Population genetics of Phytophthora palmivora from Indonesia using microsatellite markers

Eirene Brugman1, Arif Wibowo2, Ani Widiastuti3

1Universitas Gadjah Mada, Sleman, Indonesia
2Universitas Gadjah Mada, Sleman, Indonesia
3Universitas Gadjah Mada, Sleman, Indonesia


Black pod rot disease caused by Phytophthora palmivora is one of the primary cacao diseases found in many cacao plantations in Indonesia. Population genetics is essential to study pathogen population dynamics and population evolutionary potential related to pathogen’s fitness, resistance, and long-term adaptability. This study aims to evaluate the genetic diversity and population structure of the P.palmivora from Sulawesi and Java islands, as the two geographical locations representing Indonesia’s leading cacao-growing area. The simple sequence repeat (SSR) markers were used to determine the genotype of 44 P. palmivora isolates from Sulawesi (24) and Java (20). All SSR loci used in this study were polymorphic. The total number of observed multilocus genotypes (MLG) from both populations was 34. Both populations revealed high genotypic diversity from the average Simpson index (λ=0.934) and the evenness (0.883). The index of association test indicated that the Sulawesi population was clonal and sexual recombination was present in the Java population. Analysis of molecular variance (AMOVA) and Bayesian clustering showed that all genetic diversity was from within individuals and the were five genetic clusters proportionally shared among all isolates from both islands. The genetic differentiation among populations is low (Fst=0.006), implying the lack of population structure related to geographic location. Minimum spanning network analysis showed no particular grouping of MLGs, and there were shared MLGs from both populations that indicated long-distance migration of P. Palmivora. These results revealed the high genotypic diversity of P. palmivora from both islands that formed one highly diverse group.


Eirene Brugman previously received her bachelor’s degree at the Faculty of Agriculture, Diponegoro University, in 2017. Her thesis examines the application of soil solarization and biocontrol agents in controlling late blight disease by Phytophthora infestans. She continued her graduate study at Gadjah Mada University, Department of Plant Protection. She has research interests in evolutionary biology, mycology, and pathogen population genetics. She recently finished the research on population genetics of Phytophthora palmivora in Indonesia based on microsatellite markers.

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