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| Screening and Characteristic Analysis of Mitochondrial Genome SNPs in Ridgetail White Prawn Exopalamon carinicauda |
| ZHU Jixuan1, DAI Qin1, DUAN Jiancheng1, GAO Na1, GAO Wei1, YAN Binlun1,2, GAO Huan1,2,3 |
1. Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China;
2. Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Lianyungang 222005, China;
3. The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China |
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Abstract The potential SNP sites of ridgetail white prawn Exopalaemon carinicauda were screened to obtain single nucleotide polymorphisms (SNP) sites in the mitochondrial genome (mtDNA) of ridgetail white prawn with average body length of (5.23±0.33) cm collected from the culture ponds in coastal areas of Lianyungang and Nantong, Jiangsu Province, using high-resolution melting curve (HRM) technology by 109 pairs of primers designed based on the full sequence of mtDNA. HRM analysis showed that the amplification products of 9 pairs of primers in 80 pairs contained SNP sites, which contained 16 SNPs in total. Statistical results showed that the SNP sites in the mitochondrial genome of ridgetail white prawn were haplotypes with a frequency of 0.10/100 bp, among which the transformation mutations (G/A and C/T) accounted for 87.5% of the total SNPs, and the translation mutations (A/T) accounted for 12.5%, without insertion, deletion and other mutations. Location analysis revealed that the 16 SNPs obtained were distributed in COX1, cob, COX2, tRNAAsp, nad1, nad4, and nad5. In the 7 regions, there was the maximal SNPs in the COX1 gene region, with 5 SNP sites, followed by 3 SNP sites in the cob region. Moreover, further comparison of the corresponding amino acids encoded by SNPs showed that the synonymous SNP accounts for 43.7% of the total number, while the non synonymous SNP accounts for 56.3%, which may lead to changes in the properties and functions of proteins. The screening of SNPs in this study will be helpful for the further work of pedigree identification and genetic diversity analysis of ridgetail white prawn.
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Received: 24 February 2020
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