Affordable assays for genotyping single nucleotide polymorphisms in insects

Insect Molecular Biology

Volumn 16, Issue 4, 2007, Pages 377-387

  Black IV, W C ^a   Vontas, J G ^b  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b AGRICULTURAL UNIVERSITY OF ATHENS   (Greece)

Author keywords

Genotype; Insecticide resistance; Single nucleotide polymorphisms

Indexed keywords

DNA;

ANIMAL; ECONOMICS; GENETICS; GENOTYPE; HUMAN; INSECT; METHODOLOGY; NUCLEOTIDE SEQUENCE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; DNA; DNA MUTATIONAL ANALYSIS; GENOTYPE; HUMANS; INSECTS; POLYMORPHISM, SINGLE NUCLEOTIDE;

HEXAPODA;

EID: 34447623604     PISSN: 09621075     EISSN: 13652583     Source Type: Journal    
DOI: 10.1111/j.1365-2583.2007.00736.x     Document Type: Review

References (76)

1. Ahmadian, A., Gharizadeh, B., Gustafsson, A.C., Sterky, F., Nyren, P., Uhlen, M. Lundeberg, J. (2000) Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem 280 : 103 110.
2. Akey, J.M., Sosnoski, D., Parra, E., Dios, S., Hiester, K., Su, B., Bonilla, C., Jin, L. Shriver, M.D. (2001) Melting curve analysis of SNPs (McSNP): a gel-free and inexpensive approach for SNP genotyping. Biotechniques 30 : 358 362, 364, 366 7.
3. Andreev, D., Rocheleau, T., Phillips, T.W., Beeman, R.W. Ffrench-Constant, R.H. (1994) A PCR diagnostic for cyclodiene insecticide resistance in the red flour beetle Tribolium castaneum. Pesticide Sci 41 : 345 349.
4. Andrews, M.C., Callaghan, A., Field, L.M., Williamson, M.S. Moores, G.D. (2004) Identification of mutations conferring insecticide-insensitive AChE in the cotton-melon aphid, Aphis gossypii Glover. Insect Mol Biol 13 : 555 561.
5. Anstead, J.A., Williamson, M.S., Eleftherianos, L. Denholm, I. (2004) High-throughput detection of knockdown resistance in Myzus persicaeusing allelic discriminating quantitative PCR. Insect Biochem Mol Biol 34 : 871 877.
6. Ban, Y., Greenberg, D.A., Concepcion, E., Skrabanek, L., Villanueva, R. Tomer, Y. (2003) Amino acid substitutions in the thyroglobulin gene are associated with susceptibility to human and murine autoimmune thyroid disease. Proc Natl Acad Sci USA 100 : 15119 15124.
7. Barany, F. (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA 88 : 189 193.
8. Bass, C., Schroeder, I., Turberg, A., Field, L.M. Williamson, M.S. (2004) Identification of mutations associated with pyrethroid resistance in the para-type sodium channel of the cat flea, Ctenocephalides felis. Insect Biochem Mol Biol 34 : 1305 1313.
9. Beck, E.T., Bosio, C.F., Geske, D.A., Blair, C.D., Beaty, B.J. Black, W.C. (2005) An analysis of gene flow among Midwestern populations of the mosquito Ochlerotatus triseriatus. Am J Trop Med Hyg 73 : 534 540.
10. Bhattacharyya, A. Lilley, D.M. (1989) The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res 17 : 6821 6840.
11. Black, W.C., Gorrochotegui-Escalante, N. Duteau, N.M. (2006) Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay. J Med Entomol 43 : 238 247.
12. Botstein, D. Risch, N. (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 (S uppl 228 237.
13. Bourguet, D., Fonseca, D., Vourch, G., Dubois, M.P., Chandre, F., Severini, C. Raymond, M. (1998) The acetylcholinesterase gene Ace: a diagnostic marker for the Pipiensand Quinquefasciatusforms of the Culex pipienscomplex. J Am Mosq Control Assoc 14 : 390 396.
14. Brun-Barale, A., Bouvier, J.C., Pauron, D., Berge, J.B. Benoit, S. (2005) Involvement of a sodium channel mutation in pyrethroid resistance in Cydia pomonella L., and development of a diagnostic test. Pest Manag Sci 61 : 549 554.
15. Cassanelli, S., Cerchiari, B., Giannini, S., Bizzaro, D., Mazzoni, E. Manicardi, G.C. (2005) Use of the RFLP-PCR diagnostic test for characterizing MACE and kdr insecticide resistance in the peach potato aphid Myzus persicae. Pest Manag Sci 61 : 91 96.
16. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S. Fodor, S.P. (1996) Accessing genetic information with high-density DNA arrays. Science 274 : 610 614.
