From Mitchell-Olds and Schmitt, “Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis”, Nature, 2006, Box 1: Association studies use linkage disequilibrium to identify polymorphisms that may be responsible for complex trait variation. Linkage disequilibrium quantifies statistical correlations between polymorphic sites: when linkage disequilibrium is present then information from one locus provides some predictive information about the genotype at a second locus. Association studies take advantage of recombinations accumulated over thousands of generations, and hence may aid identification of individual genes responsible for QTL. In the past (top panel), a new mutation (triangle) occurs at a quantitative trait locus. The original population contains an ancestral chromosome on which the new mutation occurred (black line), as well as other chromosomes (grey lines). After many generations of recombination, the present-day population (lower panel) contains short chromosome regions derived from the original population. Molecular markers near the causal polymorphism (b) will be correlated with phenotype, whereas
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