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Mammalian Genome

, Volume 16, Issue 10, pp 792–800 | Cite as

A QTL resource and comparison tool for pigs: PigQTLDB

  • Zhi-Liang Hu
  • Svetlana Dracheva
  • Wonhee Jang
  • Donna Maglott
  • John Bastiaansen
  • Max F. Rothschild
  • James M. Reecy
Article

Abstract

During the past decade, efforts to map quantitative trait loci (QTL) in pigs have resulted in hundreds of QTL being reported for growth, meat quality, reproduction, disease resistance, and other traits. It is a challenge to locate, interpret, and compare QTL results from different studies. We have developed a pig QTL database (PigQTLdb) that integrates available pig QTL data in the public domain, thus, facilitating the use of this QTL data in future studies. We also developed a pig trait classification system to standardize names of traits and to simplify organization and searching of the trait data. These steps made it possible to compare primary data from diverse sources and methods. We used existing pig map databases and other publicly available data resources (such as PubMed) to avoid redundant developmental work. The PigQTLdb was also designed to include data representing major genes and markers associated with a large effect on economically important traits. To date, over 790 QTL from 73 publications have been curated into the database. Those QTL cover more than 300 different traits. The data have been submitted to the Entrez Gene and the Map Viewer resources at NCBI, where the information about markers was matched to marker records in NCBI’s UniSTS database. Having these data in a public resource like NCBI allows regularly updated automatic matching of markers to public sequence data by e-PCR. The submitted data, and the results of these calculations, are retrievable from NCBI via Entrez Gene, Map Viewer, and UniSTS. Efforts were undertaken to improve the integrated functional genomics resources for pigs.

Keywords

Quantitative Trait Locus Quantitative Trait Locus Location Quantitative Trait Locus Study Multiple Quantitative Trait Locus Quantitative Trait Locus Data 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors thank Drs. Jack Dekkers from Iowa State University, Gary Rohrer from USDA Meat and Animal Research Center (MARC), Andy Law from the Roslin Institute (UK), and Lizhen Wang from Sygen International for their useful discussions in the process of the database design. Thanks also go to Drs. David Adelson from Texas A&M University and Per Johnson from Göteborg University (Sweden) for sharing their materials on cattle and rat QTL database design, respectively. The data for the template chromosome maps are made possible with data mainly from the USDA-MARC comprehensive pig genome map. This work was supported in part by USDA-NAGRP Pig Genome and Bioinformatics Coordination Programs, the Iowa Agriculture and Home Economics Experiment Station, and State of Iowa Hatch funds.

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Zhi-Liang Hu
    • 1
  • Svetlana Dracheva
    • 2
  • Wonhee Jang
    • 2
  • Donna Maglott
    • 2
  • John Bastiaansen
    • 3
  • Max F. Rothschild
    • 1
  • James M. Reecy
    • 1
  1. 1.Department of Animal Science, Center for Integrated Animal GenomicsIowa State UniversityAmesUSA
  2. 2.National Center for Biotechnology InformationU.S. National Library of MedicineBethesdaUSA
  3. 3.Sygen InternationalKingston BagpuizeUK

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