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Distribution, DNA barcoding and genetic diversity of potato cyst nematodes in Indonesia

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Abstract

Global trading of plant materials, in combination with agricultural practices, may facilitate the spreading of cyst nematodes to so far non-infected areas. Recently Potato Cyst Nematode (PCN) was recognized to be present in Indonesia and both diversity and distribution require further study. Assessment of PCN populations was done by collecting soil samples, determination of morphological characteristics in combination with ITS rDNA and COI mtDNA sequencing. Thirty-seven soil samples were collected from potato fields in the Indonesia archipelago. The results showed the presence of Globodera rostochiensis in 22 out of 37 sampling fields, namely North Sumatra (6 fields), Central Java (12 fields), East Java (3 fields), and -for the first time- in Sulawesi (North Sulawesi) (1 field). The highest observed density was found in Banjarnegara (Central Java), i.e., 872 cysts 100 ml soil−1. Globodera pallida was not recovered. Both ITS and COI characterisation of Indonesian PCN (G. rostochiensis) revealed the virtual absence of sequence variation as compared to most PCN from the rest of the world; the COI sequences were identical to the most common and mostly distributed haplotype around the world. Microsatellite genotyping indicated a higher genetic diversity for populations from East Java than for populations from North Sumatra, suggesting that cysts at the origin of populations in North Sumatra were coming from populations in East Java. These data on species identification, population density, genetic diversity, and distribution of potato cyst nematode over the Indonesian archipelago constitute the very basis for the design of environmentally-sound and effective PCN control strategies.

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Notes

  1. Based on estimation of presence of eggs in the Dieng Kulon population. The average of eggs Globodera from Dieng Kulon = 300 eggs/cyst; therefore 872 cyst 100 ml−1 = 872 x ~ 300 eggs 100 ml soil−1 = ~2616 eggs ml soil−1

  2. Conversion dried soil in Dieng Kulon-Banjarnegara from ml to gram: 100 ml = 78 g

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Acknowledgements

This work was funded by the Ministry of Agriculture, Nature and Food Quality, The Netherlands (project number 1300023185), in collaboration with the Indonesian Agricultural Quarantine Agency (IAQA) and Ghent University Belgium. The authors would like to thank Plant Quarantine of IAQA officers in Medan, Padang, Semarang, Surabaya, Lombok, Makassar, Manado, Mr. Kristiadi from Indonesian Soil Research Institute, and Mr. Rusli from Food Crop Agriculture and Horticulture Service-North Sumatra for assistance on soil sampling.

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  1. Nematology Research Unit, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium

    Nurul Dwi Handayani, Prabowo Lestari, Marjolein Couvreur & Wim Bert

  2. Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, E Building 5th Floor, Jl. Harsono RM. 3 Ragunan, Jakarta, 12550, Indonesia

    Nurul Dwi Handayani & Prabowo Lestari

  3. IGEPP, INRAE, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France

    Magali Esquibet, Josselin Montarry & Eric Grenier

  4. Directorate General of Estate Crops, Ministry of Agriculture, C Building, Jl. Harsono RM. 3 Ragunan, Jakarta, 12550, Indonesia

    Antarjo Dikin

  5. Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1 RADIX building (107), 6708 PB, Wageningen, The Netherlands

    Johannes Helder

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Handayani, N.D., Esquibet, M., Montarry, J. et al. Distribution, DNA barcoding and genetic diversity of potato cyst nematodes in Indonesia. Eur J Plant Pathol 158, 363–380 (2020). https://doi.org/10.1007/s10658-020-02078-7

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