Association Mapping in Cacao Populations from Hawaii

The development of varieties in perennial crops is a long term process due to their lengthy and slow growing reproductive cycle.  Detection of QTLs of importance becomes very challenging due to the use of F₁ populations.  Association mapping represents an excellent alternative for the discovery of alleles associated with specific traits since it does not require the development of a segregating population.  One hundred productive and fifty-one unproductive trees of cacao (Theobroma cacao L.) were selected from a population that was previously characterized with 80 SSR markers and indicated that it was is an admixture population of Marañon, Amelonado, Contamana, Criollo, Curaray, Iquitos, Nacional and Nanay genetic groups.  Also a few associations between SSR markers and traits were observed. The objectives of this study were to characterize the population structure and genetic diversity of this Hawaiian population and to examine the possible association between SNP markers and yield traits in productive as well as unproductive selected plants.  Characterization of the population structure was conducted by using the software Structure. In addition, GenStat software was employed to estimate association between SNP markers and horticultural traits.  Preliminary results indicated the presence of admixture and some association between SNP markers and horticultural traits may be present in this population.