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Development of the new microsatellite multiplex PCR panel and genetic variation of farmed snakeskin gourami, Trichopodus pectoralis

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Abstract

Genetically distinct populations have been used to found genetically diverse base populations, which are a prerequisite for successful selective breeding programs. Genetic markers are very useful in this regard as a tool for characterization of genetic diversity. In the present study, a panel of eight multiplex microsatellite primers was developed and seven of them were used to assess genetic diversity of farmed snakeskin gourami, which have been domesticated for more than 30 years. The microsatellites developed showed number of alleles per locus (A) of 3 to 22 alleles, expected heterozygosity (He) range of 0.328–0.923, and Polymorphic Information Content (PIC) range of 0.227–0.915. Four farmed populations of snakeskin gourami (n = 50 fish/population) possessed moderate genetic diversity (FST = 0.056; pairwise FST = − 0.047–0.041; genetic distance = 0.034–0.087), with all but one population pair significantly different as revealed by pairwise FST. Population structuring assigned the studied populations to two clusters. Genetic variation within populations was characterized, with average number of alleles/locus of 6.7–8.0 and expected heterozygosity of 0.65–0.68. Effective population size ranged from 13.2 to 37.7. Our study was the first to report a multiplex microsatellite panel for snakeskin gourami, and it showed genetic distinction among farmed stocks of this species.

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Funding

This work was supported by Thailand Research Fund and Betagro Science Center Co. Ltd. (Contract No. DPG5980003; Distinguished Research Professor TRF FY 2016) awarded to UN.

We thank the following people: the farm owners for allowing us to collect fin-clipped samples of snakeskin gourami; Assist. Prof. Chareerat Mongkolsiriwatana, Research Unit of Genetic Technology and Applications, Department of Science, Faculty of Liberal Arts and Science for providing AW with facilities to conduct all microsatellite works; Mr.Chatchai Thaithungchin for his assistance in sample collection; and Mr. David John Anderson who provided English editing of the manuscript. Finally, we expressed the sincere thanks to the anonymous referees for their invaluable comments that significantly improved our manuscript.

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Authors and Affiliations

  1. Division of Genetics, Department of Sciences, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand

    Anyalak Wachirachaikarn

  2. Research Unit of Genetic Technology and Applications, Department of Science, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand

    Anyalak Wachirachaikarn

  3. Graduate Program in Aquaculture, Department of Aquaculture, the Graduate School of Kasetsart University, Kasetsart University, Bangkok, Thailand

    Onprang Sutthakiet

  4. Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand

    Wansuk Senanan

  5. Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand

    Uthairat Na-Nakorn

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  1. Anyalak Wachirachaikarn
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All of the protocols were approved by the Kasetsart University Animal Ethics Committee -ID ACKU 61-FIS-004.

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Wachirachaikarn, A., Sutthakiet, O., Senanan, W. et al. Development of the new microsatellite multiplex PCR panel and genetic variation of farmed snakeskin gourami, Trichopodus pectoralis. Aquacult Int 28, 751–765 (2020). https://doi.org/10.1007/s10499-019-00492-1

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