The application and performance of single nucleotide polymorphism markers for population genetic analyses of lepidoptera

Frontiers in Genetics

Volumn 2, Issue JUNE, 2011, Pages

  Coates, Brad Steven ^a   Bayles, Darrell O ^a   Wanner, Kevin W ^b   Robertson, Hugh M ^c   Hellmich, Richard L ^a,d   Sappington, Thomas W ^a,d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b MONTANA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d IOWA STATE UNIVERSITY   (United States)

Author keywords

Performance; Population genetics; Single nucleotide polymorphism

Indexed keywords

LEPIDOPTERA; OSTRINIA NUBILALIS;

EID: 84865466839     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00038     Document Type: Article

References (69)

1. Adams, M. D., Kelly, J. M., Gocayne, J. D., Dubnick, M., Polymeropou-los, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Mereno, R. R, Kerlavage, A. R., McCombie, W. R., and Venter, J. C. (1991). Complementary DNA sequencing: expressed sequence tags and the human genome project. Science 252, 1651-1656.
2. Beldade, P., Saenko, S. V., Pul, N., and Long, A. D. (2010). A gene-based linkage map of Bicyclus any-nana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome. PLoS Genet. 5, el000366. doi: 10.1371/joumal.pgen.l000366
3. Bennett, S. (2004). Solexa Ltd. Pharma-cogenomics 5, 433-438.
4. Bourguet, D., Bethenod, M. T., Pasteur, N., and Viard, F. (2000). Gene flow in the European corn borer Ostrinia nubilalis: implications for the sus-tainability of transgenic insecticidal maize. Proc. R. Soc. Lond. B Biol. Sci. 267, 117-122.
5. Brooks, S. A., Gabreski, N., Miller, D., Brisbin, A., Brown, H. E., Streeter, C, Mezey, J., Cook, D., and Antczak, D. F. (2010). Whole-genome SNP association in the horse: identification of a deletion in myosin Va responsible for Lavender Foal syndrome. PLoS Genet. 6, el000909. doi: 10.1371/journal. pgen. 1000909
6. Brumfield, R. T, Beerli, P., Nickerson, D. A., and Edwards, S. V. (2003). The utility of single nucleotide polymorphisms in inference of population history. Trends Ecol Evol. (Amst.) 18,249-256.
7. Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Buchanan, A., Sten-gard, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., and Sing, C. F. (1998). Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63, 595-612.
8. Coates, B. S., Hellmich, R. L., and Lewis, L. C. (2005). Polymorphic CA/GT and GA/CT microsatellite loci for Ostrinia nubilalis (Lep-idoptera: Crambidae). Mol. Ecol. Notes 5, 10-12.
9. Coates, B. S., Kroemer, J. A., Sumer-ford, D. V., and Hellmich, R. L. (2011). A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatel-lites. Insect Mol. Biol. 20,15-27.
10. Coates, B. S., Sumerford, D. V., Hellmich, R. L., and Lewis, L. C. (2004). Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnacalis. Int. J. Biol. Sci. 1, 13-18.
11. Coates, B. S., Sumerford, D. V., Hellmich, R. L., and Lewis, L. C. (2008). Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs). Insect Mol. Biol. 17,607-621.
12. Coates, B. S., Sumerford, D. V., Hellmich, R. L., and Lewis, L. C. (2009a). Repetitive genomic elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research. Genome 52, 57-67.
13. Coates, B. S., Sumerford, D. V, Miller, N. J., Kim, K. S., Sappington, T. W, Siegfried, B. D., and Lewis, L. C. (2009b). Comparative performance of single nucleotide polymorphism and microsatellite markers for population genetic analysis. J. Hered. 100, 556-564.
14. Coates, B. S, Sumerford, D. V, Hellmich, R. L., and Lewis, L. C. (2010). A Helitron-like transposon super-family from Lepidoptera disrupts (GAAA)n microsatellites and is responsible for flanking sequence similarity within a microsatellite family. J. Mol. Evol. 70, 278-288.
