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Domestication of all plants and animals led to a reduction in genetic diversity (Ladizinsky, 1985; Doebley, 1989; Gepts, 2004), and thus all genes in any domesticated plant necessarily have a history that includes a recent demographic event, the bottleneck associated with domestication (Fig. 11.2). Population subdivision in the wild ancestor, ongoing introgression between the crop and wild relatives, and multiple domestication events can also have demographic impacts. Genes important for domestication were also subjected to conscious or unconscious directional selection, experiencing a reduction in variation over and above that associated with any demographic events (Fig. 11.2). The level of diversity remaining at a given locus in a domesticate is thus expected to be inversely proportional to the locus’s adaptive importance during domestication. Thus, the major genes contributing to agronomically important traits may lack variation entirely (Whitt et al., 2002).

With a candidate gene in hand, molecular population genetic methods can be used to test adaptive hypotheses. Conceptually, the approach is simple: under the selection scenario described in Fig. 11.2, one expects that genes contributing to adaptive traits will have low genetic variation relative to nonselected genes. In addition, a strongly selected gene may have other discriminating features, such as an excess of low frequency polymorphisms or high intralocus LD (Przeworski, 2002). It is thus essen-

FIGURE 11.2 Schematic representation of a population bottleneck and its effect on a neutral gene and a selected gene. In Upper, shaded circles representgenetic diversity. The bottleneck reduces diversity in neutral genes, but selection decreases diversity beyond that caused by the bottleneck alone. Lower illustrates sequence haplotypes of these two hypothetical genes. The neutral gene lost several haplotypes through the domestication bottleneck, but the selected gene is left with only one haplotype containing the selected site.

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