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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY

Location: Reproduction Research

Title: Integrating the USMARC genetic map for the pig with the pig physical map

Authors
item Wiedmann, Ralph
item Freking, Bradley
item Nonneman, Danny
item Snelling, Warren
item Keele, John
item Harhay, Gregory
item Rohrer, Gary

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 5, 2007
Publication Date: January 2, 2008
Citation: Wiedmann, R.T., Freking, B.A., Nonneman, D.J., Snelling, W.M., Keele, J.W., Harhay, G.P., Rohrer, G.A. Integrating the USMARC genetic map for the pig with the pig physical map. 2008. Annual International Plant & Animal Genome Conference. Poster No. P565, pg 259.

Technical Abstract: A comprehensive genetic linkage map containing 3418 markers and spanning 2,326 cM of the autosomal genome was generated and integrated with the available physical maps for the pig. Marker types consisted of 1531 microsatellites and 1887 markers based on single feature polymorphisms, insertion/deletion events and single nucleotide polymorphisms (SNP). The first path connecting the linkage and BAC maps was created by comparing the marker sequences against the mapped BAC sequences. Because the total sequence available from the mapped BACs is no more than 20-25% of the pig genome, additional paths were needed to position most of the genetic markers to the physical map. The Harvard Sus scrofa gene index was used both as a connecting bridge between marker sequence and BAC end sequence and also as an effective way to map pig marker sequence to a unique locus of the human genome. In the latter case, the swine-human comparative map was then used to place the markers onto the swine BAC map. The primers that amplified the marker sequence were also compared to the BAC sequence and the gene indexes, providing additional paths of connection. A comparison of the BAC physical map and the genetic map revealed a sigmoidal relationship that is consistent with higher recombination at the telomeres and lower at the centromeres. There were no major discrepancies between the physical and genetic maps. This integrated map will facilitate directed marker development as well as assist in genome sequence assembly.

Last Modified: 9/3/2014
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