Abstract
Coilia ectenes, also called Coilia nasus, is an ecologically important species endemic to China. Due to habitat fragmentation, over-harvesting and water pollution, the natural germplasm of C. ectenes has declined dramatically in the recent decades. Thus, developing sufficient molecular markers for the conservation and molecular-aided selection of this species is urgent. In this study, 50 polymorphic single nucleotide polymorphism (SNP) markers were developed in C. ectenes based on the transcriptome database and characterized by genotyping 40 individuals using SNaPshot method. The minor allele frequency, the observed heterozygosity (HO), expected heterozygosity (HE) and polymorphism information content ranged from 0.1250 to 0.4875, 0.1750 to 0.7000, 0.2188 to 0.4997 and 0.1948 to 0.3744, respectively. Among these SNPs, sixteen loci were found to deviate significantly from the Hardy–Weinberg equilibrium after sequential Bonferroni correction (p < 0.05). These novel polymorphic SNPs will enable future genetics improvement of this species.
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References
Cheng QQ, Zhang QY, Ma CY, Guan WB (2011) Genetic structure and differentiation of four lake populations of Coilia ectenes (Clupeiformes: Engraulidae) based on mtDNA control region sequences. Biochem Syst Ecol 39(4–6):544–552
Fan JJ, Bai JJ, Ma DM (2018) Isolation and characterization of 40 SNP in largemouth bass (Micropterus salmoides). