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Inter-Simple Sequence Repeats (ISSR), Microsatellite-Primed Genomic Profiling Using Universal Primers

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2222))

Abstract

Inter-simple sequence repeat (ISSR) markers are highly polymorphic, relatively easy to develop, and inexpensive compared to other methods and have numerous applications. Importantly, the same ISSR primers can potentially be used universally across plant phylogenetic diversity. The basic technique of ISSRs is flexible and can be modified with options for implementation for a broad range of projects and budgets. Ranked in increasing order of technical demand and costs, these are manual agarose and manual polyacrylamide with silver staining and automated using fluorescently labeled primers and capillary electrophoresis. Overall manual agarose-based ISSRs are a sound, safe, easy, and low-cost method for reliably inferring plant genetic diversity. Here, we provide detailed protocols to undertake this fingerprinting method and provide guidance to the literature for the many options available for this technique.

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References

  1. Jeffreys AJ, Wilson V, Thein S (1985) Hypervariable “minisatellite” regions in human DNA. Nature 314:67–73

    Article  CAS  PubMed  Google Scholar 

  2. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 17:7213–7218

    Article  Google Scholar 

  3. Meyer W, Mitchell TG, Freedman EZ et al (1993) Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J Clin Microbiol 31:2274–2280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mullis KF, Faloona F, Scharf S et al (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273

    Article  CAS  PubMed  Google Scholar 

  5. Saiki RK, Gelfand DH, Stoffel S et al (1998) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    Article  Google Scholar 

  6. Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA finger- printing. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Zietkiewicz E, Rafalski A, Labuda D (1994) Genomic fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    Article  CAS  PubMed  Google Scholar 

  9. Gupta M, Chyi YS, Romero-Severson J et al (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89:998–1006

    Article  CAS  PubMed  Google Scholar 

  10. Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939–943

    Article  CAS  PubMed  Google Scholar 

  11. Hillis DM (1994) Homology in molecular biology. In: Hall BK (ed) Homology: the hierarchical basis of comparative biology. Academic Press, London

    Google Scholar 

  12. Dowling TE, Moritz C, Palmer JD et al (1996) Nucleic acids III: analysis of fragments and restriction sites. In: Hillis DM, Mortiz C, Mable BK (eds) Molecular systematics. Sinauer Associates Inc, Sunderland

    Google Scholar 

  13. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Molec Ecol 3:91–99

    Article  CAS  Google Scholar 

  14. Bussell JD, Waycott M, Chappill JA (2005) Arbitrarily amplified DNA markers as characters for phylogenetic analyses. Perspect Plant Ecol Evol Syst 7:3–16

    Article  Google Scholar 

  15. Ganie SH, Upadhyay P, Das S et al (2015) Authentication of medicinal plants by DNA markers. Plant Gene 4:83–99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Goodwin ID, Aitkin EAB, Smith LW (1997) Application of inter simple sequence repeat markers (ISSR) to plant genetics. Electrophoresis 18:1524–1528

    Article  Google Scholar 

  17. Grover A, Sharma PC (2016) Development and use of molecular markers: past and present. Crit Rev Biotechnol 36:290–302. https://doi.org/10.3109/07388551.2014.959891

    Article  CAS  PubMed  Google Scholar 

  18. Kuluev BR, AnKh B, Gerashchenkov GA et al (2018) Random priming PCR strategies for identification of multilocus DNA polymorphism in eukaryotes. Russ J Genet 54:499–513

    Article  CAS  Google Scholar 

  19. Nadeem MA, Nawaz MA, Shahid MQ et al (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32:261–285. https://doi.org/10.1080/13102818.2017.1400401

    Article  CAS  Google Scholar 

  20. Reddy MP, Sarla N, Siddiq EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128:9–17

    Article  Google Scholar 

  21. Stevens MI, Clarke AC, Clarkson FM et al (2015) Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from māhoe (Melicytus ramiflorus). New Zeal J Ecol 39:190–197

    Google Scholar 

  22. Tamboli AS, Yadav PB, Gothe AA et al (2018) Molecular phylogeny and genetic diversity of genus Capparis (Capparaceae) based on plastid DNA sequences and ISSR markers. Plant Syst Evol 304:205–217

