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Association mapping, also known as linkage disequilibrium mapping, is a relatively new and promising genetic method for complex trait dissection. Association mapping has the promise of higher mapping resolution through exploitation of historical recombination events at the population level, that may enable gene level mapping on non-model organisms where linkage based approaches would not be feasible (Nordborg and Tavare 2002; Risch and Merikangas 1996).

Association mapping utilizes ancestral recombinations and natural genetic diversity within a population to dissect quantitative traits and is built on the basis of linkage disequilibrium concept (Geiringer 1944; Lewontin and Kojima 1960). One of the working definitions of linkage disequilibrium (here on will be referred to as LD) is the non-random co-segregation of alleles at two loci.

In contrast to linkage based studies, linkage disequilibrium based genetic association studies offer a potentially powerful approach for mapping causal genes with modest effects (Hirschhorn and Daly 2005). While linkage analysis is based upon

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