Characterization of 40 single nucleotide polymorphism (SNP) via T m-shift assay in the mud crab (Scylla paramamosain)
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.
KeywordsThe 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.
- 1.Shen Y, Lai Q (1994) Present status of mangrove crab (Scylla serrate (Forskal)) culture in China, NAGA: the ICLARM Quarterly, January 28–29Google Scholar
- 2.Fishery Bureau of Ministry of Agriculture of China (2012) China Fisheries Yearbook. Chinese Agricultural Press, BeijingGoogle Scholar
- 12.Ciobanu DC, Bastiaansen JWM, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Konghorn BP, Plastow GS, van der Steen HAM, Mileham AJ (2010) A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet 41:39–47CrossRefPubMedGoogle Scholar
- 13.Olsen MT, Volny VH, Berube M, Dietz R, Lydersen C, Kovacs K, Dodd R, Palsbøll PJ (2011) A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida). Mol Ecol Resour 11(Suppl. 1):9–19CrossRefPubMedGoogle Scholar
- 20.Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, Taylor MI, Helyar SJ, Carvalho GR, Espineira M, Atanassova M, Tinti F, Maes GE, Patarnello T, Consortium F, Bargelloni L (2011) Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLOS ONE 6:e28008PubMedCentralCrossRefPubMedGoogle Scholar
- 21.Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, Houdt J, Maes GE, Bargelloni L, Nielsen RO, Taylor MI, Ogden R, Cariani A, Carvalho GR, Consortium F, Panitz F (2012) SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PLoS ONE 7:e42089CrossRefPubMedGoogle Scholar
- 30.Hansen MH, Young S, Jørgense HH, Pascal C, Henryon M, Seeb J (2011) Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis. Mol Ecol Resour 11(Suppl. 1):67–70CrossRefPubMedGoogle Scholar
- 31.Bichenkova EV, Lang Z, Yu X, Rogert G, Douglas KT (2011) DNA-mounted self-assembly: new approaches for genomic analysis and SNP detection. BBA-Gene Regul Mech 1809:1–23Google Scholar
- 34.Campbell NR, Narum SR (2012) Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River. Mol Ecol Resour 11(Suppl. 1):20–30Google Scholar