Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Extension Of PigQTLDB: Genome-Wide Alignment Of BAC FPC Maps And RH Maps For QTL Positional Gene Mining

Zhi-liang Hu¹ , Sean Humphray ² , Carol Scott ² , Stacey N. Meyers ³ , Jane Rogers ² , Max F. Rothschild ¹ , James M. Reecy ¹

¹  Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011

²  Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

³  Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801

The creation of Pig QTL database (PigQTLdb) provides a useful public tool for locating genomic regions where the best candidate genes/markers for economically important pig traits may be identified based on confirmations from multiple QTL overlaps. However, dissection of promising genomic regions for a candidate gene search still remains a challenge as the size of such regions normally spans 2 to 20 cM or millions of base pairs. The availability of the 16X complexity BAC fingerprint map and the pig-human RH comparative map have added new opportunities to search for underlining genes of a QTL. We have performed a genome-wide alignment of the pig QTL maps with the Sanger BAC FPC maps, in an attempt to create a QTL interval-mining pipeline for end users. To date, we have produced 89 anchor points to link the two maps for 18 out of 19 pig chromosomes based on sequence blast matches, and we are in the process of adding more anchor sites on a few chromosomes to improve alignment quality. We have also aligned the QTL locations to the UIUC RH map that is further linked to human genome locations. Tools were also created for end-users to search with QTL location information (cM) for underlining BAC clones, and further to obtain the sequences and their corresponding human gene information. The map alignments will be further refined as more sequences become available from the porcine genome-sequencing project.