Release 53
(Apr 28, 2024)

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:1,652
Species:7
Genome maps:22
Measured traits:2,135
QTL/associations:266,160
Last 30 days visitor activities:
  • 11,738 visitors, who made
  • 599,848 hits, which generated
  • 46.55 GB data downloads
  • Cattle QTL

    There are 191,181 currently released QTL data (including eQTL/SNP associations) curated from 731 publications. These data are lifted to 5 genome builds. The curated data represent 680 different base traits and 347 trait variants. (see cattle data summary for more details).

    Chicken QTL

    There are 15,581 currently released QTL data (including eQTL/SNP associations) curated from 211 publications. These data are lifted to 4 genome builds. The curated data represent 372 different traits and 161 trait variants. (see chicken data summary for more details).

    Goat QTL

    There are 1501 currently released QTL data (including eQTL/SNP associations) curated from 22 publications. These data are lifted to 2 genome builds. The curated data represent 26 different base traits and 94 trait variants. (see goat data summary for more details).

    Horse QTL

    There are 2,216 currently released QTL data (including eQTL/SNP associations) curated from 85 publications. These data are lifted to 2 genome builds. The curated data represent 65 different base traits and 1 trait variants. (see horse data summary for more details).

    Pig QTL

    There are 48,875 currently released QTL data (including eQTL/SNP associations) curated from 426 publications. These data are lifted to 3 genome builds. The curated data represent 673 different base traits and 768 trait variants. (see pig data summary for more details).

    Rainbow Trout QTL

    There are 2,201 currently released QTL data (including eQTL/SNP associations) curated from 12 publications. These data are lifted to 2 genome builds. The curated data represent 47 different base traits and 6 trait variants. (see rainbow trout data summary for more details).

    Sheep QTL

    There are 4,605 currently released QTL data (including eQTL/SNP associations) curated from 165 publications. These data are lifted to 4 genome builds. The curated data represent 272 different base traits and 213 trait variants. (see sheep data summary for more details).

    QTL on JBrowse: QTL/association data on supported (default) genome assemblies are ported to JBrowse/JBrowse2 for viewing of their map locations against other map features.
    Supported maps: Currently, there are 22 genome assemblies (aka. "builds", "maps") supported on the Animal QTLdb for data curation and curated data lifts. Among them, one per species the most accepted/updated assembly is designated as the default reference for data browse on JBrowse.
    API and dbxref: Scriptable access to the Animal QTLdb using a REpresentational State Transfer (REST) protocol, and dbxref links into the database for extended information.
    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: Data is available for download at each species main page or each chromosome page, 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).
    Legacy Data Archive: Permanent deposition of traditional linkage-map-based QTL data curated into the Animal QTLdb during 1999 and 2021. The utility of such data are diminishing since sequence-based genome maps and SNP-based analysis have taking the stage as we move forward.
    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 make 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 out with a streamlined process. Prepare your data in required formats described in the Minimum Required Information Guideline in three simple steps to proceed.
    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: A general user's guide in forms of questions and answers addressing common questions such as how to access data, often related with various web tools, functions, access points and/or routes to get to certain data, etc.

     

    REFERENCES:
    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2022). Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Research, Volume 50, Issue D1, Pages D956–D961. DOI: 10.1093/nar/gkab1116

    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. DOI: 10.1093/nar/gky1084

    Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2018). Development of Animal QTLdb and CorrDB: Resynthesizing Big Data to Improve Meta-analysis of Genetic and Genomic Information. The 11th World Congress on Genetics Applied to Livestock Production (WCGALP). New Zealand, February 11-16, 2018.

    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. DOI: 10.1093/nar/gkv1233

    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; DOI: 10.1093/nar/gks1150

    Zhi-Liang Hu, Carissa A. Park, Eric R. Fritz and James M. Reecy (2010). QTLdb: A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes. Invited Lecture with full paper published electronically on The 9th World Congress on Genetics Applied to Livestock Production (WCGALP). Leipzig, Germany August 1-6, 2010.

    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). DOI: 10.1007/s00335-006-0105-8

    Zhi-Liang 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.

    Related resources:     ·  VT | LPT | LBO | CMO  ·  ·  MIQAS  ·  ·  MIBBI  ·  ·  MI  ·  ·  CorrDB  ·    

     

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