15. Eckenrode, C. J., Robbins, P. S., and Andaloro, J. T. (1983). Variations in flight patterns of European corn borer (Lepidoptera: Pyralidae) in New York. Environ. Entomol. 12, 393-396.
16. Ellegren, H. (2000). Heterogeneous mutation processes in human microsatellite DNA sequences. Nat. Genet. 24, 400-402.
17. Ellegren, H. (2009). Sequencing goes 454 and takes large-scale genomics into the wild. Mol. Ecol. 17, 1629-1635.
18. Ellegren, H., Primmer, C. R., and Sheldon, B. C. (1995). Microsatellite "evolution": directionality or bias? Nat. Genet. 11,360-362.
19. Estoup, A., Garnery, L., Solignac, M., and Cornuet, J. M. (1995). Microsatellite variation in honeybee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics 140, 679-695.
20. Excoffier, L., Laval, G., and Schneider, S. (2005). Arlequin (version 3.0): an integrated software package for population genetic analysis. Evol. Bioinf. Online 1, 47-50.
21. Falush, D., Stephens, M., and Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 7, 574-578.
22. Fay, J. C, Wyckoff, G. J., and Wu, C. I. (2001). Positive and negative selection on the human genome. Genetics 158, 1227-1234.
23. Frolov, A. N., Bourguet, D., and Ponsard, S. (2007). Reconsidering the taxonomy of several Ostrinia species in the light of reproductive isolation: a tale for Ernst Mayr. Biol. J. Linn. Soc. Lond. 91, 49-72.
24. Gabriel, S., Ziaugra, L., and Tabbaa, D. (2009). SNP genotyping using the sequenom MassARRAY iPlex platform. Curr. Prot. Hum. Genet. 2.12.1-2.12.18.
25. Hacia, J. G., Fan, J. B., Ryder, O., Jin, L., Edgemon, K., Ghandour, G., Mayer, R. A., Sun, B., Hsie, L., Robbins, C. M., Brody, L. C, Wang, D., Lander, E. S., Lipshutz, R., Foder, S. P. A., and Collins, F. S. (1999). Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 22, 164-167.
26. Hayes, B. J., Nilsen, K., Berg, P. R., Grindflek, E., and Lien, S. (2007). SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. Bioinformatics 23. 1692-1693.
27. Helyar, S. J., Hemmer-Hansen, J., Bekkevold, D., Taylor, M. I., Odgen, R., Limborg, M. T., Cariani, A., Maes, G. E., Diopere, E., Carvalho, G. R., and Nielsen, E. E. (2011). Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol. Resour. ll(Suppl. 1), 123-136.
28. Hubisz, M. J., Falush, D., Stephens, M., and Pritchard, J. K. (2009). Inferring weak population structure with the assistance of sampling group information. Mol Ecol Resour. 9, 1322-1332.
29. Ingman, M., and Gyllensten, U. (2009). SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur. J. Human Genet. 17,383-386.
30. Kern, A. D. (2009). Correcting the site frequency spectrum for divergence-based ascertainment. PLoS ONE 4, e5152. doi: 10.1371/journal.pone. 0005152
31. Kijas, J. W., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. E, McGrath, A., Wilson, P., Ingersoll, R. G., McCulloch, R., McWilliam, S., Tang, D., McEwan, J., Cockett, N., Hutton Oddy, V., Nicholas, F. W., and Raadsma, H., and for the International Sheep Genomics Consortium. (2009). A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE 4, e4668. doi: 10.1371/journal.pone. 0004668
32. Kim, K. S., Bagley, M. J., Coates, B. S., Hellmich, R. L., and Sappington, T. W. (2009). Spatial and temporal genetic analyses reveal high gene flow among European corn borer populations across the central US corn belt. Environ. Entomol 38, 1312-1323.
33. Kim, K. S., Coates, B. S., Hellmich, R. L., Sumerford, D. V., and Sappington, T. W. (2008). Isolation and characterization of microsatellite loci from the European corn borer, Ostrinia nubilalis (Hiibner) (Insecta: Lep-idoptera: Crambidae). Mol. Ecol. Resources 8, 409-411.
