QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of two bulked DNA. Oryza sativa Japonica Group

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci: QTL). QTL mapping and isolation is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. Since it requires the development and selection of DNA markers for linkage analysis, QTL analysis is however time consuming and labor intensive. Here we propose “QTL-seq”, a method for rapid identification of QTL by whole genome resequencing of two bulked DNAs of individuals showing extreme opposite extreme trait values for a given phenotype in a segregating progeny. We applied QTL-seq to rice recombinant inbred lines (RILs) and F2 populations and successfully identified QTL for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTL over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps. none provided