Skip to main content
Springer Nature Link
Log in

SSR markers: a tool for species identification in Psidium (Myrtaceae)

  • Short Communication
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  1. Barbará T, Palma-Silva C, Paggi GM, Bered F, Fay MF, Lexer C (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 16(18):3759–3767. doi:10.1111/j.1365-294X.2007.03439.x

    Article  PubMed  Google Scholar 

  2. Barroso GM, Peixoto AL, Ichaso CLF, Costa CG, Guimarães EF, Lima HC (1991) Myrtaceae. In: Sistemática de Angiospermas do Brasil. Viçosa. v. 2. Ed.: Univ. Fed. Viçosa. pp 114–126

  3. Barroso GM, Peixoto AL, Ichaso CLF, Costa CG, Guimarães EF, Lima HC (1991) Myrtaceae. In: Sistemática de Angiospermas do Brasil. Viçosa. v.2 Ed.: Univ. Fed. Viçosa

  4. Barthe S, Gugerli F, Barkley NA, Maggia L, Cardi C, Scotti I (2012) Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. PLoS ONE 7:e40699

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Bérubé Y, Ritland C, Ritland K (2003) Isolation, characterization, and cross-species utility of microsatellites in yellow cedar (Chamaecyparis nootkatensis). Genome 46:353–361

    Article  PubMed  Google Scholar 

  6. Bhargava A, Fuentes FF (2010) Mutational dynamics of microsatellites. Mol Biotechnol 44:250–266

    Article  CAS  PubMed  Google Scholar 

  7. Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theor Appl Genet 97:816–827

    Article  CAS  Google Scholar 

  8. Buschiazzo E, Gemmell NJ (2010) Conservation of human microsatellites across 450 million years of evolution. Genome Biol Evol 2:153–165

    Article  PubMed Central  PubMed  Google Scholar 

  9. da Costa IR, Forni-martins ER (2006) Chromosome studies in Brazilian species of Campomanesia Ruiz & Pávon and Psidium L. (Myrtaceae Juss.). Caryologia 59(1):7–13

    Article  Google Scholar 

  10. Cruz CD (2013) Genes—a software package for analysis in experimental statistics and quantitative genetics. Acta Sci 35(3):271–276

    Google Scholar 

  11. Curtu AL, Finkeldey R, Gailing O (2004) Comparative sequencing of a microsatellite locus reveals size homoplasy within and between European oak species (Quercus spp.). Plant Mol Biol Report 22:339–346

    Article  CAS  Google Scholar 

  12. Dayanandan S, Bawa KS, Kesseli R (1997) Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 84:1658–1663

    Article  CAS  PubMed  Google Scholar 

  13. Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IRK, Horsburgh GJ, Burke T (2013) High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 14:176

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:1213–1215

    Google Scholar 

  15. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445

    Article  CAS  PubMed  Google Scholar 

  16. Gaiotto FA, Grattapaglia D, Vencovsky R (2003) Genetic structure mating system and long-distance gene flow in heart of palm (Euterpe edulis Mart.). J Hered 94(5):399–406

    Article  CAS  PubMed  Google Scholar 

  17. Guavamap (2008) Improvement of Guava: Linkage mapping and QTL analysis as a basisfor marker-assisted selection. Available on: <http://www.neiker.net/neiker/guavamap/>Accessed 04 Apr 2015

  18. Gürcan K, Mehlenbacher SA (2010) Transferability of Microsatellite Markers in the Betulaceae. J Am Soc Hortic Sci 135(2):159–173

    Google Scholar 

  19. Hansson B, Westerberg L (2002) On the correlation between heterozygosity and fitness in natural populations. Mol Ecol 11:2467–2474

    Article  PubMed  Google Scholar 

  20. Jones OR, Wang J (2010) Colony: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555

    Article  PubMed  Google Scholar 

  21. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  22. Kirst M, Cordeiro CM, Rezende GDSP, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96(2):161–166

    Article  CAS  PubMed  Google Scholar 

  23. Küpper C, Burke T, DA SzékelyT Dawson (2008) Enhanced cross-species utility of conserved microsatellite markers in shorebirds. BMC Genomics 9(502):1–120

    Google Scholar 

  24. Landrum LR, Kawasaki ML (1997) The genera of Myrtaceae in Brazil: an illustrated synoptic treatment and identification keys. Brittonia 49:508–536

    Article  Google Scholar 

  25. Lavor P, van den Berg C, Versieux LM (2013) Transferability of 10 nuclear microsatellite primers to Vriesea minarum (Bromeliaceae), a narrowly endemic and threatened species from Brazil. Revista Brasileira de Botanica 36:165–168

    Google Scholar 

  26. McVaugh R (1968) The genera of American Myrtaceae—an interim report. Taxon 17:354–418

    Article  Google Scholar 

  27. Meglécz E, Nève G, Biffin E, Gardner MG (2012) Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 Non model eukaryote species. PLoS ONE 7:1–15

    Article  Google Scholar 

  28. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KN, Latif MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci 14(11):499–528

    Article  Google Scholar 

  29. Mittal N, Dubey A (2009) Microsatellite markers—a new practice of DNA based markers in molecular genetics. Pharmacogn Rev 3:235–246

    CAS  Google Scholar 

  30. Morin PA, Luikart G, Wayne RK, The SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  31. Nimisha S, Kherwar D, Ajay KM, Singh B, Usha K (2013) Molecular breeding to improve guava (Psidium guajava L.): current status and future prospective. Sci Hortic 164:578–588