34. Kim, K. S., Coates, B. S., Hellmich, R. L, and Sappington, T. W. (2011). Genetic structure and gene flow among European corn borer populations from the Great Plains to New York. Agri. Forest Entomol doi: 10.1 lll/j.1461-9563.2011.00533.x
35. Klun, J. A. (1975). Insect sex pheromones: intraspecific pheromonal variability of Ostrinia nubilalis in North America and Europe. Environ. Entomol. 4, 891-894.
36. Kuhner, M. K., Beerli, P., Yamato, J., and Felsenstein, J. (2000). Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156, 439-447.
37. Lao, O., van Duijn, K., Kersbergen, P., de Knijff,P.,and Kayser, M. (2006). Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry. Am. J. Hum. Genet. 78, 680-690.
38. Malausa, T., Dalecky, A., Ponsard, S., Audiot, P., Streiff, R., Chaval, Y., and Bourguet, D. (2007). Genetic structure and gene flow in French populations of two Ostrinia taxa: host races or sibling species? Mol Ecol 16, 4210-4222.
39. Marulies, M., Egholm, M., Altman, W. E., Attiya, S., Dader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y. J., Chen, Z., Dewell, S. B., Du, L., Fierro, J. M., Gomes, X. V., Godwin, B. C, He, W., Helgesen, S., Ho, C. H., Irzyk, G. P., Jando, S. C, Alenquer, M. L., Jarvie, T. P., Jirage, K. B., Kim, J. B., Knight, J. R., Lanza, J. R., Leamon, J. H., Lefkowitz, S. M., Lei, M., Li, J., Lohman, K. L, Lu, H., Makhijani, V. B., McDade, K. E., McKenna, M. P., Myers, E. W., Nickerson, E., Nobile, J. R., Plant, R., Puc, B. P., Ronan, M. T., Roth, G. T., Sarkis, G. J., Simons, J. F., Simpson, J. W., Srinivasan, M., Tartaro, K. R., Tomasz, A., Vogt, K. A., Volkmer, G. A., Wang, S. H., Wang, Y., Weiner, M. P., Yu, P., Begley, R. E, and Rothberg, J. M. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.
40. Matukumalli, L. K., Lawley, C. T., Schn-abel, R. D., Taylor, J. E, Allan, M. E, Heaton, M. P., O'Connell, J., Moore, S. S., Smith, T. P. L., Son-stegard, T. S., and Van Tassell, C. P. (2009). Development and characterization of a high density SNP geno-typing assay for cattle. PLoS ONE 4, e5350. doi: 10.1371/journal.pone. 0005350
41. Meglecz, E., Petenian, E, Danchin, E., D'Acier, A. C, Rasplus, J. Y, and Faure, E. (2004). High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia. Mol. Ecol. 13, 1693-1700.
42. Monna, L., Ohta, R., Masuda, H., Koike, H., and Minobe, Y. (2006). Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.). DNA Res. 13, 43-51.
43. Morin, P. A., Luikart, G., Wayne, R. K., and SNP workshop group. (2004). SNPs in ecology, evolution and conservation. Trends Ecol Evol. (Amst.) 19,208-216.
44. Nielsen, R. (2000). Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154,931-942.
45. Nielsen, R., and Signorovitch, J. (2003). Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol 63, 245-255.
46. Novaes, E., Drost, D. R., Farmerie, W G., Pappas, G. J., Grattapaglia, D., Sederoff, R. R., and Kirst, M. (2008). High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9, 312. doi: 10.1186/1471-2164-9-312
47. Orsini, L., Wheat, C. W, Haag, C. R., Kvist, J., Frilander, M. J., Hanski, I. (2008). Fitness differences associated with Pgi SNP genoytpes in the Glanville fritillary butterfly (Meli-taea cinxia). J. Evol. Biol. 22, 367-375.
48. Paschou, P., Ziv, E., Burchard, E. G., Choudhry, S., Rodriquez-Cintron, W, Mahoney, M. W., and Drineas, P. (2007). PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genet. 3, 1672-1686. doi: 10.1371/journal.pgen.0030160
