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Genetic variation, population structure and identification of yellow catfish, Mystus nemurus (C&V) in Thailand using RAPD, ISSR and SCAR marker

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Abstract

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four subpopulations of Mystus nemurus in Thailand. The 7 RAPD and 7 ISSR primers were selected. Of 83 total RAPD fragments, 80 (96.39%) were polymorphic loci, and of 81 total ISSR fragments, 75 (92.59%) were polymorphic loci. Genetic variation and genetic differentiation obtained from RAPD fragments or ISSR fragments showed similar results. Percentage of polymorphic loci (%P), observed number of alleles, effective number of alleles, Nei’s gene diversity (H) and Shannon’s information index revealed moderate to high level of genetic variations within each M. nemurus subpopulation and overall population. High levels of genetic differentiations were received from pairwise unbiased genetic distance (D) and coefficient of differentiation. Mantel test between D or gene flow and geographical distance showed a low to moderate correlation. Analysis of molecular variance indicated that variations among subpopulations were higher than those within subpopulations. The UPGMA dendrograms, based on RAPD and ISSR, showing the genetic relationship among subpopulations are grouped into three clusters; Songkhla (SK) subpopulation was separated from the other subpopulations. The candidate species-specific and subpopulation-specific RAPD fragments were sequenced and used to design sequence-characterized amplified region primers which distinguished M. nemurus from other species and divided SK subpopulation from the other subpopulations. The markers used in this study should be useful for breeding programs and future aquacultural development of this species in Thailand.

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Acknowledgments

This research is partially supported by The Center of Excellence on Agricultural Biotechnology, Science and Technology Postgraduate Education and Research Development Office, Office of Higher Education Commission, Ministry of Education (AG-BIO/PERDO-CHE) and Agricultural Biotechnology Research Center for Sustainable Economy, Khon Kaen University, and The Khon Kaen University’s Graduate Research Fund Academic Year 2010.The suggestion on data analysis provided by Assist. Professor. Dr. Thongchai champasri is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Biochemistry, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand

    Sugunya Kumla & Nison Sattayasai

  2. Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand

    Sugunya Kumla

  3. Agricultural Biotechnology Research Center for Sustainable Economy, Khon Kaen University, Khon Kaen, 40002, Thailand

    Sugunya Kumla

  4. Department of Fisheries, Faculty of Agriculture, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand

    Sompong Doolgindachbaporn

  5. Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand

    Runglawan Sudmoon

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  1. Sugunya Kumla
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Correspondence to Nison Sattayasai.

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Kumla, S., Doolgindachbaporn, S., Sudmoon, R. et al. Genetic variation, population structure and identification of yellow catfish, Mystus nemurus (C&V) in Thailand using RAPD, ISSR and SCAR marker. Mol Biol Rep 39, 5201–5210 (2012). https://doi.org/10.1007/s11033-011-1317-x

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