17. Chen, X., Livak, K.J. Kwok, P.Y. (1998) A homogeneous, ligase-mediated DNA diagnostic test. Genome Res 8 : 549 556.
18. Chen, X., Levine, L. Kwok, P.Y. (1999) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 9 : 492 498.
19. Clark, J.M. (2006) Control of Pediculosis: Current and future needs. Paper presented at: 11th IUPAC International Congress of Pesticide Chemistry, Kobe, Japan.
20. Clark, R.M., Linton, E., Messing, J. Doebley, J.F. (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA 101 : 700 707.
21. Deng, G.R. (1988) A sensitive non-radioactive PCR-RFLP analysis for detecting point mutations at 12th codon of oncogene c-Ha-ras in DNAs of gastric cancer. Nucleic Acids Res 16 : 6231.
22. Du, W., Awolola, T.S., Howell, P., Koekemoer, L.L., Brooke, B.D., Benedict, M.Q., Coetzee, M. Zheng, L. (2005) Independent mutations in the Rdl locus confer dieldrin resistance to Anopheles gambiae and An. arabiensis. Insect Mol Biol 14 : 179 183.
23. Ffrench-Constant, R.H., Steichen, J.C., Rocheleau, T.A., Aronstein, K. Roush, R.T. (1993) A single-amino acid substitution in a gamma-aminobutyric-acid subtype-a receptor locus is associated with cyclodiene insecticide resistance in Drosophilapopulations. Proc Natl Acad Sci USA 90 : 1957 1961.
24. Ffrench-Constant, R.H., Steichen, J.C. Brun, L.O. (1994a) A molecular diagnostic for endosulfan insecticide resistance in the coffee berry borer Hypothenemus hampei (Coleoptera, Scolytidae). Bull Entomol Res 84 : 11 16.
25. Ffrench-Constant, R.H., Steichen, J.C. Shotkoski, F. (1994b) Polymerase chain-reaction diagnostic for cyclodiene insecticide resistance in the mosquito Aedes aegypti. Med Vet Entomol 8 : 99 100.
26. Fischer, S.G. Lerman, L.S. (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci USA 80 : 1579 1583.
27. Gaylord, B.S., Massie, M.R., Feinstein, S.C. Bazan, G.C. (2005) SNP detection using peptide nucleic acid probes and conjugated polymers: applications in neurodegenerative disease identification. Proc Natl Acad Sci USA 102 : 34 39.
28. Genissel, A., Pastinen, T., Dowell, A., Mackay, T.F. Long, A.D. (2004) No evidence for an association between common nonsynonymous polymorphisms in delta and bristle number variation in natural and laboratory populations of Drosophila melanogaster. Genetics 166 : 291 306.
29. Gorrochotegui-Escalante, N., Lozano-Fuentes, S., Bennett, K.E., Molina-Cruz, A., Beaty, B.J. Black, W.C. (2005) Association mapping of segregating sites in the early trypsin gene and susceptibility to dengue-2 virus in the mosquito Aedes aegypti. Insect Biochem Mol Biol 35 : 771 788.
30. Hall, J.G., Eis, P.S., Law, S.M., Reynaldo, L.P., Prudent, J.R., Marshall, D.J. et al 2000) Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc Natl Acad Sci USA 97 : 8272 8277.
31. Hansen, K.K., Kristensen, M. Jensen, K.M.V. (2005) Correlation of a resistance-associated Rdl mutation in the German cockroach, Blattella germanica (L), with persistent dieldrin resistance in two Danish field populations. Pest Manag Sci 61 : 749 753.
32. Hawkes, N.J., Janes, R.W., Hemingway, J. Vontas, J. (2005) Detection of resistance-associated point mutations of organophosphate-insensitive acetylcholinesterase in the olive fruit fly, Bactrocera oleae (Gmelin). Pesticide Biochem Physiol 81 : 154 163.
33. Hirschhorn, J.N., Sklar, P., Lindblad-Toh, K., Lim, Y.M., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E. Lander, E.S. (2000) SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci USA 97 : 12164 12169.
34. Holland, P.M., Abramson, R.D., Watson, R. Gelfand, D.H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticusDNA polymerase. Proc Natl Acad Sci USA 88 : 7276 7280.
35. Howell, W.M., Jobs, M., Gyllensten, U. Brookes, A.J. (1999) Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat Biotechnol 17 : 87 88.
36. Hsu, J.C., Haymer, D.S., Wu, W.J. Feng, H.T. (2006) Mutations in the acetylcholinesterase gene of Bactrocera dorsalis associated with resistance to organophosphorus insecticides. Insect Biochem Mol Biol 36 : 396 402.
