Knowledge of genetic differences among commonly cultivated cacao clones, as well as the type of gene action involved for disease resistance, yield, quality, and horticultural traits. are essential for cacao breeders to select parental clones efficiently and effectively. This information is also critical for quantitative geneticists in designing and improving quantitative trait loci (QTL) localization strategies using breeding populations, whether they involve analysis of multiple populations crossed to one common parent or association genetic analysis. The objectives of this research were to 1) verify the genetic identity of parental cacao clones used to produce hybrids for field evaluation at the Centro Agronomico Tropical de Investigacion y Enzenanza (CATIE),Turrialba, Costa Rica, using molecular marker analysis, and 2) estimate general and specific combining ability (GCA and SCA) of the parental clones for resistance to frosty, pod (Moniliophthora roreri Cif. and Par.) and black pod [Phytophthora palmivora (Butl.) Butl.] diseases, total number of pods, vigor (as measured by trunk diameter), and measures of maturity (months to first flowering and pod production). Misidentification of cacao clones was found at three levels. Molecular marker analysis revealed that six parental clones differed in identity to supposedly identical accessions from other germplasm collections. Trees of the parental Clone UF 273 consisted of two clearly different genotypes, resulting in two types of progeny, requiring separate designation for correct statistical analysis. Out-crossed progeny, presumably from foreign pollen, and selfed progeny were also found. Two of the traits measured, percent healthy pods and percent pods with frosty pod, showed predominantly additive gene action, while the traits total number of pods and trunk diameter, demonstrated regulation by both additive and nonadditive gene action. Number of months to first flowering and first fruit both showed evidence of predominant regulation by nonadditive gene effects. Crosses of two parental clones, UF 712 and UF 273 Type 1, were identified as potential candidates for QTL analysis as breeding populations, given their favorable GCA estimates for frosty pod resistance and total pod production, respectively.
