Release 29
(Apr 29, 2016)
 

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 supply users with a data summary link to facilitate the manuscript review process.

Database summary:
Publications:
Species:
Traits:
QTL:
1,639
7
1,692
94,457
CNV
Traits
GWAS

This graph is partly adopted from
the RGD with kind permission

Cattle QTL

There are 71,448 QTLs from 672 publications curated into the database. Those QTLs represent 505 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 5,462 QTLs from 245 publications curated into the database. Those QTLs represent 336 different traits (see data summary for details).

Horse QTL

There are 1,139 QTLs from 61 publications curated into the database. Those QTLs represent 34 different traits (see data summary for details).

Pig QTL

There are 15,108 QTLs from 537 publications curated into the database. Those QTLs represent 599 different traits (see data summary for details).

Rainbow Trout QTL

There are 127 QTLs from 10 publications curated into the database. Those QTLs represent 14 different traits (see data summary for most recent updates).

Sheep QTL

There are 1,173 QTLs from 114 publications curated into the database. Those QTLs represent 204 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: An interface for scriptable access to the Animal QTLdb.
Curator / Editor Tools: You can register for a curator account (free) to directly curate your new data into the database. Once you are granted a curator's account, you can find a Curator's Manual to follow a step-by-stel guide to get started. The Minimum Required Information guideline is helpful for you to get your data prepared for efficient curation. A bonus benefit is that you can keep your data in private mode while comparing them against existing data already released to the public. You will be able to update your data and choose a time to release them.
Batch Data Upload: If you have a large amount of data to curate, a useful alternative is to upload them in batches for a streamlined process. To use this data route, you need to prepare your data in a well-defined format following our minimum required information standards, then follow these 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 User's Guide to QTLdb, addressing usage, application, utilities, new developments, and related issues.

 

Related Links:  ·  ·  VT / LPT / CMO  ·  ·  MIQAS  ·  ·  MIBBI  ·  ·  MI  ·  ·  Animal Trait CorrDB
REFERENCES:
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, 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. 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).

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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