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Regional population differences of the brown planthopper (Nilaparvata lugens Stål) in Cambodia using genotyping-by-sequencing

Published online by Cambridge University Press:  24 October 2017

M. Matsukawa*
Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan Japan International Research Center for Agricultural Sciences, Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
Mikako Tasaki
International Cooperation Center for Agricultural Education, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
Kazuyuki Doi
Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
Kasumi Ito
International Cooperation Center for Agricultural Education, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
Kazuhito Kawakita
Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
Toshiharu Tanaka
International Cooperation Center for Agricultural Education, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
*Author for correspondence Phone/ Fax: +029-838-6622 E-mail:


The brown planthopper Nilaparvata lugens Stål (BPH) can be found year-round in tropical region and causes severe damage to rice. Although there has been documented BPH damage to rice crops in the past decade in Cambodia, the extent of this epidemic is poorly understood. Here, we examined the time variation of BPH population in the abundance of morphotypes in 13 main rice-producing provinces (86 sites) by aspirator method and in the Takeo Province (five sites) by yellow sticky trap method. At least three generations were observed during the 3-month collection period in the rainy growing season. Regarding the occurrence of BPH morphotypes, in July the macropterous adults were restricted to south Cambodia and in August all morphotypes, adults (macropterous and brachypterous) and nymphs, appeared in all sampling sites. To explain the difference of regional distribution, the genetic differentiation was analyzed in south and northwest Cambodia (three sites) by using single nucleotide polymorphisms (SNP) analysis via genotyping-by-sequencing (GBS) using next-generation sequencing. The 2455 SNPs obtained by GBS clarified the three sub-populations and they corresponded to the expected dissemination patterns. These results provide a clue to understand the differentiation and epidemic of BPH in Cambodia.

