TY - JOUR
AU - Junjian Ni
AU - Anuradha Pujar
AU - Ken Youens-Clark
AU - Immanuel Yap
AU - Pankaj Jaiswal
AU - Isaak Tecle
AU - Chih-Wei Tung
AU - Liya Ren
AU - William Spooner
AU - Xuehong Wei
AU - Shuly Avraham
AU - Doreen Ware
AU - Lincoln Stein
AU - Susan McCouch
AB - Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.
BT - Database : the journal of biological databases and curation
C1 - http://www.ncbi.nlm.nih.gov/pubmed/20157478?dopt=Abstract
DA - 2009
J2 - Database (Oxford)
LA - ENG
N2 - Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.
PY - 2009
EP - bap005
T2 - Database : the journal of biological databases and curation
TI - Gramene QTL database: development, content and applications.
VL - 2009
SN - 1758-0463
ER -