    Article  Google Scholar 

  32. Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AAF, Souza AP (2006) Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breed 384:378–384

    Google Scholar 

  33. Parida SK, Dalal V, Singh AK, Singh NK, Mohapatra T (2009) Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics 10:140–160

    Article  PubMed Central  PubMed  Google Scholar 

  34. Pillar VD (1999) How sharp are classifications? Ecology 80(8):2508–2516

    Article  Google Scholar 

  35. Proença CEB, Gibbs PE (1994) Reproductive biology of eight sympatric Myrtaceae from Central Brazil. New Phytol 126:343–354

    Article  Google Scholar 

  36. Putman AI, Carbone I (2014) Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 4(22):4399–4428

    PubMed Central  PubMed  Google Scholar 

  37. R Core Team (2013) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available on: http://www.R-project.org

  38. Rai MK, Phulwaria M, Shekhawat NS (2013) Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species. Mol Biol Rep 40(8):5067–5071. doi:10.1007/s11033-013-2608-1

    Article  CAS  PubMed  Google Scholar 

  39. Rafalsky A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5(2):94–100

    Article  Google Scholar 

  40. Risterucci AM, Duval MF, Billotte N, Rohde W (2005) Isolation and characterization of microsatellite loci from Psidium guajava L. Mol Ecol Notes 5(4):745–748

    Article  CAS  Google Scholar 

  41. Sitther V, Zhang D, Harris DL, Yadav AK, Zee FT, Meinhardt LW, Dhekney SA (2014) Genetic characterization of guava (Psidium guajava L.) germplasm in the United States using microsatellite markers. Genetic Resour Crop Evol 61(4):829–839

    Article  CAS  Google Scholar 

  42. Sefc KM, Lopes MS, Lefort F, Botta R, Roubelakis-Angelakis KA, Ibañez J, Pejic J, Wagner HW, Glössl J, Steinkellner H (2000) Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to assess the geographic origin of cultivars. Theor Appl Genet 100:498–505

    Article  Google Scholar 

  43. Shepherd M, Kasem S, Lee D, Henry R (2006) Construction of microsatellite linkage maps for Corymbia. Silvae Genet 55:228–238

    Google Scholar 

  44. Shi J, Huang S, Fu D, Yu J, Wang X, HuaW Liu S, Liu G, Wang H (2013) Evolutionary dynamics of microsatellite distribution in Plants: insight from the comparison of sequenced brassica, arabidopsis and other angiosperm species. PLoS ONE 8:1–16

    Google Scholar 

  45. Testolin R, Marrazzo MT, Cipriani G, Quarta R, Verde I, Dettori MT, Pancaldi M, Sansavini S (2000) Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43:512–520

    Article  CAS  PubMed  Google Scholar 

  46. Valdés-Infante J, Rodríguez NN, Becker D, Velázquez B, Sourd D, Espinosa G, Rohde W (2007) Microsatellite characterization of guava (Psidium guajava L.) germplasm collection in cuba. Cultivos Trop 28:61–67

    Google Scholar 

  47. Valdés-Infante J, Rodríguez NN, Velásquez B, Rivero D, Martínez F, Espinosa G, Risterucci AM, Billotte N, Becker D, Rohde W (2010) Simple sequence repeats (SSRs) for diversity characterization of guava (Psidium guajava L.). Acta Hortic 849:155–162

    Article  Google Scholar 

Download references

Acknowledgments

We thank CAPES for financial support provided to the first author; to Universidade Federal do Espírito Santo (UFES) for all the support during project execution; to FAPES for grant support to the project “Diversity of genus Psidium in the state of Espírito Santo”.

Author information

Authors and Affiliations

  1. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Escola Nacional de Botânica Tropical, Rua Pacheco Leão, 2040, Jardim Botânico, Rio de Janeiro, CEP: 22.460-030, Brazil

    A. C. Tuler & A. L. Peixoto

  2. Departamento de Biologia, Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, CEP: 29.500-000, Brazil

    T. T. Carrijo, L. R. Nóia & M. F. da Silva Ferreira

  3. Departamento de Produção Vegetal, Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, CEP: 29.500-000, Brazil

    A. Ferreira

Authors
  1. A. C. Tuler
    View author publications

    Search author on:PubMed Google Scholar

  2. T. T. Carrijo
    View author publications

    Search author on:PubMed Google Scholar

  3. L. R. Nóia
    View author publications

    Search author on:PubMed Google Scholar

  4. A. Ferreira
    View author publications

    Search author on:PubMed Google Scholar

  5. A. L. Peixoto
    View author publications

    Search author on:PubMed Google Scholar

  6. M. F. da Silva Ferreira
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to M. F. da Silva Ferreira.

Appendix

Appendix

See Table 3.

Table 3 SSR, motif, number of alleles per locus, number of amplified species per primer, type of region, annealing temperature (AT), motif class, fragment size, fragment amplitude, presence and localization of the fragment in the genetic map of P.guajava (adapted from [17, 40]
Full size table

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tuler, A.C., Carrijo, T.T., Nóia, L.R. et al. SSR markers: a tool for species identification in Psidium (Myrtaceae). Mol Biol Rep 42, 1501–1513 (2015). https://doi.org/10.1007/s11033-015-3927-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-015-3927-1

Keywords