Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens
Corresponding Author
M. L. Fritz
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Correspondence: Dr Megan L. Fritz, 112 Derieux Place, 1549 Thomas Hall, Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA. Tel.: + 1 (919) 515-1651; e-mail: [email protected]Search for more papers by this authorS. Paa
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorJ. Baltzegar
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorF. Gould
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorCorresponding Author
M. L. Fritz
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Correspondence: Dr Megan L. Fritz, 112 Derieux Place, 1549 Thomas Hall, Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA. Tel.: + 1 (919) 515-1651; e-mail: [email protected]Search for more papers by this authorS. Paa
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorJ. Baltzegar
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorF. Gould
Department of Entomology, North Carolina State University, Raleigh, NC, USA
Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
Search for more papers by this authorAbstract
Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bacillus thuringiensis (Bt) resistance. We developed 350-bp double-digest restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection and inbreeding in this nonmodel insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily a result of the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, in which more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing three PCR-based and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Overall, we have confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.
Supporting Information
Additional Supporting Information may be found in the online version of this article at the publisher's web-site:
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Figure S1. Read counts per individual, colour-coded by population. Individuals with read counts above (3×) and below (1/3×) the grey lines were excluded from downstream analyses. Figure S2. Plot of genome-wide average number of unique alleles (± 95% confidence intervals) across populations. Each data set, represented by a unique colour, contained different numbers of consensus loci. Haplotype sampling was set to a depth of either 6 (data not shown) or 12. Mean numbers of unique loci were not different across data sets within a population, as indicated by overlapping 95% confidence intervals. Figure S3. Number of reads per individual for the mapping family. Read counts for parents and progeny are in red and black, respectively. Figure S4. Number of markers per linkage group with a nucleotide diversity value (π) of greater than zero in the inbred line. Linkage groups retaining significantly more polymorphism than expected are: 2, 3, 7, 11, 14, 15, 16 and 29. Figure S5. Number of lineages that remained following each generation of full-sibling mating (orange) during production of the inbred line. The blue line represents the average number of single pair matings (SPMs) set up per generation across remaining lineages. Only a single lineage existed following generation 5, for which the blue line represents the number of SPMs set up for the existing line. Table S1. Multiple sets of consensus loci used to calculate population genetics parameters. Consensus sets of loci containing 125, 378 and 583 loci are subsets of the largest set containing 1231 loci. The mean and maximum numbers of alleles per marker reported represent summary statistics for the entire multi-population data set. Abbreviations: Bt-sel, Bacillus thuringiensis-selected; NS, nonselected. Table S2. Replicated G-test of independence used to examine whether clustering of polymorphic markers amongst the total mapped markers (n = 441) in the inbred line was more heterogeneous than would be expected by chance. An asterisk (*) indicates a statistically significant P-value relative to a Bonferroni adjusted alpha-value of 0.002. Table S3. High Purity Salt Free (HPSF)-purified oligonucleotide sequences (Eurofins MWG Operon Limited Liability Corporation (LLC), Huntsville, AL, USA) used to create uniquely barcoded double-stranded adapters with an EcoRI overhang site. Two oligonucleotides (p1.1 and p1.2) corresponding to the same barcode were annealed according to Poland et al. (2012) to generate each adapter. Table S4. HPSF-purified oligonucleotide sequences (Eurofins MWG Operon LLC, Huntsville, AL, USA) with an MspI overhang, and primers used to add Illumina indices to each ddRAD-seq library. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- Baeshen, R., Ekechukwu, N., Toure, M., Paton, D., Coulibaly, M., Traoré, S. et al. (2014) Differential effects of inbreeding and selection on male reproductive phenotype associated with the colonization and laboratory maintenance of Anopheles gambiae. Malar J 13: 19.
- Baxter, S.W., McMillan, O., Chamberlain, N., ffrench-Constant, R.H., Jiggins, C.D. (2009) Prospects for locating adaptive genes in lepidopteran genomes. In Molecular Biology and Genetics of the Lepidoptera ( M.R. Goldsmith and F Marec., eds), pp. 105–118. CRC Press, Boca Raton, FL.
-
Benjamini, Y. and
Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Methodol 57: 289–300.
10.1111/j.2517-6161.1995.tb02031.x Google Scholar
- Bi, K., Linderoth, T., Vanderpool, D., Good, J., Nielsen, R. and Moritz, C. (2013) Unlocking the vault: next-generation museum population genomics. Mol Ecol 22: 6018–6032.
- Blanco, C. (2012) Heliothis virescens and Bt cotton in the United States. GM Crops Food 3: 201–212.
