the map and has recently focused on developing single nucleotide polymorphism (SNP) markers associated with ESTs for the pig. In addition to marker development, an automated linkage analysis routine based on CRIMAP was developed. This procedure rebuilds each linkage group and prevents linkage group expansion due to genotypic errors by preventing the addition of markers with suspect genotypes. The most recent analysis yielded maps that contain over 1,500 microsatellites and 1,400 SNP markers. The autosomal map length was 2,185 cM which represents a 1.2% expansion of the 1996 map. However, the confines of the original map were reduced by 1.3% through modified marker orders, improved genotypic error detection and elimination of markers with suspect genotypes. The current map covers an additional 2.5% of the genome through extensions of previous linkage groups. The greatest extensions were present on chromosomes 1, 4, 10 and 14 (> 10 cM). More than 1,000 genetic markers can be localized to the pig BAC map by BLAST hits of marker sequences to BAC end sequences (BES) or by location in the human genome relative to BES hits to the human genome. This integrated map will facilitate directed marker development as well as assist in genome sequence assembly.