Genetic diversity of Phytophthora palmivora isolates from Indonesia and Japan using rep-PCR and microsatellite markers
- 35 Downloads
Phytophthora palmivora infects hundreds of plant species around the world. Determining the genetic diversity among isolates is necessary to establish more effective control strategies, manage resistance and understand epidemiology, long-term evolution of the pathogen, host–pathogen coevolution, and evolutionary processes. Here genetic diversity among 81 isolates of P. palmivora from various host plants and geographical regions in Indonesia and Japan was evaluated using rep-PCR (BOX, ERIC, REP and M13) and microsatellite markers. With both methods, the isolates clustered into six groups, which corresponded more to geographic regions rather than host plants or mating types, although the respective members of each group were not always consistent between the two methods. Isolates from Indonesia, Japan and other countries clearly clustered into separate groups in the rep-PCR analysis. The rep-PCR consistently grouped the isolates from Sumatera Island with some isolates from Sulawesi, but microsatellite markers grouped them with those from the Java islands. A typical A1-mating type from one region grouped in one cluster using both methods. Both DNA fingerprinting markers also grouped the isolates from Nusa Tenggara and Papua islands with those from Japan. Genetic variation was recognized within and among populations of P. palmivora based on geographical areas, host plants and mating types. Possible explanations for the results and suggested strategies for disease management are discussed.
KeywordsPhytophthora palmivora Genetic diversity Rep-PCR Microsatellite
This research was part of doctoral study of Masanto with the collaboration of the Faculty of Agriculture, University of Gadjah Mada, Yogyakarta (Indonesia) and River Basin Research Center, Gifu University, Gifu (Japan) as part of the “6-months Sandwich Program in UGSAS-GU”. The assistance of Mrs. Kayoko Otsubo is gratefully acknowledged.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Human/animal rights statement
This article does not contain any studies with human participants or animals performed by any of the authors.
- Drenth A, Guest DI (2004) Phytophthora in the tropics. In: Drenth A, Guest DI (eds) Diversity and management of Phytophthora in Southeast Asia. ACIAR Monograph no. 114, Canberra, pp 30–41Google Scholar
- Erwin DC, Ribero OK (eds) (1996) Phytophthora diseases worldwide. APS Press, St. PaulGoogle Scholar
- Fegan M, Prior P (2005) How complex is the “Ralstonia solanacearum species complex”? In: Allen C, Prior P, Hayward AC (eds) Bacterial wilt disease and the Ralstonia solanacearum species complex. APS Press, St. Paul, pp 449–461Google Scholar
- Gallegly ME, Hong C (eds) (2008) Phytophthora: identifying species by morphology and DNA fingerprints. APS Press, St. PaulGoogle Scholar
- Indonesian Agricultural Quarantine Agency (2018) Data on transportation of cacao seedlings in Indonesia (2013–2017). Ministry of Agriculture, Jakarta, IndonesiaGoogle Scholar
- Lolong AA (2012) Alternate host of several isolates Phytophthora palmivora causing coconut budrot (in Indonesian with English summary). Bull Palma 13:1–6Google Scholar
- Marpaung AE, Silalahi FH, Purba EIY (2010) Identification of the causal agent of brown rot gummosis on citrus in Karo region (in Indonesian with English summary). J Hortic Indones 20:262–273Google Scholar
- Mohammed MS, Dickinson M, Seman IA (2015) Analysis of genetic variation in Phytophthora palmivora, the causal agent of bud rot disease of oil palm. In: Proceedings of MPOB oil palm congress and exhibition; agriculture, biotechnology and sustainability; oil palm: powering the world, sustaining the future, Kuala Lumpur, 2015. Malaysian Palm Oil Board, Kuala Lumpur, Malaysia, pp 156–163Google Scholar
- Motulo HFJ, Sinaga MS, Mandang S, Tjahjoleksono A (2004) Genetic diversity of some Phytophthora palmivora isolates causes nut fall disease on coconut plantation based on the random amplified polymorphic DNA (RAPD) (in Indonesian with English summary). Jurnal Littri 10:154–158Google Scholar
- Purwantara A, Umayah A (2010) Genetic diversity analysis of Phytophthora palmivora from cocoa in Indonesia using AFLP. Indones J Biotechnol Res Estate Crops 78:61–69Google Scholar
- Purwantara A, Manohara D, Warokka JS (2004) Phytophthora diseases in Indonesia. In: Drenth A, Guest DI (eds) Diversity and management of Phytophthora in Southeast Asia. ACIAR Monograph no. 114, Canberra, pp 70–76Google Scholar
- Sumardiyono C, Pusposendjojo N, Trisnowati S (1995) Resistance of fungal plant pathogens to fungicides. Indones J Plant Pathol 1:51–55Google Scholar
- Swofford DL (2002) PAUP*. phylogenetic analysis using parsimony (*and other methods) version 4.0a164. Sinauer, SunderlandGoogle Scholar
- Umayah A, Sinaga MS, Sastrosumarjo S (2007) Genetic diversity of isolates of Phythophthora palmivora from cocoa in Indonesia. Coffee Cocoa Res J 23:129–138Google Scholar
- Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40Google Scholar
- Zaccardelli M, Campanile F, Moretti C, Buonaurio R (2008) Characterization of Italian populations of Xanthomonas campestris pv. campestris using primers based on DNA repetitive sequences. J Plant Pathol 90:375–381Google Scholar