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

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• 作者：Nana Feng (1) (2)
  Hongyu Ma (1)
  Chunyan Ma (1)
  Zhen Xu (1) (2)
  Shujuan Li (1) (2)
  Wei Jiang (1) (2)
  Yuexing Liu (1) (2)
  Lingbo Ma (1)
  
• 关键词：The mud crab ; Scylla paramamosain ; SNPs ; Transcriptome ; Genetic diversity
• 刊名：Molecular Biology Reports
• 出版年：2014
• 出版时间：August 2014
• 年：2014
• 卷：41
• 期：8
• 页码：5467-5471
• 全文大小：455 KB
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• 作者单位：Nana Feng (1) (2)
  Hongyu Ma (1)
  Chunyan Ma (1)
  Zhen Xu (1) (2)
  Shujuan Li (1) (2)
  Wei Jiang (1) (2)
  Yuexing Liu (1) (2)
  Lingbo Ma (1)
  
  1. Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
  2. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
  
• ISSN：1573-4978

文摘

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.