The Role Of Haplotyping In Mapping The Pod Color Trait

T. cacao pod color is an oligogenic trait that can not be predicted in the progeny purely based on parental phenotypes (due to allelic dominance). To improve the quality of cultivated cacao, it is of interest to be able to distinguish between clones bearing red pods (such as CCN 51, linked to undesirable flavor profile) and green pods associated with desirable flavor profiles. Previous linkage studies have mapped the pod color trait onto linkage group 4, between a pair of microsatellite markers 30 cM apart.

Utilizing the Matina 1-6 genome sequence and a novel haplotyping algorithm, we have identified the parental origin of pod color in three T. cacao mapping populations with high resolution. The iXora haplotyping framework was applied to phase genotypes from these populations, with up to hundreds of progeny and several hundred markers per chromosome. The results support the hypothesis of a single allele responsible for the pod color trait, and identifying this allele allows for molecular testing for the pod color phenotype.

The iXora analysis framework is available for non-commercial use from http://researcher.ibm.com/project/3430