37. Kim, H.J., Hawthorne, D.J., Peters, T., Dively, G.P. Clark, J.M. (2005) Application of DNA-based genotyping techniques for the detection of kdr-like pyrethroid resistance in field populations of Colorado potato beetle. Pesticide Biochem Physiol 81 : 85 96.
38. Kolaczinski, J.H., Fanello, C., Herve, J.P., Conway, D.J., Carnevale, P. Curtis, C.F. (2000) Experimental and molecular genetic analysis of the impact of pyrethroid and non-pyrethroid insecticide impregnated bednets for mosquito control in an area of pyrethroid resistance. Bull Entomol Res 90 : 125 132.
39. Kristensen, M. (2005) Identification of sodium channel mutations in human head louse (Anoplura: Pediculidae) from Denmark. J Med Entomol 42 : 826 829.
40. Kulkarni, M.A., Rowland, M., Alifrangis, M., Mosha, F.W., Matowo, J., Malima, R. et al 2006) Occurrence of the leucine-to-phenylalanine knockdown resistance (kdr) mutation in Anopheles arabiensispopulations in Tanzania, detected by a simplified high-throughput SSOP-ELISA method. Malar J 5 : 56 63.
41. Kwock, P.-Y. (2001) Methods for genotyping Single Nucleotide Polymorphisms. Annu Rev Genomics Hum Genet 2 : 235 258.
42. Lee, S.H., Yoon, K.S., Gao, J.R., Ahn, Y.J. Clark, J.M. (2005) Control and resistance management of human pediculosis. New Discoveries Agrochemicals 892 : 383 393.
43. Liu, W.O., Oefner, P.J., Qian, C., Odom, R.S. Francke, U. (1997) Denaturing HPLC-identified novel FBN1 mutations, polymorphisms, and sequence variants in Marfan syndrome and related connective tissue disorders. Genet Test 1 : 237 242.
44. Lou, X.J., Panaro, N.J., Wilding, P., Fortina, P. Kricka, L.J. (2004) Mutation detection using ligase chain reaction in passivated silicon-glass microchips and microchip capillary electrophoresis. Biotechniques 37 : 392, 394, 396 398.
45. Lyamichev, V., Mast, A.L., Hall, J.G., Prudent, J.R., Kaiser, M.W., Takova, T. et al 1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 17 : 292 296.
46. Lynd, A., Ranson, H., McCall, P.J., Randle, N.P., Black, W.C., Walker, E.D. Donnelly, M.J. (2005) A simplified high-throughput method for pyrethroid knock-down resistance (kdr) detection in Anopheles gambiae. Malar J 4 : 16 21.
47. Martinez-Torres, D., Chevillon, C., Brun-Barale, A., Berge, J.B., Pasteur, N. Pauron, D. (1999) Voltage-dependent Na+ channels in pyrethroid-resistant Culex pipiensL. mosquitoes. Pesticide Sci 55 : 1012 1020.
48. McPeek, M.S. (2000) From mouse to human: fine mapping of quantitative trait loci in a model organism. Proc Natl Acad Sci USA 97 : 12389 12390.
49. Menendez, D., Krysiak, O., Inga, A., Krysiak, B., Resnick, M.A. Schonfelder, G. (2006) A SNP in the flt-1 promoter integrates the VEGF system into the p53 transcriptional network. Proc Natl Acad Sci USA 103 : 1406 1411.
50. Myakishev, M.V., Khripin, Y., Hu, S. Hamer, D.H. (2001) High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res 11 : 163 169.
51. Newton, C.R., Graham, A., Heptinstall, L.E., Powell, S.J., Summers, C., Kalsheker, N., Smith, J.C. Markham, A.F. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17 : 2503 2516.
52. Nichols, R. Dixon, J.E. (1988) Rapid identification of clones using the same degenerate oligonucleotide mixture for both screening and sequencing. Anal Biochem 170 : 110 115.
53. Nickerson, D.A., Kaiser, R., Lappin, S., Stewart, J., Hood, L. Landegren, U. (1990) Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci USA 87 : 8923 8927.
54. Nikiforov, T.T., Rendle, R.B., Goelet, P., Rogers, Y.H., Kotewicz, M.L., Anderson, S., Trainor, G.L. Knapp, M.R. (1994) Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 22 : 4167 4175.
55. Okimoto, R. Dodgson, J.B. (1996) Improved PCR amplification of multiple specific alleles (PAMSA) using internally mismatched primers. Biotechniques 21 : 20 22, 24, 26.
56. Oleykowski, C.A., Bronson Mullins, C.R., Godwin, A.K. Yeung, A.T. (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26 : 4597 4602.
57. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K. Sekiya, T. (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86 : 2766 2770.
58. Papp, A.C., Pinsonneault, J.K., Cooke, G. Sadee, W. (2003) Single nucleotide polymorphism genotyping using allele-specific PCR and fluorescence melting curves. Biotechniques 34 : 1068 1072.
59. Risch, N. (2001) Implications of multilocus inheritance for gene-disease association studies. Theor Popul Biol 60 : 215 220.
60. Robin, C., Lyman, R.F., Long, A.D., Langley, C.H. Mackay, T.F. (2002) hairy: a quantitative trait locus for Drosophilasensory bristle number. Genetics 162 : 155 164.
61. Roehrdanz, R.L. Degrugillier, M.E. (1998) Long sections of mitochondrial DNA amplified from fourteen orders of insects using conserved polymerase chain reaction primers. Ann Entomol Soc Am 91 : 771 778.
62. Schweitzer, B. Kingsmore, S. (2001) Combining nucleic acid amplification and detection. Curr Opin Biotechnol 12 : 21 27.
63. Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. Flook, P. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene-sequences and a compilation of conserved polymerase chain-reaction primers. Ann Entomol Soc Am 87 : 651 701.
64. Stoneking, M., Hedgecock, D., Higuchi, R.G., Vigilant, L. Erlich, H.A. (1991) Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48 : 370 382.
65. Syvanen, A.C., Ikonen, E., Manninen, T., Bengtstrom, M., Soderlund, H., Aula, P. Peltonen, L. (1992) Convenient and quantitative determination of the frequency of a mutant allele using solid-phase minisequencing: application to aspartylglucosaminuria in Finland. Genomics 12 : 590 595.
66. Tyagi, S. Kramer, F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14 : 303 308.
67. Verhaeghen, K., Van Bortel, W., Roelants, P., Backeljau, T. Coosemans, M. (2006) Detection of the East and West African kdr mutation in Anopheles gambiaeand Anopheles arabiensisfrom Uganda using a new assay based on FRET/Melt Curve analysis. Malar J 5 : 16.
68. Wang, J., Chuang, K., Ahluwalia, M., Patel, S., Umblas, N., Mirel, D., Higuchi, R. Germer, S. (2005) High-throughput SNP genotyping by single-tube PCR with Tm-shift primers. Biotechniques 39 : 885 893.
69. Wilkins, E.E., Howell, P.I. Benedict, M.Q. (2007) IMP PCR primers detect single nucleotide polymorphisms for Anopheles gambiaespecies identification, Mopti and Savanna rDNA types, and resistance to dieldrin in Anopheles arabiensis. Malar J 5 : 125 132.
70. Williamson, M.S., MartinezTorres, D., Hick, C.A., Castells, N. Devonshire, A.L. (1996) Analysis of sodium channel gene sequences in pyrethroid-resistant houseflies - Progress toward a molecular diagnostic for knockdown resistance (kdr). Mol Genet Evol Pesticide Resistance 645 : 52 61.
71. Winter, A., Kramer, W., Werner, F.A., Kollers, S., Kata, S., Durstewitz, G., Buitkamp, J., Womack, J.E., Thaller, G. Fries, R. (2002) Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA: diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Proc Natl Acad Sci USA 99 : 9300 9305.
72. Witowski, N.E., Leiendecker-Foster, C., Gerry, N.P., McGlennen, R.C. Barany, G. (2000) Microarray-based detection of select cardiovascular disease markers. Biotechniques 29 : 936 938, 940, 942 passim.
73. Wolfe, J.L., Kawate, T., Sarracino, D.A., Zillmann, M., Olson, J., Stanton, V.P. Jr. Verdine, G.L. (2002) A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides. Proc Natl Acad Sci USA 99 : 11073 11078.
74. Wu, D.Y. Wallace, R.B. (1989) The ligation amplification reaction (LAR) - amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4 : 560 569.
75. Xiao, Z., Xiao, J., Jiang, Y. Zhang, S., Yu, M., Zhao, J., Wei, D. Cao, H. (2006) A novel method based on ligase detection reaction for low abundant YIDD mutants detection in hepatitis B virus. Hepatol Res 34 : 150 155.
76. Zhong, X.B., Reynolds, R., Kidd, J.R., Kidd, K.K., Jenison, R., Marlar, R.A. Ward, D.C. (2003) Single-nucleotide polymorphism genotyping on optical thin-film biosensor chips. Proc Natl Acad Sci USA 100 : 11559 11564.