Conservation Genetics Resources

, Volume 4, Issue 3, pp 811–814 | Cite as

Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

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

Abstract

A set of 15 new microsatellite loci was developed and characterized for the widespread mangrove tree species Sonneratia alba (Lythraceae) by using next-generation sequencing. Forty-eight S. alba samples from seven populations in the Indo-West Pacific region were genotyped; all loci were polymorphic, with the number of alleles ranging from three to eight. The mean observed heterozygosity per locus was 0.21 for a population from Sabah, Malaysia. No null allele or significant linkage disequilibrium was detected, indicating the robustness of the markers. Only one locus (SA103) showed deviation from Hardy–Weinberg equilibrium. As characterization of these microsatellite loci was done with samples covering most of the species’ distribution range, the markers can be applied to genetic diversity studies over the broad geographical range of the species.

Keywords

Conservation Diversity Mangrove Pyrosequencing SSR 

Notes

Acknowledgments

The authors thank Drs. Sanjay Deshmukh (Mumbai), Romanus Prabowo (Java), Jurgenne Primavera (Panay), Monica Suleiman (Sabah), Mr. Seigo Murakami (KKWC) 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.

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

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

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