Genetic diversity analysis of black pepper (Piper spp.) with RAPD markers


Piper spp
genetic diversity

How to Cite

Rasphone S, Hồ THN, Dang TL, Nguyen BLQ, Truong HTH. Genetic diversity analysis of black pepper (Piper spp.) with RAPD markers. hueuni-jns [Internet]. 2022Dec.31 [cited 2023Sep.28];131(1D):49-5. Available from:


Black pepper is a well-known export commodity in Vietnam, but pepper production has been decreasing in recent years. The lack of knowledge about the origin and genetic characteristics of pepper varieties may create variety degradation and loss of product quality. Therefore, it is necessary to study the genetic diversity of existing local and imported pepper varieties and effectively propagate and create new varieties with high yields and quality. In this study, RAPD markers were used with 100 RAPD UBC primers to study genetic diversity. Twelve RAPD primers were selected to amplify 39 pepper cultivars, and 40 polymorphic DNA bands were created with sizes ranging from 200 to 1400 bp. Five of the 12 primers amplified all 39 cultivars. The genetic diversity of lines/cultivars in the pepper population is relatively high. The phylogenetic tree of the 39 cultivars has two branches showing similarity ranging from 41.8 to 51%. The first branch includes five pepper individuals, and the second consists of 34 individuals. There is a high diversity among the pepper cultivars in the same population.


  1. Ravindran PN. Black Pepper: Piper nigrum (1st ed.). London: CRC Press; 2000.
  2. Abdulazeez MA, Sani I, James BD, Abdullahi AS. Chapter 31 - Black Pepper (Piper nigrum L.) Oils. In: Preedy VR, editor. Essential Oils in Food Preservation, Flavor and Safety. San Diego: Academic Press; 2016. p. 277-85.
  3. Hirasa K, Takemasa M. Spice Science and Technology. Boca Raton: CRC Press; 1998.
  4. Embuscado ME. Bioactives From Spices and Herbs. In: Melton L, Shahidi F, Varelis P, editors. Encyclopedia of Food Chemistry. Oxford: Academic Press; 2019. p. 497-514.
  5. Hoang H. Pepper market report in the third quarter of 2021 [Internet]. Ho Chi Minh: Vietnambiz; 2021. Available from:
  6. Garcia AAF, Benchimol LL, Barbosa AMM, Geraldi IO, Souza Jr CL, Souza APd. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology. 2004;27.
  7. Guo-Liang J. Molecular Markers and Marker-Assisted Breeding in Plants. In: Sven Bode A, editor. Plant Breeding from Laboratories to Fields. Rijeka: IntechOpen; 2013. p. Ch. 3.
  8. Rasphone S, Thanh LD, Nguyen N, Nguyen NQ, Duong OT, Hung NVP, et al. Phylogenetic analysis of Black peper (Piper Spp.) population collected in different locations of Vietnam based on the ITSU1-4 gene region. Research square. 2021.
  9. Birren B, Green ED, Klapholz S, Meyers RM. Genome Analysis: A Laboratory Manual Vol.-1 Analyzing DNA. New York: Cold Spring Harbor Laboratory Press; 1997. 675 p.
  10. Truong HTH, Kim JH, Cho MC, Chae SY, Lee HE. Identification and development of molecular markers linked to Phytophthora root rot resistance in pepper (Capsicum annuum L.). European Journal of Plant Pathology. 2013;135(2):289-97.
  11. Francis Y, Rongcai Y, Timothy B. POPGENE. Version 1.32. City of Edmonton: University of Alberta; 2000.
  12. NTSYSpc. Version 2.1. Applied Biostatistics Inc; 2000.
  13. Nei M. Molecular Evolutionary Genetics. New York Chichester, West Sussex: Columbia University Press; 1987.
  14. Sokal RR, Michener CD. A statistical method for evaluating systematic relationships. The University of Kansas science bulletin. 1958;38:1409-1438.
  15. Thermo Fisher. Interpretation of Nucleic Acid 260/280 Ratios. Thermo Scientific. 2012.
  16. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 1978;89(3):583-90.
  17. Verma S, Karihaloo JL, Tiwari SK, Magotra R, Koul AK. Genetic diversity in Eremostachys superba Royle ex Benth. (Lamiaceae), an endangered Himalayan species, as assessed by RAPD. Genetic Resources and Crop Evolution. 2007;54(2):221-9.
  18. Kizhakkayil J, Sasikumar B. Genetic diversity analysis of ginger (Zingiber officinale Rosc.) germplasm based on RAPD and ISSR markers. Scientia Horticulturae. 2010;125(1):73-6.
  19. Rangappa K. Molecular and morphological characterization of seven varieties of Zingiber officinale. J Cytol Genet. 2008;9:101-107.
Creative Commons License

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

Copyright (c) 2022 Array