49. Pavy, N., Parsons, L. S., Paule, C, MacKay, J., and Bousquet, J. (2006). Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 6, 174. doi: 10.1186/1471-2164-7-174
50. Pemberton, J. M., Slate, J., Bancroft, D. R., and Barrett, J. A. (1995). Nonamplifying alleles at microsatellite loci - a caution for parentage and population studies. Mol Ecol 4, 249-252.
51. Pritchard, J. K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multi-locus genotype data. Genetics 155, 945-959.
52. Ronaghi, M., Uhlen, M., and Nyren, P. (1998). DNA sequencing: a sequencing method based on realtime pyrophosphate. Science 281, 363-365.
53. Simon, S. A., Zhai, J., Nandety, R. S., McCormick, K. P., Zeng, J., Mejai, D., and Meyers, B. C. (2009). Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol 60,305-333.
54. Sjogren, P., and Wyoni, P. I. (1994). Conservation genetics and detection of rare alleles in finite populations. Conserv. Biol 8, 267-270.
55. Slatkin, M. (1985). Rare alleles as indicators of gene flow. Evolution 39, 53-65.
56. Stadler, T., Haubold, B., Merino, C, Stephan, W, and Pfaffelhuber, P. (2009). The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182,205-216.
57. Swofford, D. L., and Berlocher, S. H. (1987). Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony. Syst. Zool 36, 293-325.
58. Tang, K., Fu, D. J., Julien, D., Braun, A., Cantor, C. R., and Koster, H. (1999). Chip-based genotyping by mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 96, 10016-10020.
59. Tautz, D. (1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl Acids Res. 17, 6463-6471.
60. Tay, W. T., Behere, G. T., Batterhan, P., and Heckel, D. G. (2010). Generation of microsatellite repeat families by RTE transposons in lepi-dopteran genomes. BMC Evol Biol 10, 144. doi: 10.1186/1471-2148-10-144
61. Tsuchihashi, Z., and Dracopoli, N. C. (2002). Progress in high throughput SNP genotyping methods. Pharma-cogenomicsj. 2,103-110.
62. Van't Hof, A. E., Brakefield, P. M., Saccheri, I. J., and Zwaan, B. J. (2007). Evolutionary dynamics of multilocus microsatellite arrangements in the genome of the butterfly Bicyclus anynana, with implications for other Lepidoptera. Heredity 98, 320-328.
63. Vera, J. C, Wheat, C. W, Fesce-myer, H. W, Frilander, M. J., Crawford, D. L., Hanski, I., and Mar-den, J. H. (2008). Rapid tran-scriptome characterization for a non-model organism using 454 pyrosequencing. Mol. Ecol. 17, 1636-1647.
64. Wanner, K. W., Nichols, A. S., Allen, J. E., Bunger, P. L., Garczynski, S. E, Lin, C. E., Robertson, H. M., and Luetje, C.W (2010). Sex pheromone receptor specificity in the European corn borer moth, Ostrinia nubilalis. PLoS ONE 5, e8685. doi: 10.1371/jour-nal.pone.0008685
65. Weber, J. L., and May, P. E. (1989). Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. AA, 388-396.
66. Wiedmann, R. T., Smith, T. P. L., and Nonneman, D. J. (2008). SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genomics 9, 81. doi: 10.1186/1471-2156-9-81
67. Williams, L. M., Ma, X., Boyko, A. R., Bustamante, C. D., and Olek-siak, M. E (2010). SNP identification, verification, and utility for population genetics in a non-model species. BMC Genomics 11, 32. doi: 10.1186/1471-2156-11-32
68. Wilson, A. F., and Sorant, A. J. (2000). Equivalence of single-and multilocus markers: power to detect linkage with composite markers derived from biallelic loci. Am. J. Hum. Genet. 66, 1610-1615.
69. Yamamoto, K., Narukawa, J., Kadono-Okuda, K., Nohata, J., Sasanuma, M., Suetsugu, Y., Banno, Y, Fujii, J., Goldsmith, M. R., and Mita, K. (2006). Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences. Genetics 173, 151-161.