Skip to main content

Microsatellites: Evolution and Contribution

  • Protocol
  • First Online:
Microsatellites

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1006))

Abstract

Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Armour J et al (1999) Minisatellites and mutation processes in tandemly repetitive DNA. Oxford University Press, Oxford

    Google Scholar 

  2. Hancock JM (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. Oxford University Press, Oxford

    Google Scholar 

  3. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401

    PubMed  CAS  Google Scholar 

  4. Tautz D (1989) Hypervariabflity of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    Article  PubMed  CAS  Google Scholar 

  5. McDonald DB, Potts WK (1997) DNA microsatellites as genetic markers for several scales. Academic, New York

    Google Scholar 

  6. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    Article  PubMed  CAS  Google Scholar 

  7. Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J Hered 88:335–342

    Article  PubMed  CAS  Google Scholar 

  8. Schlötterer C (1998) Microsatellites. IRL, Oxford

    Google Scholar 

  9. Queller DC et al (1993) Microsatellites and kinship. Trends Ecol Evol 8:285–288

    Article  PubMed  CAS  Google Scholar 

  10. Sonah H et al (2011) Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 6:e21298

    Article  PubMed  CAS  Google Scholar 

  11. Kelkar YD et al (2011) A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res 21:2038–2048

    Article  PubMed  CAS  Google Scholar 

  12. Nadir E et al (1996) Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proc Natl Acad Sci 93:6470–6475

    Article  PubMed  CAS  Google Scholar 

  13. Morgante M et al (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  PubMed  CAS  Google Scholar 

  14. Temnykh S et al (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  15. Weber J, May P (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396

    PubMed  CAS  Google Scholar 

  16. Milbourne D et al (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245

    Article  PubMed  CAS  Google Scholar 

  17. Sharopova N et al (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481

    Article  PubMed  CAS  Google Scholar 

  18. Song QJ et al (2002) Characterization of trinucleotide SSR motifs in wheat. Theor Appl Genet 104:286–293

    Article  PubMed  CAS  Google Scholar 

  19. Temnykh S et al (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  20. Crow J (1993) How much do we know about spontaneous human mutation rates? Environ Mol Mutagen 21:122–129

    Article  PubMed  CAS  Google Scholar 

  21. Zhu Y et al (2000) A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol 50:324–338

    PubMed  CAS  Google Scholar 

  22. Ellegren H (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet 16:551–558

    Article  PubMed  CAS  Google Scholar 

  23. Jin L et al (1996) Mutation rate varies among alleles at a microsatellite locus:Phylogenetic evidence. Proc Natl Acad Sci 93:15285–15288

    Article  PubMed  CAS  Google Scholar 

  24. Tachida H, Iizuka M (1992) Persistence of repeated sequences that evolve by replication slippage. Genetics 131:471–478

    PubMed  CAS  Google Scholar 

  25. Tautz D, Schlötterer C (1994) Simple sequences. Curr Opin Genet Dev 4:832–837

    Article  PubMed  CAS  Google Scholar 

  26. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2:1123–1128

    Article  PubMed  CAS  Google Scholar 

  27. Harding RM et al (1992) The evolution of tandemly repetitive DNA: recombination rules. Genetics 132:847–859

    PubMed  CAS  Google Scholar 

  28. Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221

    PubMed  CAS  Google Scholar 

  29. Eisen J (1999) Mechanistic basis for microsatellite instability. Oxford University Press, Oxford

    Google Scholar 

  30. Brohede J, Ellegren H (1999) Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences. Proc Biol Sci 266:825–833

    Article  PubMed  CAS  Google Scholar 

  31. Goldstein D, Schlotterer C (1999) Microsatellites, evolution and applications. Oxford University Press, Oxford

    Google Scholar 

  32. Jakupciak JP, Wells RD (1999) Genetic instabilities in (CTGΒ  ·  CAG) repeats occur by recombination. J Biol Chem 274:23468–23479

    Article  PubMed  CAS  Google Scholar 

  33. Richard GF, Paques F (2000) Mini- and microsatellite expansions: the recombination connection. EMBO Rep 1:122–126

    Article  PubMed  CAS  Google Scholar 

  34. Charlesworth B et al (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220

    Article  PubMed  CAS  Google Scholar 

  35. Bruford M et al (1996) Microsatellites and their application to conservation genetics. Oxford University Press, Oxford

    Google Scholar 

  36. Kostia S et al (1995) Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244–1248

    Article  PubMed  CAS  Google Scholar 

  37. Röder MS et al (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333

    Article  PubMed  Google Scholar 

  38. Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977–983

    Article  PubMed  CAS  Google Scholar 

  39. Gupta PK et al (1999) Molecular markers and their applications in wheat breeding. Plant Breed 118:369–390

    Article  CAS  Google Scholar 

  40. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome Nature 436:793–800

    Google Scholar 

  41. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11:424–429

    Article  PubMed  CAS  Google Scholar 

  42. Eujayl I et al (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422

    Article  PubMed  CAS  Google Scholar 

  43. Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25

    Article  CAS  Google Scholar 

  44. Thiel TT et al (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  45. Chapman M et al (2009) Development, polymorphism, and cross-taxon utility of EST–SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet 120:85–91

