Juan C. Motamayor^1,2 , J. Steven Brown¹ , David N. Kuhn¹ , Raymond J. Schnell¹

¹  USDA-ARS, Subtropical Horticulture Research Station, Miami, FL, USA.

²  MARS Inc., Hackettstown, NJ, USA.

Although the potential of Linkage Disequilibrium (LD) mapping to associate markers to agronomic and horticultural traits has been already recognized in cacao, its real efficiency depends on the nature and structure of the LD in the genome of the populations under study. LD is dependent on several factors, such as recombination, mutation, migration, selection, mating system, and genetic drift. However, only the LD caused by recombination is useful for mapping purposes. Selection, genetic drift and mating system, will cause spurious association between markers and scored traits within populations undergoing such processes. Recently, a study of the genetic diversity of cacao reported an important amount of differentiation, potentially caused by genetic drift, among the cacao genetic groups and populations. Knowing the amount and the structure of the LD in these populations will greatly facilitate future association mapping studies to identify markers linked to traits of agronomic interest in cacao. In this paper we show the amount and structure of linkage disequilibrium and the degree of linkage disequilibrium decay among 93 microsatellite markers distributed across the 10 cacao linkage groups at an average of 9.83 cM. Six cultivated and natural cacao populations were analyzed for this study. An important proportion of the linkage disequilibrium found was caused by spurious associations among markers and its consequence is discussed for planning future association mapping platforms.