-
Boller, E. (1972) Behavioral aspects of mass-rearing of insects. Entomophaga 17: 9–25.
10.1007/BF02371070 Google Scholar
- Catchen, J., Amores, A., Hohenlohe, P., Cresko, W., Postlethwait, J. and De Koning, D. (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 1: 171–182.
- Catchen, J., Hohenlohe, P., Bassham, S., Amores, A. and Cresko, W. (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22: 3124–3140.
- Charlesworth, B. and Charlesworth, D. (2010) Elements of Evolutionary Genetics. Roberts and Company Publishers, Greenwood, CO.
- Charlesworth, D. and Willis, J.H. (2009) The genetics of inbreeding depression. Nat Rev Genet 10: 783–796.
- Collard, B., Mace, E., McPhail, M., Wenzl, P., Cakir, M., Fox, G. et al. (2009) How accurate are the marker orders in crop linkage maps generated from large marker datasets? Crop Pasture Sci 60: 362–372.
- Collins, A.M. (1984) Artificial selection of desired characteristics in insects. In Advances and Challenges in Insect Rearing ( E.G. King and N.C Leppla., eds), pp. 9–19. USDA Technical Bulletin.
- Davey, J.W., Cezard, T., Fuentes-Utrilla, P., Eland, C., Gharbi, K. and Blaxter, M.L. (2012) Special features of RAD sequencing data: implications for genotyping. Mol Ecol 22: 3151–3164.
- Dekker, T., Ibba, I., Siju, K.P., Stensmyr, M.C. and Hansson, B.S. (2006) Olfactory shifts parallel superspecialism for toxic fruit in Drosophila melanogaster sibling, D. sechellia. Curr Biol 16: 101–109.
- Dobzhansky, T. and Spassky, N. (1954) Environmental modification of heterosis in Drosophila pseudoobscura. Proc Natl Acad Sci USA 40: 407–415.
- Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S. et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
-
Etzel, L.K. and
Legner, E.F. (1999) Culture and colonization. In Handbook of Biological Control ( T.S. Bellows and T.W Fisher., eds), pp. 125–176. Academic Press, San Diego, CA.
10.1016/B978-012257305-7/50054-0 Google Scholar
- Falconer, D.S. and Mackay T.F.C. (1996) Introduction to Quantitative Genetics, 4th edn. Longman Group Ltd. Essex, UK.
- Fox, C.W., Scheibly, K.L., Smith, B.P. and Wallin, W.G. (2007) Inbreeding depression in two seed-feeding beetles Callosobruchus maculatus and Stator limbatus (Coleoptera: Chrysomelidae). Bull Entomol Res 97: 49–54.
- Fritz, M.L., Walker, E.D., Miller, J.R., Severson, D.W. and Dworkin, I. (2015) Divergent host preferences of above- and below-ground Culex pipiens mosquitoes and their hybrid offspring. Med Vet Entomol 29: 115–123.
-
Fritz, M.L.,
Paa, S.,
Baltzegar, J. and
Gould, F. (2016) Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens. Dryad Digital Repository. doi:10.5061/dryad.567v8
10.5061/dryad.567v8 Google Scholar
- Gahan, L.J., Gould, F. and Heckel, D.G. (2001) Identification of a gene associated with Bt resistance in Heliothis virescens. Science 293: 857–860.
- Gahan, L.J., Gould, F., Lopez Jr., J.D., Micinski, S. and Heckel, D.G. (2007) A polymerase chain reaction screen of field populations of Heliothis virescens for a retrotransposon insertion conferring resistance to Bacillus thuringiensis. J Econ Entomol 100: 187–194.
- Gahan, L.J., Pauchet, Y., Vogel, H. and Heckel, D.G. (2010) An ABC transporter mutation is correlated with insect resistance to Bacillus thuringiensis Cry1Ac toxin. PLoS Genet 6: e1001248.
- Gerloff, C.U., Ottmer, B.K. and Schmid-Hempel, B. (2003) Effects of inbreeding on immune response and body size in a social insect, Bombus terrestris. Funct Ecol 17: 582–589.
- Goldman, I.F., Arnold, J. and Carlton, B.C. (1986) Selection for resistance to Bacillus thuringiensis subspecies israelensis in field and laboratory populations of the mosquito Aedes aegypti. J Invertebr Pathol 47: 317–324.
- Gordon, D., Abajian, C. and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195–202.
