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Characterization of 20 SNP markers in the blood clam (Tegillarca granosa) using T m-shift assay

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Abstract

The blood clam (Tegillarca granosa) is an important aquaculture clam. But so far the number of SNP available is very limited. In this study, novel single nucleotide polymorphism (SNP) were identified and genotyped in blood clam (T. granosa) using T m-shift assay. Thirty-eight SNP genotyping assays were designed for validation based on allele-specific polymerase chain reaction (AS-PCR) and melting temperature T m-shift analysis, 20 of them showed polymorphisms with the minor allele frequency ranging from 0.100 to 0.480. The observed and expected heterozygosity ranged from 0.127 to 0.850 and from 0.110 to 0.538, respectively. Two loci showed a significantly deviation from Hardy–Weinberg equilibrium (p < 0.05). No significant linkage disequilibrium between pairs of loci was detected after sequential Bonferroni correction (p > 0.001). These loci will be useful for investigation genetic population structure, construction of genetic linkage maps and molecule-assisted breeding for T. granosa.

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References

  • Dai W, Guo YJ, Wang XM, Tan ZJ (2010) RFLP analysis of the ribosomal DNA ITS region of three geographical population of Tegillarca granosa. Agric Sci Technol 11(2):92–94

    CAS  Google Scholar 

  • Dong Y, Shi S, Bao Y, Yao HH, Jing Y, Lin ZH (2015) Development of 90 EST-SNP markers in blood clam (Tegillarca granosa) using high resolution melting (HRM). Conserv Genet Resour 7(2):309–314

    Article  Google Scholar 

  • Liu B, Teng SS, Shao YQ (2012) Isolation and Characterization of 39 novel polymorphic EST-SSR loci from the Blood clam, Tegillarca granosa. Conserv Genet Resour 10:1005–1007

    Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. CSHL press, New York

    Google Scholar 

  • Wang RX, Li TW, Lu ZM, Su XR, Lin ZH, Chai XL (2005a) Study on genetic variation by isozyme in different populations of blood clam Tegillarca granosa. Oceanol Limnol Sin 36(3):227–234

    CAS  Google Scholar 

  • Wang J, Chuang K, Ahluwalia M, Patel S, Umblas N, Mirel D, Higuchi R, Germer S (2005b) High-throughtput SNP genotyping by single-tube PCR with T m-shift primers. Biotechniques 39:885–893

    Article  CAS  PubMed  Google Scholar 

  • Xu YP, Sun KY, Yang GM, Li QW, Bao BL, Ren DM (2006) Primary research on the genetic diversity of three populations of Tegillarca granosa in Yueqing Bay. J ShangHai Fish Univ 15(2):234–239

    CAS  Google Scholar 

  • Yeh FC, Yang R, Boyle TJ, Ye Z, Xiyan JM (2000) POPGENE 32, microsoft windows-based freeware for population genetic analysis. In: Molecular biology and biotechnology centre. University of Alberta, Edmonton

Download references

Acknowledgments

The study was supported by the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A410), the National Project for Agricultural Technology System (No. CARS-48), National Infrastructure of Fishery Germplasm Resources of China (No. 2015DKA30470), and Zhejiang Major Program of Science and Technology (No. 2012C12907-4).

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Authors and Affiliations

  1. Zhejiang Mariculture Research Institute, 6-1 Hetong Bridge, Wenzhou, 325000, China

    Bo Liu, Shuang-shuang Teng, Yan-Qing Shao, Xue-Liang Chai, Guo-Qiang Xiao, Jun Fang & Jiong-Ming Zhang

  2. Qingdao Agricultural University, Qingdao, 266109, China

    Bo Liu

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  1. Bo Liu
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  2. Shuang-shuang Teng
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  3. Yan-Qing Shao
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  4. Xue-Liang Chai
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  5. Guo-Qiang Xiao
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  6. Jun Fang
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  7. Jiong-Ming Zhang
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Liu, B., Teng, Ss., Shao, YQ. et al. Characterization of 20 SNP markers in the blood clam (Tegillarca granosa) using T m-shift assay. Conservation Genet Resour 8, 239–242 (2016). https://doi.org/10.1007/s12686-016-0543-x

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  • DOI: https://doi.org/10.1007/s12686-016-0543-x

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