The art and science of cloning QTLs in plants

Recent technical progress in the area of molecular biology and genomics have made possible the molecular dissection of major loci (Quantitative Trait Loci: QTLs) responsible for the genetic control of quantitative traits. Until now, most plant QTLs have been cloned through a positional cloning approach after their identification in experimental crosses. In some cases it has been possible to establish an association between sequence variation at a candidate gene and a phenotype by the analysis of existing genetic accessions. Several refinements of these strategies are made possible by deploying appropriate genetic materials and the latest developments in genomics platforms (e.g. transcriptomics) which allow us to identify eQTLs (expression QTLs), i.e. functional polymorphisms influencing the level of expression of a particular gene. A strategy based on reverse genetics could also be deployed to clone QTLs. We foresee that while QTL analysis and cloning addressing naturally occurring genetic variation will shed light on mechanisms of plant adaptation, more emphasis on approaches relying on candidate gene identification and reverse genetics will accelerate the pace of discovery of the genes underlining QTLs. Although QTL cloning is still in its infancy, further refinement of genomics tools and platforms will make QTL cloning a more routine procedure.