Abstract
Estuarine tapertail anchovy (Coilia nasus) is a widely distributed and commercially important aquaculture species. However, excessive fishing and changes in aquatic ecology have almost caused extinction of the species in the middle reaches of the Yangtze River. Therefore, it is very urgent to perform genetic research on C. nasus to protect the wild population. In this study, we sequenced the liver transcriptome of C. nasus using Illumina Hiseq 2500 platform. We obtained 65,129 unigenes with an average length of 606 bp and a total of 62,947 putative SNPs were detected. Among them, 31 SNPs were selected for the validation experiments. All of the 31 loci were found to be polymorphic and showed bi-allelic in 58 individuals of C. nasus. These SNP markers should not only be useful for population conservation, but also for construction of genetic linkage map and economic performance improvement of C. nasus.
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References
Fang DA, Zhou YF, Duan JR, Zhang MY, Xu DP, Liu K, Xu P, Wei Q (2015) Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing. Genet Mol Res 14:14181–14188
Francis CY, Rong CY, Boyle T (2000) Popgene Microsoft Windows-based freeware for population genetic analysis. In: Molecular biology and biotechnology centre. University of Alberta, Edmonton
Han ZQ, Han G, Wang ZY, Gao TX (2015) The possible physical barrier and coastal dispersal strategy for Japanese grenadier anchovy, Coilia nasus in the East China Sea and Yellow Sea: evidence from AFLP markers. Int J Mol Sci 16:3283–3297
Jiang T, Yang J, Liu H, Shen XQ (2012) Life history of Coilia nasus from the Yellow Sea inferred from otolith Sr:Ca ratios. Environ Biol Fishes 95:503–508
Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124–1132
Liu B, Teng SS, Shao YQ, Chai XL, Xiao GQ, Fang J, Zhang JM (2016) Characterization of 20 SNP markers in the blood clam (Tegillarca granosa) using T m-shift assay. Conserv Genet Resour. doi:10.1007/s12686-016-0543-x
Vignal A, Milan D, Sancristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305
Zhang M, Xu D, Liu K, Shi W (2005) Studies on biological characteristics and change of resource of Coilia nasus Schlegel in the lower reaches of the Yangtze River. Resour Environ Yangtze Basin 14:693–698
Acknowledgments
This work was supported by a grant from the Key Technology R&D Program of Jiangsu Province (Grant No. BE2014307), the Special Fund of the Chinese Central Government for Basic Scientific Research Operations in Commonwealth Research Institutes (Grant No. 2015JBFR06), the Natural Science Foundation of Jiangsu Province, China (Grant No. BK20140121).
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Du, F., Xu, G., Li, Y. et al. Development of SNP markers and validation 31 SNPs in Coilia nasus . Conservation Genet Resour 9, 99–101 (2017). https://doi.org/10.1007/s12686-016-0630-z
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DOI: https://doi.org/10.1007/s12686-016-0630-z