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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

Thai, Binh Thanh, Tan, Mun Hua, Lee, Yin Peng, Gan, Han Ming, Tran, Trang Thi and Austin, Christopher M. 2016, Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing, Molecular Biology Reports, vol. 43, no. 5, pp. 391-396, doi: 10.1007/s11033-016-3966-2.

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Title Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing
Author(s) Thai, Binh Thanh
Tan, Mun Hua
Lee, Yin Peng
Gan, Han Ming
Tran, Trang Thi
Austin, Christopher M.
Journal name Molecular Biology Reports
Volume number 43
Issue number 5
Start page 391
End page 396
Total pages 6
Publisher Springer
Place of publication Berlin, Germany
Publication date 2016-05
ISSN 0301-4851
1573-4978
Keyword(s) Aquaculture
Clam
Genotype
Illumina
Molecular markers
Population genetics
Animals
Bivalvia
High-Throughput Nucleotide Sequencing
Microsatellite Repeats
Sequence Analysis, DNA
Vietnam
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Summary 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.
Language eng
DOI 10.1007/s11033-016-3966-2
Field of Research 070401 Aquaculture
070402 Aquatic Ecosystem Studies and Stock Assessment
0601 Biochemistry And Cell Biology
Socio Economic Objective 970105 Expanding Knowledge in the Environmental Sciences
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2016, Springer
Persistent URL http://hdl.handle.net/10536/DRO/DU:30091040

Document type: Journal Article
Collection: School of Life and Environmental Sciences
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