DNA isolation and AFLP™ genetic fingerprinting of Theobroma cacao (L.)

Accurate identification of parental plants and their hybrids is essential for an effective breeding programme. Traditional classification of cocoa varieties relies on the characterisation of agricultural traits at plant maturity. A rapid and reliable method is described, based on genotypic analysis. An efficient DNA isolation procedure was developed, yielding unsheared DNA of high purity. Two genetic fingerprinting techniques, RAPD and AFLP(TM) were evaluated for their suitability in distinguishing cocoa varieties. RAPD analysis was unsatisfactory due to the low frequency of polymorphisms and poor reproducibility. AFLP(TM) was reliable in distinguishing phenotypically identical, known varieties of cocoa. Importantly, AFLP(TM) also revealed intra- and inter-varietal variation.