- Gould, F., Anderson, A., Reynolds, A., Bumgarner, L. and Moar, W. (1995) Selection and genetic analysis of a Heliothis virescens (Lepidoptera: Noctuidae) strain with high levels of resistance to Bacillus thuringiensis toxins. J Econ Entomol 88: 1545–1559.
- Groot, A., Gemeno, C., Brownie, C., Gould, F. and Schal, C. (2005) Male and female antennal responses in Heliothis virescens and H. subflexa to conspecific and heterospecific sex pheromone compounds. Environ Entomol 34: 256–263.
- Groot, A.T., Classen, A., Inglis, O., Blanco, C.A., Lopez, J., Teran Vargas, A. et al. (2011) Genetic differentiation across North America in the generalist moth Heliothis virescens and the specialist H. subflexa. Mol Ecol 20: 2676–2692.
- Hartl, D.L. and Clark, A.G. (2007) Principles of Population Genetics, 4th edn. Sinauer Associates, Inc., Sunderland, MA.
- Hoy, M.A. (1990) Genetic improvement of parasites and predators. FFTC-NARC International Seminar on 'The use of parasitoids and predators to control agricultural pests', Tukuha Science City, Ibaraki-ken, 305 Japan, October 2–7, 1989. pp. 15.
- Huettel, M.D. (1976) Monitoring the quality of laboratory-reared insects: a biological and behavioral perspective. Environ Entomol 5: 807–814.
- Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403–1405.
- Joyner, K. and Gould, F. (1985) Developmental consequences of cannibalism in Heliothis zea (Lepidoptera: Noctuidae). Ann Entomol Soc Am 78: 24–28.
- Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M. et al. (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384–1395.
- Keenan, K., McGinnity, P., Cross, T.F., Crozier, W.W. and Prodöhl, P.A. (2013) diveRsity: an R package for the estimation of population genetics parameters and their associated errors. Methods Ecol Evol 4: 782–788.
- Keller, L.F. and Waller, D.M. (2002) Inbreeding effects in wild populations. Trends Ecol Evol 17: 230–241.
- Kim, S.H., Cheng, K.M., Ritland, C., Ritland, K. and Silversides, F.G. (2007) Inbreeding in the Japanese quail estimated by pedigree and microsatellite analyses. J Hered 98: 378–381.
- Kosambi, D.D. (1944) The estimation of map distance from recombination values. Ann Eugenics 12: 172–175.
- Li, R., Li, Y., Fang, X., Yang, H., Wang, J., Kristiansen, K. et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124–1132.
- Mackauer, M. (1976) Genetic problems in the production of biological control agents. Annu Rev Entomol 21: 369–385.
- Mackay, T.F.C., Richards, S., Stone, E.A., Barbadilla, A., Ayroles, J.F., Zhu, D. et al. (2012) The Drosophila melanogaster genetic reference panel. Nature 482: 173–178.
- Magoc, T. and Salzberg, S. (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957–2963.
- Margarido, G.R.A., Souza, A.P. and Garcia, A.A.F. (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144: 78–79.
- Mita, K., Kasahara, M., Sasaki, S., Nagayasu, Y., Yamada, T., Kanamori, H. et al. (2004) The genome sequence of silkworm, Bombyx mori. DNA Res 11: 27–35.
- Mollinari, M., Margarido, G.R., Vencovsky, R. and Garcia, A.A. (2009) Evaluation of algorithms used to order markers on genetic maps. Heredity 103: 494–502.
- Mukhopadhyay, J., Rangel, E.F., Ghosh, K. and Munstermann, L.E. (1997) Patterns of genetic variability in colonized strains of Lutzomyia longipalpis (Diptera: Psychodidae) and its consequences. Am J Trop Med Hyg 57: 216–221.
- Munstermann, L.E. (1994) Unexpected genetic consequences of colonization and inbreeding: allozyme tracking in Culicidae (Diptera). Ann Entomol Soc Am 87: 157–164.
-
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
10.1111/j.1365-294X.2006.02908.x Google Scholar
- Nickerson, D.A., Tobe, V.O. and Taylor, S.L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 25: 2745–2751.
- Nielsen, R., Paul, J.S., Albrechtsen, A. and Song, Y.S. (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12: 443–451.
- Norris, D.E., Shurtleff, A.C., Toure, Y.T. and Lanzaro, G.C. (2001) Microsatellite DNA polymorphism and heterozygosity among field and laboratory populations of Anopheles gambiae s.s. (Diptera: Culicidae). J Med Entomol 38: 336–340.
- Oppenheim, S.J., Gould, F. and Hopper, K.R. (2012) The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa. Evolution 66: 3336–3351.
