Integrating Quantitative Trait Loci (QTL) from Many Studies: Approaches from Soybean, Common Bean, and Peanut

Quantitative trait loci (QTL) analysis is often the starting point for dissecting underlying genetic mechanisms of complex traits. To make use of the many QTL mapping studies in legumes, methods are needed for integrating QTLs from various studies within a species. We describe the approaches used in public databases for soybean (soybase.org), common bean (legumeinfo.org) and peanut (peanutbase.org). In SoyBase, QTL coordinates have been projected onto a composite reference map by manual interpolation with respect to common markers. In LegumeInfo and PeanutBase, we have projected QTLs from the experiment maps to the consensus maps where possible, using a percentile length calculation method along with linked marker information. Briefly, the lengths of individual linkage groups and the QTL intervals are recorded from a publication linkage map using the ImageJ software and converted into centimorgans using a perl script. The publication linkage groups lengths are adjusted to the corresponding consensus linkage groups, and QTL intervals are placed using closely linked marker and flanking marker information. The associated QTL descriptive information (trait descriptions, R-squared values, additivity, parents, etc.) is collected into standardized spreadsheet forms and then loaded into databases at legumeinfo.org and peanutbase.org. To avoid discrepancies in trait nomenclature between different publications and species, unified trait ontologies are utilized for each trait. Overall, the QTL methods described here can facilitate the use of published QTL information to design breeding experiments, conduct meta-QTL analysis, and facilitate reverse genetic experiments.