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SNP Arrays for Species Identification in Salmonids

  • Roman WenneEmail author
  • Agata Drywa
  • Matthew Kent
  • Kristil Kindem Sundsaasen
  • Sigbjørn Lien
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1452)

Abstract

The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper.

Key words

SNP array Salmon Genotyping Brown trout Rainbow trout 

Notes

Acknowledgements

This work was partially funded from statutory topic IV.1. in the Institute of Oceanology PAS and project No. 397/N-cGRASP/2009/0 of the Ministry of Science and Higher Education in Poland to R.W.

References

  1. 1.
    Bourret V, Kent MP, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Varspoor E, Bernatchez L, Lien S (2013) SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Mol Ecol 22(3):532–551. doi: 10.1111/mec.12003 CrossRefPubMedGoogle Scholar
  2. 2.
    Kochzius M, Nölte M, Weber H, Silkenbeumer N, Hjörleifsdottir S, Hreggvidsson GO, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Garcia VE, Turan C, Hervet C, Campo FD, Antoniou A, Landi M, Blohm D (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10(2):207–217. doi: 10.1007/s10126-007-9068-3 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Martinsohn JT, Ogden R (2009) FishPopTrace Consortium. FishPopTrace—developing SNP-based population genetic assignment methods to investigate illegal fishing. Forensic Sci Int-Gen 2(1):294–296. doi: 10.1016/j.fsigss.2009.08.108 CrossRefGoogle Scholar
  4. 4.
    Dominik S, Henshall JM, Kube PD, King H, Lien S, Kent MP, Elliott NG (2010) Evaluation of an Atlantic salmon SNP chip as a genomic tool for the application in a Tasmanian Atlantic salmon (Salmo salar) breeding population. Aquaculture 308(Suppl 1):56–61. doi: 10.1016/j.aquaculture.2010.05.038 CrossRefGoogle Scholar
  5. 5.
    Gidskehaug L, Kent M, Hayes BJ, Lien S (2011) Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics 27(3):303–310. doi: 10.1093/bioinformatics/btq673 CrossRefPubMedGoogle Scholar
  6. 6.
    Karlsson S, Moen T, Lien S, Glover KA, Hindar K (2011) Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip. Mol Ecol Res 11(Suppl 1):247–253. doi: 10.1111/j.1755-0998.2010.02959.x CrossRefGoogle Scholar
  7. 7.
    Lien S, Gidskehaug L, Moen T, Hayes BJ, Berg PR, Davidson WS, Omholt SW, Kent MP (2011) A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homologies and striking differences in sex-specific recombination patterns. BMC Genomics 12:615–625. doi: 10.1186/1471-2164-12-615 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Brenna-Hansen S, Jieying I, Kent PM, Boulding EG, Domink S, Davidson WS, Lien S (2012) Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis. BMC Genomics 13:432–444. doi: 10.1186/1471-2164-13-432 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Gutierrez AP, Lubieniecki KP, Davidson EA, Lien S, Kent MP, Fukui S, Withler RE, Davidson WS (2012) Genetic mapping of quantitative trait loci (QTL) for body-weight in Atlantic salmon (Salmo salar) using a 6.5 K SNP array. Aquaculture 358–359:61–70. doi: 10.1016/j.aquaculture.2012.06.017 CrossRefGoogle Scholar
  10. 10.
    Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä J-P, Vasemägi A, Primmer CR (2013) Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar). BMC Genomics 14:439–451. doi: 10.1186/1471-2164-14-439 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Perrier C, Bourret V, Kent MP, Bernatchez L (2013) Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon. Mol Ecol 22(22):5577–5593. doi: 10.1111/mec.12500 CrossRefPubMedGoogle Scholar
  12. 12.
    Bourret V, Dionne M, Kent MP, Lien S, Bernatchez L (2013) Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation. Evolution 67(12):3469–3487. doi: 10.1111/evo.12139 CrossRefGoogle Scholar
  13. 13.
    Ozerov M, Vasemägi A, Wennevik V, Niemelä E, Prusov S, Kent MP, Vähä J-P (2013) Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.). BMC Genomics 14:12–23. doi: 10.1186/1471-2164-14-12 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Glover KA, Pertoldi C, Besnier F, Wennevik V, Kent MP, Skaala Ø (2013) Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs. BMC Genet 14:74–92. doi: 10.1186/1471-2156-14-74 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Sodeland M, Gaarder M, Moen T, Thomassen M, Kjøglum S, Kent M, Lien S (2013) Genome-wide association testing reveals quantitative trait loci for fillet texture and fat content in Atlantic salmon. Aquaculture 408–409:169–174. doi: 10.1016/j.aquaculture.2013.05.029 CrossRefGoogle Scholar
  16. 16.
    Johnston SE, Orell P, Pritchard VL, Kent MP, Lien S, Niemelä E, Erkinaro J, Primmer CR (2014) Genome-wide SNP analysis reveals a genetic basis for sea–age variation in a wild population of Atlantic salmon (Salmo salar). Mol Ecol 23(14):3452–3468. doi: 10.1111/mec.12832 CrossRefPubMedGoogle Scholar
