Conservation Genetics Resources

, Volume 7, Issue 2, pp 451–453 | Cite as

Development and characterization of nine novel microsatellite markers for the milkfish Chanos chanos

  • Brian S. SantosEmail author
  • Maria Rowena R. Romana-Eguia
  • Zubaida U. Basiao
  • Minoru Ikeda
Microsatellite Letters


The milkfish, Chanos chanos, is an important aquaculture resource in Southeast Asia. Using NGS data, 72 microsatellite markers were developed. PCR product confirmation using agarose gel electrophoresis allowed the identification of 24 utilizable markers. Milkfish samples (n = 48) from a hatchery stock in Palawan, Philippines were analyzed for genetic variability at the aforementioned 24 loci. Consequently, nine of these microsatellite loci were noted to have high success rate in amplification, exhibited polymorphism with 19 maximum number of alleles and no null alleles. These are the first microsatellite markers to be developed and characterized for C. chanos that will efficiently enable genetic stock delineation and monitoring as well as marker-aided genetic improvement research.


Chanos chanos Microsatellite markers Milkfish Population genetic structure 



Funds for this study were provided by the Department of Science and Technology-Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRD) and the Southeast Asian Fisheries Development Center, Aquaculture Department (SEAFDEC/AQD; study code Br-02-F2012B).


  1. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  2. Faircloth BC (2008) Msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 8:92–94CrossRefPubMedGoogle Scholar
  3. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  4. Shaw PW, Turan C, Wright JM, O’Connell M, Carvalho GR (1999) Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses. Heredity 83:490–499CrossRefPubMedGoogle 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 4:535–538CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Brian S. Santos
    • 1
    Email author
  • Maria Rowena R. Romana-Eguia
    • 2
  • Zubaida U. Basiao
    • 1
  • Minoru Ikeda
    • 3
  1. 1.Institute of BiologyUniversity of the Philippines DilimanQuezon CityPhilippines
  2. 2.Aquaculture DepartmentSoutheast Asian Fisheries Development CenterBinangonanPhilippines
  3. 3.Laboratory of Integrative Aquatic BiologyOnagawa Field Center, Graduate School of Agricultural ScienceOnagawa, OshikaJapan

Personalised recommendations