Research Papers
Copyright © Cambridge University Press 2017 

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Beissinger, T.M., Hirsch, C.N., Sekhon, R.S., Foerster, J.M., Johnson, J.M., Muttoni, G., Vaillancourt, B., Buell, C.R., Kaeppler, S.M. & Leon, N. (2013) Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics 193, 10731081.CrossRefGoogle ScholarPubMed
Danecek, P, Auton, A, Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R, Lunter, G., Marth, G., Sherry, S.T., McVean, G., Durbin, R. & 1000 Genomes Project Analysis Group (2011) The variant call format and VCFtools. Bioinformatics 27, 21562158.CrossRefGoogle ScholarPubMed
Dyck, V.A. & Thomas, B. (1979) The brown planthopper problem. pp. 317 in Brown Planthopper: Threat to Rice Production in Asia. Los Baños, Laguna, Philippines, International Rice Research Institute.Google Scholar
Excoffier, L. & Lischer, H. (2015) Arlequin ver 3.5: An Integrated Software Package for Population Genetics Data Analysis. Switzerland, Swiss Institute of Bioinformatics.Google Scholar
Glaubitz, J.C., Casstevens, T.M., Lu, F., Harriman, J., Elshire, R.J., Sun, Q. & Buckler, E.S. (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9, 111.CrossRefGoogle ScholarPubMed
Heong, K.L. & Escalada, M.M. (2008) Final Report: Research and Implementation Issues Related to Management of the Brown Planthopper/Virus Problem in Rice in Vietnam. Canberra, Australia, Australian Centre for International Agricultural Research.Google Scholar
Ho, V.C. (2013) Management of rice planthopper and related virus diseases in Mekong delta, South Vietnam (Personal communication).Google Scholar
Jairin, J., Kobayashi, T., Yamagata, Y., Sanada-Morimura, S., Mori, K., Tashiro, K., Kuhara, S., Kuwazaki, S., Urio, M., Suetsugu, Y., Yamamoto, K., Matsumura, M. & Yasui, H. (2013) A simple sequence repeat- and single-nucleotide polymorphism-based genetic linkage map of the brown planthopper, Nilaparvata lugens. DNA Research 20, 1730.CrossRefGoogle ScholarPubMed
Kakioka, R. (2013) Application of RAD sequencing to ecological and evolutionary genomics. Biological Science 64, 168176. [in Japanese].Google Scholar
Labate, J.A., Robertson, L.D., Strickler, S.R. & Mueller, L.A. (2014) Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome 57, 169180.CrossRefGoogle ScholarPubMed
Li, C., Waldbieser, G., Bosworth, B., Beck, B.H., Thongda, W. & Peatman, E. (2014) SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Molecular Ecology Resources 14, 12611270.CrossRefGoogle ScholarPubMed
Lischer, H. (2014) PGDSpider: An Automated Data Conversion Tool for Connecting Population Genetics and Genomics Programs. Switzerland, University of Berne.Google Scholar
Matsukawa, M., Ito, K., Kawakita, K. & Tanaka, T. (2014) Current status of the occurrence and farmer perceptions of rice planthopper in Cambodia. Japan Agricultural Research Quarterly 48, 167173.CrossRefGoogle Scholar
Matsumoto, Y., Matsumura, M., Sanada-Morimura, S., Hirai, Y., Sato, Y. & Noda, H. (2013) Mitochondrial cox sequences of Nilaparvata lugens and Sogatella furcifera (Hemiptera, Delphacidae): low specificity among Asian planthopper populations. Bulletin of Entomological Research 103, 382392.CrossRefGoogle ScholarPubMed
Matsumura, M., Takeuchi, H., Satoh, M., Sanada-Morimura, S., Otuka, A., Watanabe, T. & Thanh, D.V. (2008) Species-specific insecticide resistance to imidacloprid and fipronil in the rice planthoppers Nilaparvata lugens and Sogatella furcifera in East and South-East Asia. Pest Management Science 64, 11151121.CrossRefGoogle ScholarPubMed
Morin, P.A., Luikart, G., Wayne, R.K. & SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution 19, 208216.CrossRefGoogle Scholar
Mun, J.H., Song, Y.H., Heong, K.L. & Roderick, G.K. (1999) Genetic variation among Asian populations of rice planthoppers, Nilaparvata lugens and Sogatella furcifera (Homoptera: Delphacidae): mitochondrial DNA sequences. Bulletin of Entomological Research 89, 245253.CrossRefGoogle Scholar
Nagata, T. & Masuda, T. (1980) Insecticide susceptibility and wing-form ratio of the brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) and the white backed planthopper, Sogatella furcifera (Horvath) (Hemiptera: Delphacidae) of Southeast Asia. Applied Entomology and Zoology 15, 1019.CrossRefGoogle Scholar
