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Conservation Genetics Resources

, Volume 4, Issue 4, pp 951–954 | Cite as

Isolation and characterization of 14 microsatellite markers for Rhizophora mucronata (Rhizophoraceae) and their potential use in range-wide population studies

  • Yoshimi Shinmura
  • Alison K. S. Wee
  • Koji Takayama
  • Sankararamasubramanian Halasya Meenakshisundaram
  • Takeshi Asakawa
  • Onrizal
  • Bayu Adjie
  • Erwin Riyanto Ardli
  • Sarawood Sungkaew
  • Norhaslinda Binti Malekal
  • Nguyen Xuan Tung
  • Severino G. Salmo III
  • Orlex Baylen Yllano
  • M. Nazre Saleh
  • Khin Khin Soe
  • Emiko Oguri
  • Noriaki Murakami
  • Yasuyuki Watano
  • Shigeyuki Baba
  • Edward L. Webb
  • Tadashi KajitaEmail author
Technical Note

Abstract

A set of 14 new microsatellite markers was developed for mangrove species Rhizophora mucronata (Rhizophoraceae) by using pyrosequencing. Fifty-six samples from 9 populations of R. mucronata in the Indo-West Pacific region were genotyped; all loci were polymorphic, with the number of alleles ranging from 2 to 9. The mean expected heterozygosity per locus was 0.16 in a population from Sabah, no significant linkage disequilibrium was found among loci, and significant deviation from Hardy–Weinberg equilibrium was found in 3 loci. The polymorphic microsatellite markers with samples covering most of the species’ distribution range can be applied in genetic diversity studies covering a broad geographical range of the species.

Keywords

Genetic diversity Mangrove Pyrosequencing SSR 

Notes

Acknowledgments

The authors thank Drs. Sanjay Deshmukh (Mumbai), Romanus Prabowo (Java), Jurgenne Primavera (Panay), Monica Suleiman (Sabah), Mrs. Katy Beaver (PCA, Seychelles) and Department of Environment and Natural Resources, Region VI (Panay) for field works to collect materials. We also thank Mr. Junya Ono, Mr. Tsuyoshi Takano and Mr. Futa Yamaji for their help in DNA extraction. This work was supported by the Singapore Ministry of Education (grant number R154-000-440-112), by the JSPS KAKENHI 22405005 to TK, and JSPS JENESYS Programme 2009 and 2011 to the Graduate School of Science, Chiba University.

References

  1. Brownstein M, Carpten J, Smith J (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20(1004–1006):1008–1010Google Scholar
  2. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  3. Duke NC (2006) Rhizophora apiculata, R. mucronata, R. stylosa, R. × annamalai, R. × lamarckii (Indo-West Pacific stilt mangrove). In: Elevitch CR (ed) Traditional trees of pacific islands—their culture, environment, and use. Permanent Agriculture Resources, Holualoa, pp 641–660Google Scholar
  4. Islam MS, Lian CL, Kameyama N, Wu B, Hogetsu T (2004) Development of microsatellite markers in Rhizophora stylosa using a dual-suppression-polymerase chain reaction technique. Mol Ecol Notes 4:110–112CrossRefGoogle Scholar
  5. Islam MS, Lian CL, Kameyama N, Wu B, Hogetsu T (2008) Chloroplast microsatellite markers for the mangrove tree species Bruguiera gymnorrhiza, Kandelia candel, and Rhizophora stylosa, and cross-amplification in other mangrove species. Conserv Genet 9:989–993CrossRefGoogle Scholar
  6. Kondo K, Nakamura T, Tsuruda K, Saito N, Yaguchi Y (1987) Pollination in Bruguiera gymnorrhiza and Rhizophora mucronata (Rhizophoraceae) in Ishigaki Island, The Ryukyu Islands, Japan. Biotropica 19:377–380CrossRefGoogle Scholar
  7. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedGoogle Scholar
  8. Meglécz 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 26:403–404PubMedCrossRefGoogle Scholar
  9. Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  10. Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106PubMedCrossRefGoogle Scholar
  11. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234PubMedCrossRefGoogle Scholar
  12. Shinmura Y, Wee AKS, Takayama K et al (2012) Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing. Conserv Genet Resour. doi: 10.1007/s12686-012-9650-5 Google Scholar
  13. Spalding M, Kainuma M, Collins L (2010) World atlas of mangroves. Earthscan, LondonGoogle Scholar
  14. Takayama K, Tamura M, Tateishi Y, Kajita T (2009) Isolation and characterization of microsatellite loci in a mangrove species, Rhizophora stylosa (Rhizophoraceae). Conserv Genet Resour 1:175–178CrossRefGoogle Scholar
  15. Takayama K, Lopez PS, Konig C, Kohl G, Novak J, Stuessy TF (2011) A simple and cost-effective approach for microsatellite isolation in non-model plant species using small-scale 454 pyrosequencing. Taxon 60:1442–1449Google Scholar
  16. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Yoshimi Shinmura
    • 1
  • Alison K. S. Wee
    • 2
  • Koji Takayama
    • 3
  • Sankararamasubramanian Halasya Meenakshisundaram
    • 4
  • Takeshi Asakawa
    • 1
  • Onrizal
    • 5
  • Bayu Adjie
    • 6
  • Erwin Riyanto Ardli
    • 7
  • Sarawood Sungkaew
    • 8
  • Norhaslinda Binti Malekal
    • 9
  • Nguyen Xuan Tung
    • 10
  • Severino G. Salmo III
    • 11
  • Orlex Baylen Yllano
    • 12
  • M. Nazre Saleh
    • 13
  • Khin Khin Soe
    • 14
  • Emiko Oguri
    • 15
  • Noriaki Murakami
    • 15
  • Yasuyuki Watano
    • 1
  • Shigeyuki Baba
    • 16
  • Edward L. Webb
    • 2
  • Tadashi Kajita
    • 1
    Email author
  1. 1.Department of Biology, Graduate School of ScienceChiba UniversityInage-ku, ChibaJapan
  2. 2.Department of Biological SciencesNational University of SingaporeSingaporeSingapore
  3. 3.Department of Systematic and Evolutionary BotanyUniversity of ViennaViennaAustria
  4. 4.Biotechnology ProgrammeM.S. Swaminathan Research FoundationChennaiIndia
  5. 5.Forestry Sciences DepartmentUniversitas Sumatera UtaraMedanIndonesia
  6. 6.Bali Botanical GardenIndonesian Institute of SciencesBaliIndonesia
  7. 7.Faculty of BiologyJenderal Soedirman UniversityPurwokertoIndonesia
  8. 8.Forest Biology Department, Faculty of ForestryKasetsart UniversityBangkokThailand
  9. 9.Institute for Tropical Biology and ConservationUniversiti Malaysia Kota KinabaluKota KinabaluMalaysia
  10. 10.Mangrove Ecosystem Research CentreHanoi National University of EducationHanoiVietnam
  11. 11.Department of Environmental Science, School of Science and EngineeringAteneo de Manila UniversityQuezon CityPhilippines
  12. 12.Biology Department, College of Sciences and TechnologyAdventist University of the PhilippinesCavitePhilippines
  13. 13.Department of Forest Production, Faculty of ForestryUniversiti Putra MalaysiaSerdangMalaysia
  14. 14.Department of BotanyUniversity of YangonYangonMyanmar
  15. 15.Makino Herbarium, Department of Biological SciencesTokyo Metropolitan UniversityTokyoJapan
  16. 16.Tropical Biosphere Research CenterUniversity of the RyukyusIriomoteJapan

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