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Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål)

Published online by Cambridge University Press:  06 September 2011

S. Jing ,
B. Liu ,
L. Peng ,
X. Peng ,
L. Zhu ,
Q. Fu  and
G. He
S. Jing
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
B. Liu
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
L. Peng
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
X. Peng
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
L. Zhu
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
Q. Fu
Affiliation:
China National Rice Research Institute, Hangzhou 310006, People's Republic of China
G. He*
Affiliation:
State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, People's Republic of China
*
*Author for correspondence Fax: +86 27 68752327 E-mail: [email protected]
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Abstract

To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens Stål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

Keywords

brown planthoppersimple sequence repeatexpress sequence taggenetic diversitybiotype
Type
Research Paper
Information
Bulletin of Entomological Research , Volume 102 , Issue 1 , February 2012 , pp. 113 - 122
Copyright
Copyright © Cambridge University Press 2011

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References

Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D. & Sorrells, M.E. (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181–186.CrossRefGoogle ScholarPubMed
Behura, S.K. (2006) Molecular marker systems in insects: current trends and future avenues. Molecular Ecology 15, 3087–3113.CrossRefGoogle ScholarPubMed
Black, W.C. (1993) PCR with arbitrary primers: approach with care. Insect Molecular Biology 2, 1–6.CrossRefGoogle ScholarPubMed
Botstein, D., White, R.L., Skolnick, M. & Davis, R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32, 314.Google ScholarPubMed
Carson, H.L. (1990) Increased genetic variance after a population bottleneck. Trends in Ecology and Evolution 5, 228–230.CrossRefGoogle ScholarPubMed
Cato, S.A., Gardner, R.C., Kent, J. & Richardson, T.E. (2001) A rapid PCR-based method for genetically mapping ESTs. Theoretical and Applied Genetics 102, 296–306.CrossRefGoogle Scholar
Claridge, M.F. & Den Hollander, J. (1982) Virulence to rice cultivars and selection for virulence in populations of the brown planthopper Nilaparvata lugens. Entomologia Experimentalis et Applicata 32, 213–221.CrossRefGoogle Scholar
Claridge, M.F. & Hollander, J.D. (1980) The “biotypes” of the rice brown planthopper, Nilaparvata lugens. Entomologia Experimentalis et Applicata 27, 23–30.CrossRefGoogle Scholar
Denno, R.F. & Roderick, G.K. (1990) Population biology of planthoppers. Annual Review of Entomology 35, 489–520.CrossRefGoogle Scholar
Dupo, A.L.B. & Barrion, A.T. (2009) Taxonomy and general biology of delphacid planthoppers in rice agroecosytems. pp. 3–156in Heong, K.L. & Hardy, B. (Eds) Planthoppers: New Threats to the Sustainability of Intensive Rice Production Systems in Asia. Los Baños, Philippines, International Rice Research Institute.Google Scholar
Excoffier, L., Laval, G. & Schneider, S. (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47–50.Google Scholar
Feingold, S., Lloyd, J., Norero, N., Bonierbale, M. & Lorenzen, J. (2005) Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theoretical and Applied Genetics 111, 456–466.CrossRefGoogle ScholarPubMed
Ghormade, V., Kulkarni, S., Doiphode, N., Rajamohanan, P.R. & Deshpande, M.V. (2010) Chitin deacetylase: A comprehensive account on its role in nature and its biotechnological applications. pp. 1054–1066in Méndez-Vilas, A. (Ed.) Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology. Badajoz, Spain, Formatex.Google Scholar