National Institute of Statistics (2012) Statistical Yearbook of Cambodia 2011. Cambodia, National Institute of Statistics, Ministry of Planning, Phnom Penh.Google Scholar
Nesbitt, H.J. & Phaloeun, C. (1997) Rice-based farming systems. pp. 3137 in Nesbitt, H.J. (ed) Rice Production in Cambodia. Manila, Philippines, International Rice Research Institute.Google Scholar
Otuka, A., Sakamoto, T., Chien, H.V., Matsumura, M. & Sanada-Morimura, S. (2014) Occurrence and short-distance migration of Nilaparvata lugens (Hemiptera: Delphacidae) in the Vietnamese Mekong delta. Applied Entomology and Zoology 49, 97107.CrossRefGoogle Scholar
Poland, J.A., Brown, P.J., Sorrells, M.E. & Jannink, J.L. (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7, 18.CrossRefGoogle ScholarPubMed
Pujolar, J.M., Jacobsen, M.W., Als, T.D., Frydenberg, J., Munch, K., Jonsson, B., Jian, J.B., Cheng, L., Maes, G.E., Bernatchez, L. & Hansen, M.M. (2014) Genome-wide single-generation signatures of local selection in the panmictic European eel. Molecular Ecology 23, 25142528.CrossRefGoogle ScholarPubMed
Raj, A., Stephens, M. & Pritchard, J.K. (2013) fastSTRUCTURE: variational inference of population structure in large SNP. Genetics 197, 573589.CrossRefGoogle Scholar
Riley, J.R., Reynolds, D.R. & Farrow, R.A. (1987) The migration of Nilaparvata lugens (Stål) (Delphacidae) and other Hemiptera associated with rice during the dry season in the Philippines: a study using radar, visual observations, aerial netting and ground trapping. Bulletin of Entomological Research 77, 145169.CrossRefGoogle Scholar
Rousset, F. (2015) Genepop 4.4 for Windows/Linux/Mac OS X.Google Scholar
Silva-Brandão, L.K., Silva, O.A.B.N., Brandão, M.M., Omoto, C. & Sperling, F.A.H. (2015) Genotyping-by-sequencing approach indicates geographic distance as the main factor affecting genetic structure and gene flow in Brazilian population of Grapholita molesta (Lepidoptera, Tortricidae). Evolutionary Applications 8, 476485.CrossRefGoogle ScholarPubMed
Stapley, J., Reger, J., Feulner, P.G.D., Smadja, C., Galindo, J., Ekblom, R., Bennison, C., Ball, A.D., Beckerman, A. & Slate, J. (2010) Adaptation genomics: the next generation. Trends in Ecology & Evolution 25, 705712.CrossRefGoogle ScholarPubMed
Wada, T., Ito, K., Takahashi, A. & Tang, J. (2007) Variation of pre-ovipositional period in the brown planthopper Nilaparvata lugens, collected in tropical, subtropical and temperate Asia. Journal of Applied Entomology 131, 698703.CrossRefGoogle Scholar
Wada, T., Ito, K., Takahashi, A. & Tang, J. (2009) Starvation tolerance of macropter brown planthopper Nilaparvata lugens, from temperate, subtropical, and tropical populations in East and South-East Asia. Entomologia Experimentalis et Applicata 130, 7380.CrossRefGoogle Scholar
White, T.A., Perkins, S., Heckel, G. & Searle, J. (2013) Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Molecular Ecology 22, 29712985.CrossRefGoogle ScholarPubMed
Wilson, A.W., Wickett, N., Grabowski, P., Fant, J., Borevitz, J. & Mueller, G.M. (2015) Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology. Mycologia 107, 217226.CrossRefGoogle ScholarPubMed
Wong, L.P., Lai, J.K., Saw, W.Y., Ong, R.T., Cheng, A.Y., Pillai, N.E., Liu, X., Xu, W., Chen, P., Foo, J., Tan, L.W., Koo, S., Soong, R., Wenk, M.R., Lim, W., Khor, C., Little, P., Chia, K. & Teo, Y. (2014) Insight into the genetic structure and diversity of 38 south Asian Indians from deep whole-genome sequencing. PLoS Genetics 10, 115.CrossRefGoogle ScholarPubMed
Xue, J., Zhou, X., Zhang, C., Yu, L., Fan, H., Wang, Z., Xu, H., Xi, Y., Zhu, Z., Zhou, W., Pan, P., Li, B., Colbourne, J.K., Noda, H., Suetsugu, Y., Kobayashi, T., Zheng, Y., Liu, S., Zhang, R., Liu, Y., Luo, Y., Fang, D., Chen, Y., Zhan, D., Lv, X., Cai, Y., Wang, Z., Huang, H., Cheng, R., Zhang, X., Lou, Y., Yu, B., Zhuo, J., Ye, Y., Zhang, W., Shen, Z., Yang, H., Wang, J., Wang, J., Bao, Y. & Cheng, J. (2014) Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation. Genome Biology 15, 521539.CrossRefGoogle ScholarPubMed
Zhang, K., Zhu, W., Rong, X., Zhang, Y., Ding, X., Liu, J., Chen, D., Du, Y. & Hong, X. (2013) The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes. Genomics 14, 417428.Google ScholarPubMed
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