A Broad Assessment of Microsatellite Linkage Disequilibrium (LD) in Wild, Cultivated, and Mapping Populations of Theobroma cacao L

Linkage disequilibrium (LD) is the nonrandom association of alleles. Practically, LD measures the difference between the observed haplotype frequencies in a given population as compared to their expected frequencies, which is the product of their allele frequencies.  Linkage disequilibrium analyses in several species have frequently indicated a non-linear relationship between physical distances and LD values. The structure of this relationship can provide insight into the possibility and efficacy of association mapping analyses, which in turn have been used to identify markers regulating important phenotypic traits.  In this study, we measure the amount of LD in various cacao populations.