Despite these drawbacks, LD mapping has had some successes. One early example successfully linked phenotypic variation in malting quality in barley to haplotype variation at the β-amylase2 gene, a locus involved in starch hydrolysis. Differences in the coding region of barley β-amylase2 affect thermostability of the enzyme (Ma et al., 2001; Clark et al., 2003), and SNP genotyping confirmed that cultivars with high malting quality and the high-thermostability enzyme share a common haplotype (Polakova et al., 2003; Malysheva-Otto and Roder, 2006). Resequencing of candidate genes has also been used in foxtail millet and rice to determine the genetic basis of waxy or sticky grains. Mutations at the waxy (granule-bound starch synthase) locus result in changes in amylose content in the endosperm, resulting in the sticky grains popular in eastern and southern Asia (Domon et al., 2002; Kawase et al., 2005; Olsen et al., 2006). LD mapping has also been used to verify associations inferred from QTL or other approaches (Thornsberry et al., 2001; Szalma et al., 2005; Balasubramanian et al., 2006; Breseghello and Sorrells, 2006b).
A promising future direction for LD mapping is the use of synthetic populations derived from a relatively small number of founders (Breseghello and Sorrells, 2006a), facilitating QTL and LD mapping in a single population while minimizing complications due to population structure (Flint-Garcia et al., 2005; Breseghello and Sorrells, 2006a; Yu and Buckler, 2006).
Extensive work is required to isolate a candidate gene for a particular trait, but a phenotype–genotype association is no guarantee that the trait or its candidate gene has been historically important or is an adaptation. It is tempting to conclude that observable phenotypic differences are adaptive, particularly in domesticated organisms where selection is strong and the direction of selection can be surmised. However, many of the differences between domesticates and their progenitors may not be adaptive, at least from a human perspective; for example, QTLs decreasing protein content in wheat (Uauy et al., 2006) and seed size in sunflower (Burke et al., 2002) are unlikely to have been directly selected during domestication. A number of alternative processes can explain observed phenotype–genotype associations, including genetic drift, selection on a correlated trait, pleiotropy, or even natural selection working in opposition to anthropogenic selection. It therefore behooves us to endeavor to test adaptive hypotheses rather than assume them to be true (Gould and Lewontin, 1979).
To understand the process of adaptation during domestication, one must first consider the genetic history associated with domestication.