    Article  PubMed  CAS  Google Scholar 

  46. Choudhary S et al (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608

    Article  PubMed  CAS  Google Scholar 

  47. Gadaleta A et al (2010) Development and characterization of EST-derived SSRs from a ‘totipotent’ cDNA library of durum wheat. Plant Breed 129:715–717

    Article  CAS  Google Scholar 

  48. Nunome T et al (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet 119:1143–1153

    Article  PubMed  Google Scholar 

  49. Wei W et al (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451

    Article  PubMed  CAS  Google Scholar 

  50. Chabane K et al (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Resour Crop Evol 52:903–909

    Article  CAS  Google Scholar 

  51. Cho YG et al (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  52. Eujayl I et al (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS. Euphytica 119:39–43

    Article  CAS  Google Scholar 

  53. Scott KD et al (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  54. Gupta PK et al (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  PubMed  CAS  Google Scholar 

  55. Wilhelm J et al (2003) Validation of an algorithm for automatic quantification of nucleic acid copy numbers by real-time polymerase chain reaction. Anal Biochem 317:218–225

    Article  PubMed  CAS  Google Scholar 

  56. Wittwer CT (2009) High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 30:857–859

    Article  PubMed  CAS  Google Scholar 

  57. Vossen RHAM et al (2009) High-resolution melting analysis (HRMA)—more than just sequence variant screening. Hum Mutat 30:860–866

    Article  PubMed  CAS  Google Scholar 

  58. Wittwer CT et al (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49:853–860

    Article  PubMed  CAS  Google Scholar 

  59. Stephens AJ et al (2008) High-resolution melting analysis of the spa repeat region of Staphylococcus aureus. Clin Chem 54:432–436

    Article  PubMed  CAS  Google Scholar 

  60. Tindall EA et al (2009) Assessing high-resolution melt curve analysis for accurate detection of gene variants in complex DNA fragments. Hum Mutat 30:876–883

    Article  PubMed  CAS  Google Scholar 

  61. Mackay JF et al (2008) A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Meth 4:8

    Article  Google Scholar 

  62. Wu SB et al (2008) High resolution melting analysis of almond SNPs derived from ESTs. Theor Appl Genet 118:1–14

    Article  PubMed  CAS  Google Scholar 

  63. Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50:1748–1754

    Article  PubMed  CAS  Google Scholar 

  64. Smith BL et al (2010) High-resolution melting analysis (HRMA): a highly sensitive inexpensive genotyping alternative for population studies. Mol Ecol Resour 10:193–196

    Article  PubMed  CAS  Google Scholar 

  65. Bosmali I et al (2012) Microsatellite and DNA-barcode regions typing combined with high resolution melting (HRM) analysis for food forensic uses: a case study on lentils (Lens culinaris). Food Res Int 46:141–147

    Article  CAS  Google Scholar 

  66. Ganopoulos I et al (2011) Adulterations in Basmati rice detected quantitatively by combined use of microsatellite and fragrance typing with high resolution melting (HRM) analysis. Food Chem 129:652–659

    Article  CAS  Google Scholar 

  67. Ganopoulos I et al (2011) Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products. Food Contr 22:532–541

    Article  CAS  Google Scholar 

  68. Ganopoulos I et al (2012) Microsatellite genotyping with HRM (high resolution melting) analysis for identification of the PGI common bean variety Plake Megalosperma Prespon. Eur Food Res Tech 234:501–508

    Article  CAS  Google Scholar 

  69. Mader E et al (2008) A strategy to setup codominant microsatellite analysis for high-resolution-melting-curve-analysis (HRM). BMC Genet 9:69

    Article  PubMed  Google Scholar 

  70. Reed GH et al (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8:597–608

    Article  PubMed  CAS  Google Scholar 

  71. Powell W et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  72. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  73. Joshi SP et al (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240

    CAS  Google Scholar 

  74. Provan J et al (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147

    Article  PubMed  Google Scholar 

  75. Neeraja C et al (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776

    Article  PubMed  CAS  Google Scholar 

  76. Kalia R et al (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  77. Wang M et al (2009) Microsatellite markers in plants and insects. Part I: applications of ­biotechnology. Genes Genomes Genomics 3:54–67

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Madesis, P., Ganopoulos, I., Tsaftaris, A. (2013). Microsatellites: Evolution and Contribution. In: Kantartzi, S. (eds) Microsatellites. Methods in Molecular Biology, vol 1006. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-389-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-389-3_1

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-388-6

  • Online ISBN: 978-1-62703-389-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics