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Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing

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Abstract

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy–Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7–36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.

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Acknowledgments

Funding for this project was provided by the Government of Vietnam through its Aquaculture Biotechnology programs (606a/HD-KHCN-CNSH).The authors also wish to acknowledge the support of Monash University Malaysia through its Tropical Medicine and Biology Multidisciplinary Platform. We would like to thank Fisheries College for support in this project and Mr. Nguyen Thanh Nhon and Mr. Nguyen Van Ha who helped to collect the samples.

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Authors and Affiliations

  1. Fisheries College, Dinh Bang, Tu Son, Bac Ninh, Vietnam

    Binh Thanh Thai

  2. Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia

    Mun Hua Tan, Yin Peng Lee, Han Ming Gan & Christopher M. Austin

  3. School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia

    Mun Hua Tan, Yin Peng Lee, Han Ming Gan & Christopher M. Austin

  4. Hanoi National University of Education, Hanoi, Vietnam

    Trang Thi Tran

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  1. Binh Thanh Thai
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  2. Mun Hua Tan
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Correspondence to Binh Thanh Thai.

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Thai, B.T., Tan, M.H., Lee, Y.P. et al. Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing. Mol Biol Rep 43, 391–396 (2016). https://doi.org/10.1007/s11033-016-3966-2

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  • DOI: https://doi.org/10.1007/s11033-016-3966-2

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