Rice root genetic architecture: meta-analysis from a drought QTL database

During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.