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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.
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Database highlights
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Publications: | 2,859 |
Species: | 7 |
Genome maps: | 22 |
Measured traits: | 1,546 |
QTL/associations: | 277,842 |
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Cattle QTL
There are 192,247 currently released QTL data (including
eQTL/SNP associations) curated from 1,179 publications.
These data are lifted to 5 genome builds.
The curated data represent 552 different base traits and
385 trait variants. (see cattle data summary for more
details).
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Chicken QTL
There are 18,602 currently released QTL data (including
eQTL/SNP associations) curated from 406 publications.
These data are lifted to 4 genome builds.
The curated data represent 244 different traits and
186 trait variants.
(see chicken data summary
for more details).
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![](/icons/cruse-transp.png) |
Goat QTL
There are 2145 currently released QTL data (including
eQTL/SNP associations) curated from 36 publications.
These data are lifted to 2 genome builds.
The curated data represent 81 different base traits and
110 trait variants.
(see goat data summary for more details).
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Horse QTL
There are 2,216 currently released QTL data (including
eQTL/SNP associations) curated from 109 publications.
These data are lifted to 2 genome builds.
The curated data represent 60 different base traits and
1 trait variants.
(see horse data summary for
more details).
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![](/icons/cruse-transp.png) |
Pig QTL
There are 55,688 currently released QTL data (including
eQTL/SNP associations) curated from 836 publications.
These data are lifted to 3 genome builds.
The curated data represent 407 different base traits and
944 trait variants.
(see pig data summary for
more details).
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![](/icons/cruse-transp.png) |
Rainbow Trout QTL
There 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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![](/icons/cruse-transp.png) |
Sheep QTL
There are 4,743 currently released QTL data (including
eQTL/SNP associations) curated from 270 publications.
These data are lifted to 4 genome builds.
The curated data represent 167 different base traits and
217 trait variants.
(see sheep data summary for
more details).
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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.
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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.
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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.
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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.
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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).
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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.
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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.
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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.
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Video Tutorials: Video tutorials to show how to use newly developed
database tools to access and analyze information stored in the Animal QTLdb.
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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.
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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.
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