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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Publications at this Location » Publication #211105

Title: Sequencing the Pig Genome Using a Mapped BAC by BAC Approach

item Humphray, Sean
item Scott, Carol
item Clark, Richard
item Marron, Brandy
item Plumb, Robert
item Bender, Clare
item Camm, Nick
item Davis, Jayne
item Jenks, Andrew
item Noon, Angela
item Patel, Manish
item Sehra, Harminder
item Rogatcheva, Margarita
item Milan, Denis
item Chardon, Patrick
item Rohrer, Gary
item Nonneman, Danny - Dan
item De Jong, Pieter
item Meyers, Stacey
item Archibald, Alan
item Beever, Jonathon
item Schook, Lawrence
item Rogers, Jayne

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/30/2006
Publication Date: 1/2/2007
Citation: Humphray, S.J., Scott, C., Clark, R., Marron, B., Plumb, R., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Rogatcheva, M., Milan, D., Chardon, P., Rohrer, G.A., Nonneman, D.J., De Jong, P., Meyers, S., Archibald, A., Beever, J., Schook, L., Rogers, J. 2007. Sequencing the pig genome using a mapped BAC by BAC approach. Plant and Animal Genome Conference Proceedings. Abstract P34, p. 110.

Interpretive Summary:

Technical Abstract: We have generated a highly contiguous physical map covering >98% of the pig genome in just 176 contigs. The map is localised to the genome through integration with the UIUC RH map as well BAC end sequence alignments to the human genome. Over 265k HindIII restriction digest fingerprints totalling 16.2 genome equivalents form the basis of the map assembly. Most of the map coverage is from the CH-242 library generated from a single Duroc sow. Mapped clones have also been used to generate over 620k BAC end sequences with an average read length of 635bp. The map represents an entry point for rapid electronic positional cloning of genes and fine mapping of QTLs. We are using the map as a basis for sequencing the pig genome by detecting the most economic set of minimally overlapping CH-242 BACs. Sequence clones are identified in a series of iterative sets using first mapped data and BES alignment to human with bridging clones subsequently selected on the basis of the map and BES alignments to pig sequence clones. A Duroc fosmid library (generated from the same animal as the CH-242 BAC library) is currently being end sequenced and will improve both sequencing efficiency in regions where clones of <40kb are required and further enable map gap closure. The map and project progress summaries are available via pre-ensembl (