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.

Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations1

“…Previous studies have reported quantitative trait loci (QTL) for IMF in several breeds (Hu et al, 2013). Comparison with QTL detected in previous studies showed some agreement with 18 of our consensus selection signatures, but candidate regions on SSC 3, 9 (92.2-123.6 Mb), 13, 14, 15, and 16 were ex clusively identified in our study.…”

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

“…With more and more QTLs having been integrated, a QTL database (Hu et al, 2013) can be a potential resource for studying the genetic mechanisms that underlie growth and immune traits. Until now, there are more than 500 growth-related QTLs and~300 immunity-related QTLs in the pig QTL database.…”

Genome-wide association study of growth traits in the Jinghai Yellow chicken

“…To date, more than 1500 QTLs, covering most of the genome, have been found to be associated with growth traits (Hu et al, 2013). Previous genomic studies have generally employed low-density microsatellites as markers.…”