    Article  CAS  Google Scholar 

  23. Wolfe A, Liston A (1998) Contributions of PCR-based methods to plant systematics and evolutionary biology. In: Soltis DE, Soltis PS, Doyle JJ (eds) Plant molecular systematics II. Kluwer Academic Publishers, Boston. https://doi.org/10.1007/978-1-4615-5419-6

    Chapter  Google Scholar 

  24. Wu Y, Yang DY, Tu PF et al (2011) Genetic differentiation induced by spaceflight treatment of Cistanche deserticola and identification of inter-simple sequence repeat markers associated with its medicinal constituent contents. Adv Space Res 47:591–599

    Article  CAS  Google Scholar 

  25. Kumar A, Mishra P, Baskaran K et al (2016) Higher efficiency of ISSR markers over plasmid psbA-trnH region in resolving taxonomical status of genus Ocimum L. Ecol Evol 6:7671–7682

    Article  PubMed  PubMed Central  Google Scholar 

  26. Savelkoul PH, Aarts HJ, de Haas J et al (1999) Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37:3083–3091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Bornet B, Branchard M (2001) Nonanchored inter simple sequence repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant Mol Biol Rep 19:209–215

    Article  CAS  Google Scholar 

  28. Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5:69–76

    Article  CAS  PubMed  Google Scholar 

  29. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  30. Deng Q, Deng Q, Liu L et al (2019) DNA extraction and optimization of ISSR-PCR reaction system for Pyracantha. IOP Conf Ser Earth Environ Sci 237:052025. https://doi.org/10.1088/1755-1315/237/5/052025

    Article  Google Scholar 

  31. Mondal A, Pal T, De KK (2018) Fluorescent inter simple sequence repeat (F-ISSR) markers and capillary electrophoresis to assess genetic diversity and relatedness within commercial sugarcane varieties. Int J Agric Technol 14:717–730

    CAS  Google Scholar 

  32. Stevens MI, Hunger SA, Hills SFK et al (2007) Phantom hitch-hikers mislead estimates of genetic variation in Antarctic mosses. Plant Syst Evol 263:191–201

    Article  Google Scholar 

  33. Camacho FJ, Gernandt DS, Liston A et al (1997) Endophytic fungal DNA, the source of contamination in spruce needle DNA. Mol Ecol 6:983–987

    Article  CAS  Google Scholar 

  34. Smith DE, Klein AS (1996) Erratum. Mol Phylogenet Evol 5:286–287

    Article  Google Scholar 

  35. White TJ, Bruns T, Lee S et al (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ et al (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego

    Google Scholar 

  36. Baldwin BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Mol Phylogenet Evol 1:3–16

    Article  CAS  PubMed  Google Scholar 

  37. Archibald JK, Mort ME, Crawford DJ et al (2006a) The utility of automated analysis of inter-simple sequence repeat (ISSR) loci for resolving relationships in the Canary Island species of Tolpis (Asteraceae). Am J Bot 93:1154–1162

    Article  CAS  PubMed  Google Scholar 

  38. Archibald JK, Mort ME, Crawford DJ et al (2006b) Evolutionary relationships within recently radiated taxa: comments on methodology and analysis of inter-simple sequence repeat data and other hypervariable, dominant markers. Taxon 55:747–756

    Article  Google Scholar 

  39. Arens P, Odinot P, van Heusden AW et al (1995) GATA and GACA repeats are not evenly distributed throughout the tomato genome. Genome 38:84–90

    Article  CAS  PubMed  Google Scholar 

  40. Prince LM (2015) Plant genotyping using fluorescently tagged inter-simple sequence repeats (ISSRs): basic principles and methodology. In: Batley J (ed) Plant genotyping. Methods in molecular biology (methods and protocols), vol 1245. Humana Press, New York

    Google Scholar 

  41. Oliveira EC, Amaral Júnior AT, LSA G et al (2010) Optimizing the efficiency of the touchdown technique for detecting inter-simple sequence repeat markers in corn (Zea mays). Genet Mol Res 9:835–842

