CSGRqtl, a Comparative Quantitative Trait Locus Database for Saccharinae Grasses

Abstract

CSGRqtl is a comparative genomic database that facilitates the cross-utilization of information among members of the Saccharinae clade of grasses, and between Saccharinae and other taxa. CSGRqtl is developed as a specific data mining resource for Saccharinae crops, weeds, and models, complementing and supplementing another database, Gramene (Ware et al., 2002), that includes a variety of mapping data for a broad spectrum of grass taxa. To facilitate data comparisons, a plant trait ontology defined by Gramene is applied to categorize Saccharinae QTLs. Using the Sorghum bicolor (L.) Moench (S.bicolor) genome sequence as a central reference, CSGRqtl provides approximate physical positions for QTL likelihood peaks. In order to facilitate QTL mapping and further study of the functions and evolution of candidate genes that may underlie QTLs, CSGRqtl integrates gene annotations, genetic markers and paleo-duplicated regions, and provides a series of query functionalities to navigate different data components, on the basis of QTL alignments. The goals of CSGRqtl are to provide both for practical needs of crop improvement by serving as a toolbox for QTL visualization and manipulation, and to facilitate investigation of fundamental questions about similarities and differences in the genetic control of traits across paleo-duplicated ‘subgenomes’ and across the genomes of divergent taxa. Availability: http://helos.pgml.uga.edu/qtl/