  17. 17.
    Sandlund OT, Karlsson S, Thorstad EB, Berg OK, Kent MP, Norum ICJ, Hindar K (2014) Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation. Ecol Evol 4(9):1538–1554. doi: 10.1002/ece3.1040 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Zueva KJ, Lumme J, Veselov AE, Kent MP, Lien S, Primmer CR (2014) Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution? PLoS One 9(3), e91672. doi: 10.1371/journal.pone.0091672 CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Shen R, Fan JB, Campbell D, Chang WH, Chen J, Doucet D, Yeakley J, Bibikova M, Garcia EW, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A (2005) High-throughput SNP genotyping on universal bead arrays. Mutat Res 573(1-2):70–82. doi: 10.1016/j.mrfmmm.2004.07.022 CrossRefPubMedGoogle Scholar
  20. 20.
    Steemers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArray™ platform. Biotechnol J 2(1):41–49. doi: 10.1002/biot.200600213 CrossRefPubMedGoogle Scholar
  21. 21.
    Smith MJ, Pascal CE, Grauvogel Z, Habicht C, Seeb JE, Seeb LW (2011) Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales. Mol Ecol Resour 11(Suppl 1):268–277. doi: 10.1111/j.1755-0998.2010.02965.x CrossRefPubMedGoogle Scholar
  22. 22.
  23. 23.
    Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen MM, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, Mcbride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69–78. doi: 10.1101/sqb.2003.68.69 CrossRefPubMedGoogle Scholar
  24. 24.
    Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32:56–61Google Scholar
  25. 25.
    Illumina (2010) Infinium genotyping data analysis. Technical Note: Illumina DNA analysis. Publication Number 970-2007-005, January 2010Google Scholar
  26. 26.
    Guo SW, Thompson NEA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372CrossRefPubMedGoogle Scholar
  27. 27.
    Slatkin M, Voelm L (1991) FST in a hierarchical island model. Genetics 127(3):627–629PubMedPubMedCentralGoogle Scholar
  28. 28.
    Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567. doi: 10.1111/j.1755-0998.2010.02847.x CrossRefPubMedGoogle Scholar
  29. 29.
    Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370CrossRefGoogle Scholar
  30. 30.
    Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Press, Sunderland, MA, 376 ppGoogle Scholar
  31. 31.
    Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x CrossRefPubMedGoogle Scholar
  32. 32.
    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentralGoogle Scholar
  33. 33.
    Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. doi: 10.1007/s12686-011-9548-7 CrossRefGoogle Scholar
  34. 34.
    Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2000) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171. 1996–2004. Université de Montpellier II, MontpellierGoogle Scholar
  35. 35.
    Benzécri JP (1992) Correspondence analysis handbook. Statistics, textbooks and monographs, Vol 225. Marcel Dekker, New York, NY, p 688Google Scholar
  36. 36.
    Kalinowski ST, Manlove KR, Taper ML (2007) ONCOR: a computer program for genetic stock identification. Department of Ecology, Montana State University, Bozeman, MT, http://www.montana.edu/kalinowski/Software/ONCOR.htm
  37. 37.
    Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci U S A 94(17):9197–9201CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Drywa A, Poćwierz-Kotus A, Dobosz S, Kent MP, Lien S, Wenne R (2014) Identification of multiple diagnostic SNP loci for differentiation of three salmonid species using SNP-arrays. Mar Genomics 15:5–6. doi: 10.1016/j.margen.2014.03.003 CrossRefPubMedGoogle Scholar
  39. 39.
    Drywa A, Poćwierz-Kotus A, Wąs A, Dobosz S, Kent MP, Lien S, Bernaś R, Wenne R (2013) Genotyping of two populations of Southern Baltic sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array. Mar Genomics 9:25–32. doi: 10.1016/j.margen.2012.08.001 CrossRefPubMedGoogle Scholar
  40. 40.
    Poćwierz-Kotus A, Bernaś R, Dębowski P, Kent MP, Lien S, Kesler M, Titov S, Leliuna E, Jespersen H, Drywa A, Wenne R (2014) Genetic differentiation of southeast Baltic populations of sea trout inferred from single nucleotide polymorphisms. Anim Genet 45(1):96–104. doi: 10.1111/age.12095 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Roman Wenne
    • 1
    Email author
  • Agata Drywa
    • 1
  • Matthew Kent
    • 2
  • Kristil Kindem Sundsaasen
    • 2
  • Sigbjørn Lien
    • 2
  1. 1.Institute of OceanologyPolish Academy of SciencesSopotPoland
  2. 2.Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHANorwegian University of Life Sciences, NMBUÅsNorway

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