Use of microsatellite markers of germplasm identity analysis in cocoa

Molecular genetic markers provide, among other applications, the opportunity to verify identity in germplasm collections. DNA-based polymorphisms are a powerful tool in genetic characterisation. RFLP markers were the first to be used for plant genome studies, for mapping and for diversity analyses. However, RFLPs are labour intensive, time consuming, require a large quantity of DNA and purification by ultra centrifugation. The PCR based techniques, including microsatellite analysis, require less DNA than RFLP markers and are therefore convenient for genetic analysis on young plants. An additional advantage of the use of microsatellites is the codominant mode of inheritance, which in contrast to the dominant PCR markers based on arbitary primers, allows easy transfer of markers between genetic maps of different crosses. Compared to RFLPs, microsatellites detect more alleles and a higher level of polymorphism and are equally powerful tools for estimation of heterozygosity. Results obtained on cocoa accessions included in the CFC/ICCO/IPGRI project on "Cocoa Germplasm Utilization and Conservation, a Global Approach" are presented here, including about 150 comparisons of DNA samples from nine collections concerning 28 different accessions. It is concluded that identification problems occur frequently, on average in about 30% of the samples examined in our study. These identification problems occur both in comparisons between accessions from different collections and between trees within accessions from the same collection. Such identification problems constitute a serious problem for comparative analysis of clones obtained from different sites or even from different trees within the same accession. Convenient loci number for identification analyses using microsatellites, sample collection methodology as well as conditions required for comparisons between different microsatellite analyses or between laboratories are briefly discussed. (Résumé d'auteur)