    Article  CAS  PubMed  Google Scholar 

  42. Goulao LF, Oliveira CM (2014) Multilocus profiling with AFLP, ISSR, and SAMPL. In: Besse P (ed) Molecular plant taxonomy, methods and protocols. Humana Press, New York

    Google Scholar 

  43. Prince LM (2009) The relationship of Monardella viminea to closely related taxa based on analyses of ISSRs. USFWS Report P0750003

    Google Scholar 

  44. Applied Biosystems (2010) Application Note, ISSR Plant Genotyping. Publication 106AP31-01. Life Technologies Corporation, USA. http://tools.invitrogen.com/content/sfs/brochures/cms_079244.pdf

  45. Somasundaram SM, Subbaraya U, Durairajan SG et al (2019) Comparison of two different electrophoretic methods in studying the genetic diversity among plantains (Musa spp.) using ISSR markers. Electrophoresis 40:1265–1272

    Article  CAS  Google Scholar 

  46. Liu B, Wendel JF (2001) Inter simple sequence repeat (ISSR) polymorphisms as a genetic marker system in cot ton. Molec Ecol Notes 1:205–208

    Article  CAS  Google Scholar 

  47. Barth S, Melchinger AE, Lübberstedt T (2002) Genetic diversity in Arabidopsis thaliana L. Heynh. Investigated by cleaved amplified polymorphic sequence (CAPS) and inter-simple sequence repeat (ISSR) markers. Mol Ecol 11:495–505

    Article  CAS  PubMed  Google Scholar 

  48. Grierson ERP (2014) The Development and Genetic Variation of Sophora prostrata—A New Zealand divaricating shrub. Unpublished MSc Thesis, University of Waikato

    Google Scholar 

  49. Crawford DJ, Mort ME (2004) Single-locus molecular markers for inferring relationships at lower taxonomic levels: observations and comments. Taxon 53:631–635

    Article  Google Scholar 

  50. Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26:297–302

    Article  Google Scholar 

  51. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Hollingsworth PM, Ennos RA (2004) Neighbour joining trees, dominant markers and population genetic structure. Heredity 92:490–449

    Article  CAS  PubMed  Google Scholar 

  53. Nelson MF, Anderson NO (2013) How many marker loci are necessary? Analysis of dominant marker data sets using two popular population genetic algorithms. Ecol Evol 3:3455–3470. https://doi.org/10.1002/ece3.725

    Article  PubMed  PubMed Central  Google Scholar 

  54. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50

    CAS  Google Scholar 

  56. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Porras-Hurtado L, Ruiz Y, Santos C et al (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 4:98. https://doi.org/10.3389/fgene.2013.00098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Wolfe AD (2005) ISSR techniques for evolutionary biology. Methods Enzymol 395:134–144. https://doi.org/10.1016/S0076-6879(05)95009-X

    Article  CAS  PubMed  Google Scholar 

  60. Gemmill CEC, Allan GJ, Wagner WL et al (2002) Evolution of insular pacific Pittosporum (Pittosporaceae): origin of the Hawaiian radiation. Mol Phylogenet Evol 22:31–42

    Article  CAS  PubMed  Google Scholar 

  61. Carter SN, Miller S, Meyer SJ et al (2018) A new species of Pittosporum described from the poor Knights Islands, northland, Aotearoa/New Zealand. Syst Bot 43:633–643. https://doi.org/10.1600/036364418X697355

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. School of Science, University of Waikato, Hamilton, New Zealand

    Chrissen E. C. Gemmill

  2. Plant & Food Research, Palmerston North, New Zealand

    Ella R. P. Grierson

Authors
  1. Chrissen E. C. Gemmill
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  2. Ella R. P. Grierson
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Corresponding author

Correspondence to Chrissen E. C. Gemmill .

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Editors and Affiliations

  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

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Gemmill, C.E.C., Grierson, E.R.P. (2021). Inter-Simple Sequence Repeats (ISSR), Microsatellite-Primed Genomic Profiling Using Universal Primers. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_14

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  • DOI: https://doi.org/10.1007/978-1-0716-0997-2_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0996-5

  • Online ISBN: 978-1-0716-0997-2

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