Genetic Diversity of Potato Cyst Nematode Using Internal Transcribed Spacer Region (Its) and Simple Sequence Repeat Markers

  • M. W. Mbiyu University of Nairobi
  • W. M. Muiru University of Nairobi
  • J. W. Kimenju University of Nairobi
  • M. W. Nyongesa Kenya Agricultural Livestock Research Organization
  • S. Haukeland International Centre for Insect Physiology and Ecology


Genetic diversity of potato cyst nematodes (Globodera spp) is important in potato breeding programmes worldwide. The objective of this study was to identify and determine the genetic diversity of potato cyst nematode (PCN) populations from Nyandarua, Nakuru and Meru Counties in Kenya. Twenty simple sequence repeats (SSR) markers, four of which were newly designed for this study were used to genotype the 88 PCN samples. Fragments of DNA were amplified using 434 bp primer (ITS5/PITSr3) specific for Globodera. rostochiensis. From 20 SSR markers, four were polymorphic and specific for PCN. The expected heterozygosity (He) and Shannon’s index (I) ranged from 0.32 to 0.50 and from 0.50 to 0.69, respectively, across the 3 populations. As a result, the He and I values indicated a limited range of genetic diversity and heterozygote deficiency between the samples. The mean polymorphism information content (PIC) ranged from 0.344 to 0.365 indicating an intermediate polymorphism (PIC ≥ 0.25) across the populations. Furthermore, analysis of molecular variance (AMOVA) revealed that the highest genetic variance 96% (P<0.001) was due to intra-population variance. An unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree was constructed based on Nei’s genetic dissimilarity and the entire population was grouped into two major clusters and five sub-clusters. Principal coordinate analysis (PCoA) revealed that the variance accounted for by the first 3 principal coordinates were 27.73, 28.89 and 24.42, respectively. The Bayesian model-based population structure analysis assembled the populations into K=6 distinct genetic structures based on the highest ΔK=8.25. The fixation index (Fst) ranged from 0.02 to 0.05, indicating that the three G. rostochiensis populations had low genetic differentiation. The results from this study suggest that there was low genetic diversity among the PCN evaluated across the Counties.

How to Cite
Mbiyu, M. W., Muiru, W. M., Kimenju, J. W., Nyongesa, M. W., & Haukeland, S. (2023). Genetic Diversity of Potato Cyst Nematode Using Internal Transcribed Spacer Region (Its) and Simple Sequence Repeat Markers. East African Agricultural and Forestry Journal, 87(3&4), 14. Retrieved from