- Paradis, E. (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419–420.
- Paterson, A.H. (1996) Making genetic maps. In Genome Mapping in Plants ( A.H. Paterson, ed.), pp. 23–29. R. G. Landes Company, San Diego, CA.
- Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. and Hoekestra, H.E. (2012) Double digest RADseq: an inexpensive method of de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7: e37135.
- Poland, J.A., Brown, P.H., Sorrells, M.E. and 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: e32253.
- Pootakham, W., Jomchai, N., Ruang-areerate, P., Shearman, J.R., Sonthirod, C., Sangsrakru, D. et al. (2015) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 105: 288–295.
- Pradeep, A.R., Chatterjee, S.N. and Nair, C.V. (2005) Genetic differentiation induced by selection in an inbred population of the silkworm Bombyx mori, revealed by RAPD and ISSR marker systems. J Appl Genet 46: 291–298.
- R core team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
- Raulston, J.R. (1975) Tobacco budworm: observations on the laboratory adaptation of a wild strain. Ann Entomol Soc Am 68: 139–142.
- Roush, R.T. (1986) Inbreeding depression and laboratory adaptation in Heliothis virescens (Lepidoptera: Noctuidae). Ann Entomol Soc Am 79: 583–587.
- Rumball, W., Franklin, I., Frankham, R. and Sheldon, B. (1994) Decline in heterozygosity under full-sib and double first-cousin inbreeding in Drosophila melanogaster. Genetics 136: 1039–1049.
- Shaw, K.L. (2000) Interspecific genetics of mate recognition: inheritance of female acoustic preference in Hawaiian crickets. Evolution 54: 1303–1312.
- Sheck, A.L. and Gould, F. (1995) Genetic analysis of differences in oviposition preferences of Heliothis virescens and H. subflexa (Lepidoptera: Noctuidae). Environ Entomol 24: 341–347.
- Sheck, A.L. and Gould, F. (1996) The genetic basis of differences in growth and behavior of specialist and generalist herbivore species: selection on hybrids of Heliothis virescens and Heliothis subflexa (Lepidoptera). Evolution 50: 831–841.
- Sheck, A.L., Groot, A.T., Ward, C.M., Gemeno, C., Wang, J., Brownie, C. et al. (2006) Genetics of sex pheromone blend differences between Heliothis virescens and Heliothis subflexa: a chromosome mapping approach. J Evol Biol 19: 600–617.
- Singh, R., Tan, S.G., Panandam, J.M., Rahman, R.A., Ooi, L.C.L., Low, E.L. et al. (2009) Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm. BMC Plant Biol 9: 114.
- Sokal, R.R. and Rohlf, F.J. (1995) Biometry: The Principles and Practices of Statistics in Biological Research, 3rd edn. W.H. Freeman and Company, New York.
- Sokolowski, M.B. (1980) Foraging strategies of Drosophila melanogaster: a chromosomal analysis. Behav Genet 10: 291–302.
- Strimmer, K. (2008) fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics Appl 24: 1461–1462.
- Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
- Taylor, M.F.J., Heckel, D.G., Brown, T.M., Kreitman, M.E. and Black, G. (1993) Linkage of pyrethroid resistance to a sodium channel locus in the tobacco budworm. Insect Biochem Mol Biol 23: 763–775.
- Tomaru, M., Doi, M., Higuchi, H. and Oguma, Y. (2000) Courtship song recognition in the Drosophila melanogaster complex: heterospecific songs make females receptive in D. melanogaster, but not in D. sechellia. Evolution 54: 1286–1294.
- Turissini, D.A., Gamez, S. and White, B.J. (2014) Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito, Anopheles gambiae. Genome Biol Evol 6: 3094–3104.
- de Valdez, M.F.W., Nimmo, D., Betz, J., Gong, H.F., James, A.A., Alphey, L. et al. (2011) Genetic elimination of dengue vector mosquitoes. Proc Natl Acad Sci USA 108: 4772–4775.
- Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112: 30–40.
- Ward, M.D. (2009) Genetics of sex pheromones: mapping desaturase genes in Heliothis species. Master's Thesis, North Carolina State University, Raleigh, NC, USA.
- Watterson, G.A. (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256–276.
- Weir, B.S. and Cockerham, C.C. (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
- Xu, P., Xu, S., Wu, X., Tao, Y., Wang, B., Wang, S. et al. (2014) Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd. Plant J 77: 430–442.
- You, M., Yue, Z., He, W., Yang, X., Yang, G., Xie, M. et al. (2013) A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet 45: 220–225.
