Exploiting quantitative trait loci in gene discovery

Extensive efforts over the past 10 yr have led to the mapping of QTL for a broad array of plant phenotypes in diverse species. The resulting datasets can be compared with map locations of mutants and cloned genes. Depending on the trait and the relevant resources available, different strategies may be pursued to uncover the gene(s) underlying a QTL. As with the cloning of tb1 and CRY2, there may be a candidate gene previously defined by a null allele. In the case of BRX, FRI, and fw2.2, there were no candidate genes, but the ability to create new alleles or use transgenics provided proof that the QTL was cloned. In species with large genomes, a number of candidate genes may reside within a QTL region defined by recombination. In this case, sequencing in a number of diverse inbreds can help find the gene that carries polymorphism significantly associated for the trait. Just as the molecular biologist searches out the important domains or amino acids of a protein, the use of different QTL populations uncovers allelic variation. The availability of complete genome sequence in many plant species will greatly enhance the ability to more rapidly characterize and exploit this allelic variation.