Association mapping in plant populations.

The central problem with any of the approaches for fine mapping is the limited number of meioses that have occurred and (in the case of advanced intercross lines) the cost of propagating lines to allow for a sufficient number of meioses. An alternative approach is 'association mapping', taking advantage of events that created association in the relatively distant past. Assuming many generations, and therefore meioses, have elapsed since these events, recombination will have removed association between a QTL and any marker not tightly linked to it. Association mapping thus allows for much finer mapping than standard biparental cross approaches. In this chapter review, association is first defined quantitatively and the mechanisms that generate it are described. To motivate the discussion of rigorous methods to test for marker association with a quantitative trait allele, a detailed discussion is provided for an example from the plant breeding literature. An analysis frequently used in human genetics to find marker associations with disease susceptibility alleles, the transmission/disequilibrium test (TDT), is reviewed. A brief discussion to extend the TDT to quantitative traits and to identify QTL × environment interactions is provided. The recent developments making use of multiple-marker haplotypes to locate QTL and some points concerning the power of association mapping are also discussed.

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