ABSTRACT
Mutant variants in traits of interest are fundamental to understanding biological phenomena and in many species collections of mutants have been a cornerstone that has driven scientifi c discovery. In plants, the process of identifying a gene of interest from a mutant phenotype has traditionally been cumbersome, taking several years to identify and confi rm candidate genes. The widespread adoption of Arabidopsis as a model organism, the associated development of tools for molecular genetic analysis, and ultimately a genome sequence revolutionized the process of gene cloning and facilitated the use of genetic screens to isolate loci of interest. Indeed at the turn of the millennium, prior to the completion of the Arabidopsis genome, it was suggested that following the development of a mapping population it was possible to progress from mutant phenotype to candidate gene in as little as six to eight weeks (Somerville 2000). Although positional cloning strategies have become more widespread for crop plants, there is still a considerable time investment required to conduct these experiments and the timeframe proposed for Arabidopsis is untenable in the majority of plant systems. However, it is the author’s estimate that at the time of writing this review, approximately 50 loci have been isolated using positional cloning or a combination of genetic mapping and candidate gene analysis in tomato. The emerging genome sequence of tomato, together with the associated tool development including bacterial artifi cial chromosome (BAC) libraries, genetic markers, physical contig development, and BAC end sequencing have reduced and will continue to reduce the effort required to isolate genes using forward genetics based approaches (https://solgenomics. net/organism/Solanum_lycopersicum/genome). Highlighting examples from the literature, this review describes the factors that must be taken in to account when designing positional cloning strategies in tomato, together with the options that are available to ensure that these strategies are successful. In addition, current limitations are discussed, together with prospects for future technology and tool development.
