Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

Abstract

The Animal QTL database (QTLdb; http://www.animalgenome.org/QTLdb) is designed to house all publicly available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. An earlier version was published in the Nucleic Acids Research Database issue in 2007. Since then, we have continued our efforts to develop new and improved database tools to allow more data types, parameters and functions. Our efforts have transformed the Animal QTLdb into a tool that actively serves the research community as a quality data repository and more importantly, a provider of easily accessible tools and functions to disseminate QTL and gene association information. The QTLdb has been heavily used by the livestock genomics community since its first public release in 2004. To date, there are 5920 cattle, 3442 chicken, 7451 pigs, 753 sheep and 88 rainbow trout data points in the database, and at least 290 publications that cite use of the database. The rapid advancement in genomic studies of cattle, chicken, pigs, sheep and other livestock animals has presented us with challenges, as well as opportunities for the QTLdb to meet the evolving needs of the research community. Here, we report our progress over the recent years and highlight new functions and services available to the general public.

Figure 1.

A screenshot of an Animal QTLdb chromosomal map view with new elements or functions in boxes or in circles: (a) options to view different data types, allowing ‘QTL’, ‘eQTL’ and ‘association’ data to be displayed in various combinations; options to view ‘linkage map’, ‘genome map’ or both; and options to view different genome map builds if applicable. (b) Cytogenetic bands and genome coordinates aligned side-by-side with the linkage map. Note that the genome chromosome bar can be clicked to go to viewing QTL in GBrowse. (c) New shapes/colors for different data types. (d) All QTL/traits on a chromosome can be easily retrieved to view by selecting from a pull-down menu or by their first initials. (e) A flexible data download tool that allows users to download data in the current view or by chromsome. (f) A link to trigger Metaplot function (Figure 5 for details).

Figure 2.

A snapshot of GBrowse display of QTL and association data on part of bovine chromosome 3 in alignment with annotated genes and transcripts on UMD3.1 genome build of Bos taurus.

Figure 3.

A snapshot of an Animal QTLdb data details page, showing new parameters and features added to the database. The new parameters subject to collection into the database include data analysis types (c), test models (c) and animal breeds (b). The ATO is now linked to VT, PT and CMO (a).

Figure 4.

A new hierarchy display tool showing a partial cattle trait tree, along with main features embedded in the display.

Figure 5.

An example of QTL meta-plots, showing a pile plot and a kernel density (KD) plot, for average daily gain (ADG) QTL on pig chromosome 4. The meta-plot peak is supported by the number of reported QTL that overlap. Note this function is active only when there are more than three QTL in a chromosome view (Figure 1).