Molecular Biology Reports

, Volume 41, Issue 8, pp 5467–5471 | Cite as

Characterization of 40 single nucleotide polymorphism (SNP) via T m-shift assay in the mud crab (Scylla paramamosain)

  • Nana Feng
  • Hongyu Ma
  • Chunyan Ma
  • Zhen Xu
  • Shujuan Li
  • Wei Jiang
  • Yuexing Liu
  • Lingbo Ma


In this study, single nucleotide polymorphism (SNP) were identified, confirmed and genotyped in the mud crab (Scylla paramamosain) using T m-shift assay. High quality sequences (13, 311 bp long) were obtained by re-sequencing that contained 91 SNPs, with a density of one SNP every 146 bp. Of all 91 SNPs, 40 were successfully genotyped and characterized using 30 wild specimens by T m-shift assay. The minor allele frequency per locus ranged from 0.017 to 0.500. The observed and expected heterozygosity, and polymorphism information content (PIC) ranged from 0.000 to 0.600, from 0.033 to 0.509, and from 0.033 to 0.375, respectively, with an average of 0.142, 0.239 and 0.198 per locus. Seventeen SNPs were significantly deviated from Hardy–Weinberg equilibrium. No significant linkage disequilibrium between pairs of loci was detected after sequential Bonferroni correction (P > 0.00125). Seventeen SNPs were related with known function genes. This study provided new molecular markers for investigation of population genetic diversity, construction of genetic linkage maps and molecular marker-assisted selection in this important crustacean species.


The mud crab Scylla paramamosain SNPs Transcriptome Genetic diversity 



This study was supported by the National Non-Profit Institutes (East China Sea Fisheries Research Institute) (No. 2011M05), the National Natural Science Foundation of China (No. 31001106), the Science and Technology Commission of Shanghai Municipality (No. 10JC1418600) and the National Infrastructure of Fishery Germplasm Resources.

Supplementary material

11033_2014_3420_MOESM1_ESM.docx (40 kb)
Supplementary material 1 (DOCX 39 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
  2. 2.College of Fisheries and Life ScienceShanghai Ocean UniversityShanghaiChina

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