Cloning QTLs in plants

The utilization of a number of genomics platforms and analytical methods allow us to fine map and clone major quantitative trait loci (QTLs) responsible for the genetic control of quantitatively inherited traits. To date, most plant QTLs that were successfully cloned, have been dissected by means of a positional cloning approach within a biparental cross. In some cases, an association between allelic variation at a candidate gene and a phenotype has been established through the analysis of existing genetic accessions. The effectiveness of these strategies can be enhanced by using appropriate genetic materials (e.g. introgression libraries, panels of unrelated accessions, etc.) and the latest developments in forward- and reverse-genetic platforms. Under this respect, the ‘omics’ platforms provide a new paradigm to identifiy candidate genes and clues for their function. Completion of genome sequences and improved bioinformatics will facilitate in silico cross-matching of candidate sequences with QTLs in programmes of positional cloning or association mapping. Several QTLs have been associated to candidate genes solely based on map information and further circumstantial observation, and without completing a formal cloning procedure. Although QTL mapping and cloning have been so far almost synonymous for the dissection of the genetic control of naturally available phenotypic differences, genes involved in controlling quantitative traits could be identified also by combining quantitative genetics with insertional mutagenesis. Although QTL analysis and cloning addressing naturally occurring genetic variation will continue to shed light on mechanisms of plant adaptation, a greater emphasis on approaches relying on mutagenesis and candidate gene validation is likely to accelerate the discovery of the genes underlying QTLs.