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 highlights | |
| Publications: | 2,897 |
| Species: | 7 |
| Genome maps: | 22 |
| Measured traits: | 1,548 |
| QTL/associations: | 289,348 |
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Cattle QTLThere are 192,336 currently released QTL data (including eQTL/SNP associations) curated from 1,188 publications. These data are lifted to 5 genome builds. The curated data represent 553 different base traits and 395 trait variants. (see cattle data summary for more details). |
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Chicken QTLThere are 28,444 currently released QTL data (including eQTL/SNP associations) curated from 410 publications. These data are lifted to 4 genome builds. The curated data represent 245 different traits and 226 trait variants. (see chicken data summary for more details). |
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Goat QTLThere are 2469 currently released QTL data (including eQTL/SNP associations) curated from 40 publications. These data are lifted to 2 genome builds. The curated data represent 82 different base traits and 117 trait variants. (see goat data summary for more details). |
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Horse QTLThere are 2,225 currently released QTL data (including eQTL/SNP associations) curated from 110 publications. These data are lifted to 2 genome builds. The curated data represent 60 different base traits and 2 trait variants. (see horse data summary for more details). |
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Pig QTLThere are 56,615 currently released QTL data (including eQTL/SNP associations) curated from 845 publications. These data are lifted to 3 genome builds. The curated data represent 403 different base traits and 1074 trait variants. (see pig data summary for more details). |
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Rainbow Trout QTLThere are 2,201 currently released QTL data (including eQTL/SNP associations) curated from 23 publications. These data are lifted to 2 genome builds. The curated data represent 35 different base traits and 6 trait variants. (see rainbow trout data summary for more details). |
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Sheep QTLThere are 5,058 currently released QTL data (including eQTL/SNP associations) curated from 281 publications. These data are lifted to 4 genome builds. The curated data represent 170 different base traits and 250 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.
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.
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