Notes on the Animal QTL Database
Developments and Releases History

The initial proposals and plans on developing a (pig) QTL database was made within the NAGRP Pig Genome Coordination Program in the fall of 1998. The database design, vision layout, data preparation and preliminary exploration on the approaches was not made until 2002/2003 when I returned to Iowa State. The pig QTL data collection and tools development works were done in 2004, which result in our first paper on PigQTLdb published ( 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. As a result, two papers are published (Nucleic Acids Research, 2007, 35 [Database issue]: D604-D609; Mammalian Genome, 18: 1-4, 2007). The developmental work on extending the QTLdb's functionality has continued. In 2007, more structural data tyles are added for alignment, including SNPs, Microarray elements, and new microsatellites (see FAQ #11 for details).

During the course of the project development, many attempts were made to utilize existing tools. We contacted a number of research groups and attempted several existing tools, which 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 with the available facilities and expertise 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 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 formal release was made at the NAGRP site in December, 2004. The pig QTL data is synchronized between NCBI and NAGRP databases.

• Release 1: May 01, 2004: NCBI Implementation, with 466 pig QTL
• Release 2: Dec 20, 2004: NAGRP Implementation, with a total of 791 pig QTL
• Release 3: Jan 04, 2006: FPC and RH/human maps are aligned; 1,263 pig QTL
• Release 4: Aug 15, 2006: Pig QTL: 1,287; Cattle QTL: 630; Chicken QTL: 657.
• Release 5: Jan 05, 2007: SNPs and New microsatellite markers are aligned; Linked to genome tracks; Pig QTL: 1,675; Cattle QTL: 846; Chicken QTL: 657.
• Release 6: Jan 08, 2008: More SNPs and microarray elements are aligned; SNP minor allele frequency and oligo array expression data are displayed. Pig QTL: 1,675; Cattle QTL: 1125; Chicken QTL: 657; Sheep: 51.

The database and its peripheral tools at the NAGRP implementation was designed mainly for users to compare, confirm and locate the most plausible locations on a chromosomes for QTL. This is aimed at providing a tool for structural genomic information mining 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. Data on the NCBI and the NAGRP Animal Genome servers are cross-referenced to each other. This function allows all of the unique information on each site to appear to be integrated on the same database server via worldwide web.

A noticible extended feature developed into the QTLdb is that diverse types of structural genome features, such as microsatellites, SNPs, microarray elements, tiled FPC BACs, can be aligned with QTL map locations to aid the data mining. Further more, different map types, such as RH maps, genome sequence maps, human maps, can also be align where available data is available to establish links.

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 (2007). 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 (2007). 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).