FIGURE 11.1 Schematic of the phenotype–genotype hierarchy as represented by top-down and bottom-up approaches.

each of these approaches, discuss the methodologies available for their implementation, and assess their strengths and weaknesses.

To date, all of the successes at identifying genes underlying the adaptive changes during domestication have originated from top-down approaches, beginning with the phenotype and using genetic analyses to uncover genomic regions and eventually candidate genes responsible for the phenotype of interest. The most successful method for finding these genes has been QTL mapping, but association or LD methods are rapidly gaining favor in the plant genomics community. While it is beyond the scope of this article to provide a comprehensive review of QTL and LD mapping, we review some empirical findings and highlight some of the challenges of spanning the gap between phenotype and genotype.

Given a trait of interest, QTL mapping was the first (and is still the most widely used) method available for localizing the genetic basis of a trait (e.g., Sax, 1923). QTL mapping has led to all of the major successes in the identification and cloning of genes underlying domestication traits (Doebley et al., 2006). The best-known examples come from tomato and maize. In the mid-1980s Tanksley and coworkers (Paterson et al., 1988) initiated QTL analysis of fruit mass in a cross between wild and domesticated tomato, localizing six QTLs. With extensive mapping efforts, they were able to isolate a region encompassing the major QTL fruitweight2.2 (fw2.2). They also demonstrated the phenotypic effect of fw2.2 with transgenic analysis (Frary et al., 2000). At about the same time Doebley and coworkers