Grover, A., Aishwarya, V. & Sharma, P.C. (2007) Biased distribution of microsatellite motifs in the rice genome. Molecular Genetics and Genomics 277, 469–480.CrossRefGoogle ScholarPubMed
Guan, X.J., Fu, Q., Wang, G.R., Lai, F.X. & Zhang, Z. (2004) The DNA polymorphism of host-associated populations of Nilaparvata lugens (Stål) with different virulence. Acta Entomologica Sinica 47, 152–158.Google Scholar
Gupta, P.K., Rustgi, S., Sharma, S., Singh, R., Kumar, N. & Balyan, H.S. (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics 270, 315–323.CrossRefGoogle Scholar
Han, Y.C., Teng, C.Z., Hu, Z.L. & Song, Y.C. (2008) An optimal method of DNA silver staining in polyacrylamide gels. Electrophoresis 29, 1355–1358.CrossRefGoogle ScholarPubMed
Hansen, B.D., Harley, D.K.P., Lindenmayer, D.B. & Taylor, A.C. (2009) Population genetic analysis reveals a long-term decline of a threatened endemic Australian marsupial. Molecular Ecology 18, 3346–3362.CrossRefGoogle ScholarPubMed
Hartl, D.L. & Clark, A.G. (1997) Principles of Population Genetics. 3rd ed. Sunderland, MA, USA, Sinauer Associates, Inc.Google Scholar
Hollander, J.D. & Pathak, P.K. (1981) The genetics of the ‘biotypes’ of the rice brown planthopper, Nilaparvata lugens. Entomologia Experimentalis et Applicata 29, 76–86.CrossRefGoogle Scholar
Huang, Z., He, G., Shu, L., Li, X. & Zhang, Q. (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theoretical and Applied Genetics 102, 929–934.CrossRefGoogle Scholar
Ju, Z., Wells, M.C., Martinez, A., Hazlewood, L. & Walter, R.B. (2005) An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus. In Silico Biology 5, 439–463.Google Scholar
Kantety, R.V., La Rota, M., Matthews, D.E. & Sorrells, M.E. (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Molecular Biology 48, 501–510.CrossRefGoogle ScholarPubMed
Kumpatla, S.P. & Mukhopadhyay, S. (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48, 985–998.CrossRefGoogle ScholarPubMed
Latif, M.A., Soon Guan, T., Mohd Yusoh, O. & Siraj, S.S. (2008) Evidence of sibling species in the brown planthopper complex (Nilaparvata lugens) detected from short and long primer random amplified polymorphic DNA fingerprints. Biochemical Genetics 46, 520–537.CrossRefGoogle Scholar
Liu, K. & Muse, S.V. (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128.CrossRefGoogle ScholarPubMed
Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27, 209.Google Scholar
Metzgar, D., Bytof, J. & Wills, C. (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research 10, 72.Google ScholarPubMed
Moccia, M.D., Oger-Desfeux, C., Marais, G.A. & Widmer, A. (2009) A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping. BMC Genomics 10, 243.CrossRefGoogle Scholar
Noda, H., Kawai, S., Koizumi, Y., Matsui, K., Zhang, Q., Furukawa, S., Shimomura, M. & Mita, K. (2008) Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests. BMC Genomics 9, 117.CrossRefGoogle ScholarPubMed
Pannebakker, B.A., Niehuis, O., Hedley, A., Gadau, J. & Shuker, D.M. (2010) The distribution of microsatellites in the Nasonia parasitoid wasp genome. Insect Molecular Biology 19, 91–98.CrossRefGoogle ScholarPubMed
Pathak, M.D. (1975) Utilization of insect-plant interactions in pest control. pp. 121–148in Pimentel, D. (Ed.) Insects, Science and Society. London, UK, Academic Press.CrossRefGoogle Scholar
Pathak, M.D. & Khush, G.S. (1977) Studies on varietal resistance to the brown planthopper at I.R.R.I. The Brown Planthopper Symposium. Los Baños, Philippines, International Rice Research Institute.Google Scholar
Peakall, R.O.D. & Smouse, P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288–295.CrossRefGoogle Scholar
