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Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing

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Abstract

White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

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Funding

This research was financially supported by the Prince of Songkla University, Surat Thani Campus Collaborative Research Fund contract no. 003/2562, Coordinating Center for Thai Government Science and Technology Scholarship Students (CSTS) National Science and Technology Development Agency (NSTDA) contract no. SCH-NR2016-181 and Discipline of Excellence in Sustainable Aquaculture, Prince of Songkla University.

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Authors and Affiliations

  1. Faculty of Innovative Agriculture and Fishery Establishment Project, Prince of Songkla University, Surat Thani Campus, Surat Thani, 84000, Thailand

    Parichart Ninwichian & Jareeporn Ruangsri

  2. Discipline of Excellence in Sustainable Aquaculture, Prince of Songkla University, Songkhla, 90110, Thailand

    Jareeporn Ruangsri

  3. Faculty of Science and Industrial Technology, Prince of Songkla University, Surat Thani Campus, Surat Thani, 84000, Thailand

    Nirandon Phuwan

  4. Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, 12120, Khlong Luang, Pathum Thani, Thailand

    Bavornlak Khamnamtong & Sirawut Klinbunga

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  1. Parichart Ninwichian
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  2. Jareeporn Ruangsri
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  3. Nirandon Phuwan
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  4. Bavornlak Khamnamtong
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Contributions

All authors have contributed to and agreed on the content of the manuscript, and the respective roles of each author are listed as follows. PN: funding acquisition, sample collection, experimental design, conducted the experiments, data analysis, drafting of the research article, and final approval of the research article. JR: funding acquisition, sample collection, and final approval of the research article. NP: sample collection, conducted the experiments, data analysis, and final approval of the research article. BK: experimental design and final approval of the research article. SK: experimental design, critical revision of the research article for important intellectual content, and final approval of the research article.

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Correspondence to Parichart Ninwichian.

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All experimental procedures were performed in accordance with guidelines for the care and use of laboratory animals approved by the Institutional Animal Care and Use Committee of the Prince of Songkla University.

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Ninwichian, P., Ruangsri, J., Phuwan, N. et al. Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing. Mol Biol Rep 48, 4273–4283 (2021). https://doi.org/10.1007/s11033-021-06442-6

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