Skip to main content

Advertisement

SpringerLink
Log in

Microsatellite primer development for the seagrass Zostera nigricaulis (Zosteraceae)

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

Seagrasses are marine angiosperms with a worldwide distribution that form conspicuous beds in nearshore habitats. Despite being universally recognised as a foundation species that performs a number of important ecosystems functions (incl. sediment stabilisation, facilitation of biodiversity, nutrient cycling and carbon sequestration), global seagrass habitats are in decline. Resilience—the ability to recover from disturbance without switching to an alternative state—is paramount to the maintenance and persistence of seagrass habitats. Genetic diversity is a key component of seagrass resilience and contributes to an understanding of population structure, connectivity between populations, and reproductive strategies. Microsatellite primers were developed to investigate the resilience of the seagrass Zostera nigricaulis, which dominates subtidal habitats in the bays of south-eastern Australia. We also tested for cross-amplification of markers between Z. nigricaulis and previously developed markers for the sympatric species Z. muelleri to assess their applicability for use in assessing patterns of genetic diversity, population structure, and mating system. Using next-generation sequencing we isolated 11 novel microsatellite loci for Z. nigricaulis, 8 of which were polymorphic for the samples tested. Allelic diversity ranged from 1 to 8. None of the primer pairs developed for Z. nigricaulis cross-amplified in Z. muelleri; but 14 of 24 primer pairs previously developed for Z. muelleri amplified clearly in Z. nigricaulis samples with six of these showing polymorphism. The results demonstrate the applicability of the Z. nigricaulis microsatellite primers for use in the study of population genetics and limited cross-amplification with Z. muelleri.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

References

  • Blacket MJ, Robin C, Good RT, Lee SF, Miller AD (2012) Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Mol Ecol Resour 12(3):456–463. doi:10.1111/j.1755-0998.2011.03104.x

    Article  PubMed  CAS  Google Scholar 

  • Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ (2011) Rise of the machines—recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 11(6):1093–1101. doi:10.1111/j.1755-0998.2011.03037.x

    Article  PubMed  Google Scholar 

  • Kuo J (2005) A revision of the genus Heterozostera (Zosteraceae). Aquat Bot 81(2):97–140. doi:10.1016/j.aquabot.2004.10.005

    Article  Google Scholar 

  • Les DH, Moody ML, Jacobs SWL, Bayer RJ (2002) Systematics of seagrasses (Zosteraceae) in Australia and New Zealand. Syst Bot 27(3):468–484

    Google Scholar 

  • Meglecz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin J-F (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26(3):403–404. doi:10.1093/bioinformatics/btp670

    Article  PubMed  CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295. doi:10.1111/j.1471-8286.2005.01155.x

    Article  Google Scholar 

  • Raymond M, Rousset F (1995) GENPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86(3):248–249

    Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (Clifton, NJ) 132:365–386

    CAS  Google Scholar 

  • Sherman C, Stanley A, Keough M, Gardner M, Macreadie P (2012) Development of twenty-three novel microsatellite markers for the seagrass, Zostera muelleri from Australia. Conserv Genet Resour 4(3):689–693. doi:10.1007/s12686-012-9623-8

    Article  Google Scholar 

  • Short FT, Polidoro B, Livingstone SR, Carpenter KE, Bandeira S, Bujang JS, Calumpong HP, Curruthers TJB, Coles RG, Dennison WC, Erftemeijer PLA, Fortes MD, Freeman AS, Japtap TG, Kamal AHM, Kendrick GA, Kenworth WJ, La Nafie YA, Nasution IM, Orth RJ, Prathep A, Sanciangco JC, van Tussenbroek B, Vergara SG, Waycott M, Zieman JC (2011) Extinction risk assessment of the world’s seagrass species. Biol Conserv 144:1961–1971

    Article  Google Scholar 

  • Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10(1):249–256. doi:10.1046/j.1365-294X.2001.01185.x

    Article  PubMed  CAS  Google Scholar 

  • Waycott M, Duarte CM, Carruthers TJB, Orth RJ, Dennison WC, Olyarnik S, Calladine A, Fourqurean JW, Heck KL, Hughes AR, Kendrick GA, Kenworthy WJ, Short FT, Williams SL (2009) Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proc Natl Acad Sci USA 106(30):12377–12381. doi:10.1073/pnas.0905620106

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank A. Hirst, N. Hutchinson, C. White and D. Hatton for assistance with specimen collection. This study was financially supported by a research grant from the Victorian Department of Sustainability and Environment: ‘Seagrass resilience in Port Phillip Bay: developing better predictions of how seagrasses respond to environmental change’.

Author information

Authors and Affiliations

  1. Centre of Integrative Ecology, School of Life and Environmental Science, Deakin University, Pigdons Rd, Waurn Ponds, Geelong, VIC, 3217, Australia

    Timothy M. Smith, Paul H. York, Annalise M. Stanley & Craig D. H. Sherman

  2. Plant Functional Biology and Climate Change Cluster (C3), School of the Environment, University of Technology Sydney, Broadway, Sydney, NSW, 2007, Australia

    Peter I. Macreadie

  3. Department of Zoology, University of Melbourne, Melbourne, VIC, 3010, Australia

    Michael J. Keough

  4. Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, Hobart, TAS, 7053, Australia

    D. Jeff Ross

Authors
  1. Timothy M. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Paul H. York
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Annalise M. Stanley
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peter I. Macreadie
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michael J. Keough
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. D. Jeff Ross
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Craig D. H. Sherman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Timothy M. Smith.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Smith, T.M., York, P.H., Stanley, A.M. et al. Microsatellite primer development for the seagrass Zostera nigricaulis (Zosteraceae). Conservation Genet Resour 5, 607–610 (2013). https://doi.org/10.1007/s12686-013-9862-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-013-9862-3

Keywords

Search

Navigation