Pechan, T., Ye, L., Chang, Y., Mitra, A., Lin, L., Davis, F.M., Williams, W.B. & Luthe, D.S. (2000) A unique 33-kD cysteine proteinase accumulates in response to larval feeding in maize genotypes resistant to fall armyworm and other Lepidoptera. Plant Cell 12, 1031–1040.CrossRefGoogle ScholarPubMed
Pérez, F., Ortiz, J., Zhinaula, M., Gonzabay, C., Calderón, J. & Volckaert, F. (2005) Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Marine Biotechnology 7, 554–569.CrossRefGoogle ScholarPubMed
Powell, W., Machray, G.C. & Provan, J. (1996) Polymorphism revealed by simple sequence repeats. Trends in Plant Science 1, 215–222.CrossRefGoogle Scholar
Rohlf, F.J. (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. New York: Exeter Software 83.Google Scholar
Schlötterer, C. (2001) Genealogical inference of closely related species based on microsatellites. Genetics Research 78, 209–212.CrossRefGoogle ScholarPubMed
Serapion, J., Kucuktas, H., Feng, J. & Liu, Z. (2004) Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Marine Biotechnology 6, 364–377.CrossRefGoogle ScholarPubMed
Shufran, K.A. & Whalon, M.E. (1995) Genetic analysis of brown planthopper biotypes using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Insect Science and its Application 16, 27–34.CrossRefGoogle Scholar
Sneath, P.H.A. & Sokal, R.R. (1973) Numerical taxonomy: the principles and practice of numerical classification. San Francisco, CA, USA, W.H. Freeman.Google Scholar
Sourdille, P., Tavaud, M., Charmet, G. & Bernard, M. (2001) Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes. Theoretical and Applied Genetics 103, 346–352.CrossRefGoogle Scholar
Tang, M., Lv, L., Jing, S.L., Zhu, L.L. & He, G.C. (2010) Bacterial Symbionts of the Brown Planthopper, Nilaparvata lugens (Homoptera: Delphacidae). Applied and Environmental Microbiology 76, 1740–1745.CrossRefGoogle ScholarPubMed
Tautz, D. (1989) Hypervariabflity of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17, 6463.CrossRefGoogle ScholarPubMed
Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. & McCouch, S. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research 11, 1441–1452.CrossRefGoogle ScholarPubMed
Thiel, T., Michalek, W., Varshney, R.K. & Graner, A. (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106, 411–422.CrossRefGoogle ScholarPubMed
Varshney, R.K., Thiel, T., Stein, N., Langridge, P. & Graner, A. (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cellular & Molecular Biology Letters 7, 537–546.Google ScholarPubMed
Wang, H.X., Li, F.H. & Xiang, H.H. (2005) Polymorphic EST-SSR markers and their mode of inheritance in Fenneropenaeus chinensis. Aquaculture 249, 107–114.CrossRefGoogle Scholar
Wang, S., Zhang, L. & Matz, M. (2009) Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). Journal of Heredity 100, 329–337.CrossRefGoogle ScholarPubMed
Weng, Y., Azhaguvel, P., Michels, G.J. Jr & Rudd, J.C. (2007) Cross-species transferability of microsatellite markers from six aphid (Hemiptera: Aphididae) species and their use for evaluating biotypic diversity in two cereal aphids. Insect Molecular Biology 16, 613–622.CrossRefGoogle ScholarPubMed
Wilson, S.W., Mitter, C., Denno, R.F. & Wilson, M.R. (1994) Planthoppers: Their Ecology and Management. pp. 7–113in Denno, R.F. & Perfect, T.J. (Eds) Evolutionary Patterns of Host Plant Use by Delphacid Planthoppers and their Relatives. New York, USA, Chapman and Hall.Google Scholar
Yu, H. & Li, Q. (2008) Exploiting EST databases for the development and characterization of EST-SSRs in the Pacific oyster (Crassostrea gigas). Journal of Heredity 99, 208–214.CrossRefGoogle ScholarPubMed
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