Fig. 1. This electropherogram shows the DNA fragment profiles of SSR primers for three different loci, amplified separately using three different dyes, multiplexed and separated by capillary electrophoresis. The sample was the T. cacao accession PA44, an Upper Amazon Forastero type that is part of the USDA germplasm collection maintained in Puerto Rico. Alleles from three loci were amplified as shown in the electropherogram sample: The heterozygous locus Y16980 (mTcCIR6) is located on chromosome 6 and shows alleles sizes of 228 and 232 base pairs. The two homozygous loci, Y16996 (mTcCIR24) located on chromosome 9 and the Y16995 (mTcCIR22) locus on chromosome 1, each show a single allele at 187 and 290 bp, respectively. Internal standards, labeled with red, are run concurrently with all samples for base pair determination during the capillary electrophoresis DNA fragment separations.