Genetic fingerprinting of clones

The genetic identification of particular oil palm genotypes must be based on a replicable and reliable procedure, particularly if it is to be used as a mechanism for the protection of germplasm property rights through the certification of a variety or clone’s legitimacy.

Our research includes developing a methodology that uses microsatellite markers to generate the genetic fingerprint of the most popular ASD clones (Tornado, Titan, Sunrise, Prince, Sabre and Endurance). Fingerprints were generated on two occasions and the results were repeated in two independent molecular biology laboratories (University of Costa Rica and ASD’s own lab in Coto).

A total of 17 primers were used to detect simple sequence repeats (SSRs) in the Elaeis oleifera genome. The microsatellites were selected due to the ease of interpretation of the amplified alleles, the presence of polymorphism in prior evaluations and also for the replicability of the results.

Estimates of probability of identity (PI) and probability of exclusion (PE) were used to determine the suitability of the microsatellite marker system. PI expresses the probability of finding two individuals with the same genotype for a determined locus. Considering that each locus segregates independently, the probability of finding identical genotypes (clones) is the product of the probabilities of each one of the 17 loci included in the analysis.

The estimate of the combination of the probabilities was 3.47 x 10-13, meaning that the possibility of finding two individuals with the same genotype was an event with a probability of nearly zero. The PI of the combination of the 17 loci was also calculated using the assumption that all the individuals were full siblings, yielding a probability of 3.47 x 10-6. The combined power of exclusion for the 17 loci was >99.99%, which means that the battery of loci evaluated was suitable for the analysis of parentage among clones, the verification of contamination between clones and for evaluation of the legitimacy of the clones as well as controlled crosses.

The validation process resulted in the generation of two identical genetic fingerprints with a high probability of discriminating between clones, thus we can conclude that the protocol for the molecular identification of oil palm genotypes is reliable and replicable, even when executed in different laboratories.