Release 39
(Aug 22, 2019)
 

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features such as annotated genes.

Many scientific journals require or recommend that any original QTL/association data be deposited into a public database before a paper may be accepted for publication. We provide user/curator accounts for direct data submission, and in return we supply users with a data summary link to facilitate the manuscript review process.

Database summary:
Publications:
Species:
Traits:
QTL/associations:
2,214
7
2,062
174,241

This graph is partly adopted from
the RGD with kind permission
Last month visitor activities
  • 5,173 visitors, who made
  • 131,959 web hits, and
  • 3.01 GB data downloads
  • Cattle QTL

    There are 127,191 QTLs from 961 publications curated into the database. Those QTLs represent 628 different traits (see data summary for details).

    Catfish QTL

    There are 0 QTLs from 0 publications curated into the database. Those QTLs represent 0 different traits (see data summary for details).

    Chicken QTL

    There are 11,340 QTLs from 312 publications curated into the database. Those QTLs represent 418 different traits (see data summary for details).

    Horse QTL

    There are 2,260 QTLs from 88 publications curated into the database. Those QTLs represent 54 different traits (see data summary for details).

    Pig QTL

    There are 29,865 QTLs from 676 publications curated into the database. Those QTLs represent 688 different traits (see data summary for details).

    Rainbow Trout QTL

    There are 584 QTLs from 14 publications curated into the database. Those QTLs represent 18 different traits (see data summary for most recent updates).

    Sheep QTL

    There are 3,001 QTLs from 163 publications curated into the database. Those QTLs represent 256 different traits (see data summary for most recent updates).

    QTL on GBrowse/ JBrowse: For species that have a genome sequence assembly, QTL/association data are also ported to GBrowse and JBrowse to view against respective map features on their most recent builds.
    Data Alliances: Newly released QTL/association data are exported to our data alliances: Ensembl, Monarch Project, NCBI Entrez GeneDB, Reuters Data Citation Index, and UCSC. Users can employ tools on these respective sites for information mining in relation to animal QTL and association data.
    Data Downloads: The QTLdb data is available for download at each species front page or at individual chromosome pages, where customized data search/download is possible. The data formats include "cM" mapping data in tab-delimited form and "bp" locations in GFF, BAM, and BED formats (FAQ #23).
    API: Scriptable access to the Animal QTLdb.
    Curator / Editor Tools: You can register for a free curator account to directly get your data into the database. Once your curator's account is granted, you can find a step-by-step curation guide to help you proceed, for manual data entry or for batch data upload. You can keep your data in private status until a time when you wish to making it public.
    Batch Data Submission: A useful alternative to curate large amounts of data is to upload them in batches for our team to help you out a streamlined process. Please prepare your data in required formats described in Minimum Required Information Guideline, in these simple steps.
    Video Tutorials: Video tutorials to show how to use newly developed database tools to access and analyze information stored in the Animal QTLdb.
    Frequently Asked Questions: Questions and answers designed to serve as a general user's guide to the Animal QTLdb, addressing common questions such as functions, data scopes, database usages, applications, new developments, etc.
    Related Links:  ·  ·  VT / LPT / CMO  ·  ·  MIQAS  ·  ·  MIBBI  ·  ·  MI  ·  ·  Animal CorrDB  ·  · 
    REFERENCES:
    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2019). Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Research, Volume 47, Issue D1, 8 January 2019, Pages D701–D710.

    Zhi-Liang Hu, Carissa A. Park and James M. Reecy (2016). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44 (D1): D827-D833.

    Zhi-Liang Hu, Carissa A. Park, Xiao-Lin Wu and James M. Reecy (2013). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research, 41 (D1): D871-D879

    Zhi-Liang 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), 1-4 (2007).

    Zhi-Liang 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.


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