Development of 11 polymorphic microsatellite markers for Xylocarpus granatum (Meliaceae) using next-generation sequencing technology


Human impacts have seriously damaged mangroves, and conservation of mangroves will require information on local and regional population genetic structures. Here, we report the development and polymorphism of eleven novel microsatellite markers, developed using next-generation sequencing on 56 samples of widespread mangrove species Xylocarpus granatum (Meliaceae) from nine populations across the Indo-West Pacific region. All loci were found to be polymorphic, with the number of alleles per locus ranging from four to 19. In a population from Sabah (Malaysia), the mean observed and expected heterozygosity per locus was 0.59 and 0.58, respectively. No null allele, significant linkage disequilibrium or deviation from Hardy–Weinberg equilibrium was detected among all loci. The eleven markers developed can be valuable tools to conservation genetics of this species across its distributional range.

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  1. 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 26:403–404

    PubMed  Article  Google Scholar 

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

    Google Scholar 

  3. 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 

  4. Takayama K, López PS, Konig C, Khol 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 60:1442–1449

    Google Scholar 

  5. 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 4:535–538

    Article  Google Scholar 

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The authors thank Drs. Kyaw Kyaw Khaung and Myint Aung (Myanmar), Mr. Lukes Isechal (Palau), Mr. Cossa de Miranda Filipe (Mozambique), Dr. Jurgenne Primavera (Panay), Dr. Yoichi Tateishi and Mr. Masaharu Amano (University of the Ryukyus), Dr. Monica Suleiman (Sabah), SFD-Sabah Forestry Department (Malaysia), Palau International Coral Reef Center (Palau), Direcção Provincial da Agricultura—Zambézia (Mozambique) and Department of Environment and Natural Resources, Region VI (Panay) for their assistance during field works and material collection. This work was supported by the Singapore Ministry of Education R154-000-440-112 to ELW, by the Fujiwara Natural History Foundation to KT, by the JSPS KAKENHI 22405005 and 25290080 to TK, and JSPS JENESYS Programme 2009 and 2011 to the Graduate School of Science, Chiba University.

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Correspondence to Koji Takayama.

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Tomizawa, Y., Shinmura, Y., Wee, A.K.S. et al. Development of 11 polymorphic microsatellite markers for Xylocarpus granatum (Meliaceae) using next-generation sequencing technology. Conservation Genet Resour 5, 1159–1162 (2013).

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  • Conservation
  • Genetic diversity
  • Mangrove
  • Pyrosequencing
  • SSR
  • Indo-West Pacific