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Genetic diversity of potato blackleg pathogens, Pectobacterium wasabiae, P. carotovorum subsp. brasiliense and Dickeya dianthicola in Japan by rep-PCR fingerprinting

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Abstract

We determined the species composition of 219 isolates of potato blackleg or soft rot pathogens in Japan collected after 2000 from potato plants by species-specific PCR. Of the total, Pectobacterium wasabiae (Pw) and P. carotovorum subsp. brasiliense (Pcb) comprised 88% (Pw: 94 isolates, Pcb: 98 isolates) of the isolates and Dickeya dianthicola (Ddi) 12% (27 isolates). P. atrosepticum (Pa) was not detected. Genetic diversity of Pw, Pcb and Ddi was investigated using repetitive sequence-based PCR (rep-PCR) fingerprinting with three primer pairs complementary to repetitive sequences in the bacterial genome (BOX, ERIC and REP). One hundred and twenty-one Pw isolates, one hundred Pcb isolates and thirty-three Ddi isolates were assigned to twenty-nine, twenty-one and eleven fingerprint genotypes (FGs) based on the combination of fingerprint patterns for each rep-PCR experiment (BOX-, ERIC- and REP-PCR). The genetic diversity of Pw and Ddi isolates in Japan was considered high, with Simpson’s diversity index and Shannon’s index of 0.87 and 2.44 for Pw, and 0.84 and 2.05 for Ddi, respectively. Pcb isolates were less diversified genetically (diversity index: 0.57 and 1.58). The FGs of the isolates obtained from blackleg-affected potato plants in the seed tuber field agreed with those of the isolates in the field where the seeds produced were grown. These results support the occurrence of seed-borne transmission of the blackleg pathogen between the fields.

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Data availability

The data sets analyzed during the current study available from the corresponding author on reasonable request.

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Acknowledgments

The authors deeply appreciate Professor Dr. Yuichi Takikawa, Graduate School of Agriculture, Shizuoka University, for providing bacterial isolates and advice and Drs. Mitsuo Horita and Shingo Toyoshima for useful advice. This study was funded by the Science and Technology Research Promotion Program for the Agriculture (no. 27005C), Forestry, Fisheries, and Food industry, Ministry of Agriculture, Forestry and Fisheries.

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Funding

This study was funded by the Science and Technology Research Promotion Program for the Agriculture, Forestry, Fisheries, and Food industry (no. 27005C), Ministry of Agriculture, Forestry and Fisheries.

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Author notes

  1. Shinji Yasuoka

    Present address: Donan Agricultural Experiment Station, HRO, 680 Hon-cho, Hokuto, Hokkaido, 041-1201, Japan

Authors and Affiliations

  1. Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido, 062-8555, Japan

    Takato Nakayama, Taketo Fujimoto, Takehiro Ohki & Tetsuo Maoka

  2. Takachi Agricultural Experiment Station, Hokkaido Research Organization (HRO), 9-2 Shinseiminami, Memuro, Kasai, Hokkaido, 082-0081, Japan

    Shinji Yasuoka

  3. Agricultural Research Institute, Tokachi Federation of Agricultural Cooperatives, Nishi 24 Kita l, Obihiro, Hokkaido, 080-2464, Japan

    Takahiro Ozawa

  4. Hokkaido-chuo Station, Center for Seeds and Seedlings, NARO, 1089 Nishinosato, Kitahiroshima, Hokkaido, 061-1102, Japan

    Yoshiyuki Aono

  5. Tokachi Station, Center for Seeds and Seedlings, NARO, 210-6 Higashi 4-sen, Kofuku, Obihiro, Hokkaido, 089-1246, Japan

    Yutaka Ushio

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  1. Takato Nakayama
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Contributions

All authors contributed to the study conception and design. Collection of pathogenic bacteria was done by Shinji Yasuoka, Takahiro Ozawa, Yoshiyuki Aono and Yutaka Ushio. Material preparation, data collection and analysis were performed by Takato Nakayama. The first draft of the manuscript was written by Takato Nakayama. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Takato Nakayama.

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Nakayama, T., Yasuoka, S., Ozawa, T. et al. Genetic diversity of potato blackleg pathogens, Pectobacterium wasabiae, P. carotovorum subsp. brasiliense and Dickeya dianthicola in Japan by rep-PCR fingerprinting. Eur J Plant Pathol 159, 917–939 (2021). https://doi.org/10.1007/s10658-021-02216-9

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