Notes on the Animal QTL Database
Development and Releases

The current Animal QTL Database development is a project led by a team at the Iowa State University, under the NAGRP Bioinformatics Coordination Programs.

The initial proposal on developing a (pig) QTL database was made within the NAGRP Pig Genome Coordination Program in the fall of 1998. However the actual design, preparation and preliminary exploration on the approaches was not made until 2002/2003. The pig QTL data collection and tools development works were done in 2004, which result in our first paper on PigQTLdb published in Mammalian Genome (2005, Volume 16(10):792-800). Subsequently, the QTLdb was expanded on its functionality and utility. Additional curator/editor tools and viewer tools were developed, and cattle/chicken QTL data were added in 2005/2006.

During the course of the project, many attempts were made to utilize existing tools. The contacted groups and tools tried include: Roslin Institute for Anubis tool, Cold Spring Harbor Lab for cMAP, University of Tennessee Bioinformatics group for their Mouse/Human Bone Density QTL Database, Sweden RatMap Group for its QTL tools, Texas A&M University for a Bovine QTL Viewer, among others. For various reasons none of these tools was worked out at the Iowa State University. As the last resort we explored a Perl/GD and MySQL approach to program out the tools needed for displaying and analyzing the QTLs.

Under an agreement between the NAGRP Bioinformatics Coordinator and the NCBI, a copy of the pig database is implemented at the NCBI. As the development work went, the NCBI copy made a preliminary release with partial data in June 2004. As the data collection and new tools development came to a completion, a final release is made at the NAGRP site in December, 2004. The final QTL data is synchronized between NCBI and NAGRP databases.

An agreement has also been made between the NAGRP Bioinformatics Coordinator and the University of Melbourne for a sheep version of the database, and the database software was kindly provided by Zhiliang Hu (www.animalgenome.org) to the University of Melbourne. Jill Maddox is currently loading sheep data into the database.

The database and its peripheral tools at the NAGRP implementation is attempted mainly for users to compare, confirm and locate on a chromosomes the most feasible location for genes responsible for quantitative traits important to animal production; The NCBI implementation has all marker information matched to marker records in NCBI's UniSTS database. This allows automatic matching of markers to public sequence data by e-PCR.

A noticeable feature on the database is that the QTL information in the NAGRP Animal Genome server and at the NCBI are cross-referenced to each other for each QTL. This function allows all of the unique information on each site to appear to be integrated on the same database server via worldwide web.

Related publications throughout the course of this work:

  1. Zhiliang Hu and Max Rothschild (2003). "A Frame-Work for Developing the Pig QTL Database". The 13th North American Colloquium on Animal Cytogenetics & Gene Mapping. Louisville, Kentucky, July 13-17, 2003.

  2. Zhiliang Hu, James Reecy and Max Rothschild (2005). "A Quantitative Trait Loci Resource and Comparison Tool for Pigs: PigQTLDB". Iowa State "Animal Industry 2005 Report".

  3. Zhiliang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). "PigQTLdb: A Pig QTL Database". Plant & Animal Genome XIV Conference, San Diego, CA, January 15-19, 2005

  4. Zhiliang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). "A QTL Resource and Comparison Tool for Pigs: PigQTLDB". Mammalian Genome. (2005) Volume 16(10):792-800.

  5. Zhiliang Hu, Sean Humphray, Carol Scott, Stacey N. Meyers, Jane Rogers, Max F. Rothschild and James M. Reecy (2006). "Extension of PigQTLdb: Genome-wide Alignment of BAC FPC Maps and RH Maps for QTL Positional Gene Mining". Plant & Animal Genome XIV Conference, San Diego, CA, January 14-18, 2006

  6. Zhiliang Hu, Eric Ryan Fritz and James M. Reecy (2006). AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35 (Database issue):D604-D609; doi:10.1093/nar/gkl946.

  7. Zhiliang Hu and James M. Reecy (2006). Animal QTLdb: Beyond a Repository - A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome, Volume 18, 1-4 (2007).

First draft: January 3, 2005
Modified: January 4, 2006

By Zhiliang Hu
Associate Scientist
Dept of Animal Science
Iowa State University

Modified: October 31, 2007

By Jill Maddox
University of Melbourne