Analysis of Cocoa Clonal Seedlings Purity Through Deoxyribonucleic Acid (DNA) Barcoding and Random Amplification of Polymorphic DNA (RAPD) Fingerprinting

Main Article Content

Sulistyani Pancaningtyas
Agung Wahyu Susilo


The genetic purity of a plant indicates the similarity properties between seedlings in the field and the description of the plant in the database. Identifying plant purity through a morphological approach has several drawbacks, including time efficiency and environmental factors, and the diversity is limited and inconsistent. This condition encourages the development of detection methods using DNA molecular markers. Plant identification through fingerprinting or the use of molecular markers has not been widely carried out on a commercial scale, considering the investment costs for this analysis are still quite expensive. Another method used for plant identification through DNA Barcoding by comparing variations between DNA sequences. The primers used to identify barcodes on cocoa were derived from the chloroplast genome, including rbcL and matK. This research aims to see the consistency of the rbcL primer when applied to other cocoa clones, and the analysis of the polymorphic diversity of each cocoa clone using DNA fingerprinting RAPD. This method will be tested on clones of Sulawesi 1, Sulawesi 2, ICCRI 03, and ICCRI 09, which were propagated by SE and mother plants in the field using cocoa leaf samples. The stages include DNA extraction, sequencing, and analysis of the sequencing results. The results of seedlings uniformity analysis using DNA barcoding on cocoa plants produced from in vitro propagation showed that the multiplied seeds did not show any difference in sequence with the parent plant (DR2, Sulawesi 1, Sulawesi 2, and ICCRI 09). The analysis of the diversity of cocoa clones DR 2, MCC 2, Sulawesi 1, Sulawesi 2, and ICCRI 09 through DNA Fingerprinting RAPD showed that the OPA 15 primer produced a more apparent polymorphic band than the other three primers (OPP 08, OPW 11, and M 29).

Article Details

How to Cite
Pancaningtyas, S., & Wahyu Susilo, A. (2022). Analysis of Cocoa Clonal Seedlings Purity Through Deoxyribonucleic Acid (DNA) Barcoding and Random Amplification of Polymorphic DNA (RAPD) Fingerprinting. Pelita Perkebunan (a Coffee and Cocoa Research Journal), 38(1), 20-28.
Creative Commons License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Authors who publish with this journal agree to the following terms:

    1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
    1. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
    1. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).


Most read articles by the same author(s)