Figure 1. Diagram showing the step-wise methodology of gene identification for quantitative traits through map-based cloning. Starting from the top, each box describes a step in the process of gene identification. For qualitative variation based on single loci, an F2 population usually suffices, and the creation of a NIL is sometimes not necessary. Double arrows between ‘association mapping’ and ‘candidate gene’ indicate that QTL mapping can begin with an association mapping approach or a QTL can be verified with association mapping (see main text for details). Ultra-high resolution involves the isolation of many recombinants in a small physical region surrounding the QTL. BAC – bacterial artificial chromosome library.

Figure 2. Examples of genes underlying qualitative (a) and quantitative (b) natural variation in tomato. (a) The SELF PRUNING (SP) gene regulates flowering transition during sympodial growth in tomato. This naturally occurring mutant is the foundation of the processing tomato industry. Wild-type ‘indeterminate’ plants (SP/–) initially flower (red balls) after five to eight leaves (green sticks), and then flower consecutively after every three leaves, indefinitely. Plants that are sp/sp mutants flower normally after five to eight leaves, but a‘determinate’ growth habit then ensues as flowering terminates, on average, after one fewer leaf following the preceding sympodium. This results in a shorter stature plant. Representatives of normal and mutant SP plants are shown next to each diagram. The SP gene has been cloned, revealing that a single base-pair change is sufficient to qualitatively change tomato plant structure. SP, whose normal function is to suppress flowering similar to TERMINAL FLOWER (TFL) in Arabidopsis, is a member of a gene family involved in flowering transition, including Arabidopsis FT, which promotes flowering in a graft-transmissible way and has been the target of natural variation for flowering time in rice. (b) Quantitative trait locus (QTL) mapping for fruit weight in tomato identified the fw2.2 locus as a major target of selection during the transition of wild tomato species from small fruits to the large-fruited types that comprise present-day cultivated tomato varieties. Near isogenic lines (NILs) that carry fw2.2 from the wild species S. pennellii can reduce fruit weight up to 30%, depending on the genetic background. The image shows representative fruit from an introgression line (IL), or large NIL, carrying three linked reducing fruit weight QTL from S. pennellii, the largest contributor of which is fw2.2 (top). Those plants without the introgression have larger fruits because they carry large-fruited alleles of fw2.2 originating from cultivated S. lycopersicum (bottom). Fw2.2 was cloned and found to encode a hypothetical gene with putative structural similarity to oncogenic Ras proteins. The phenotypic change due to fw2.2 is based on genetic differences in upstream regulatory elements of the gene, as opposed to changes in coding sequence, which has become a recurring theme among genes identified through natural variation.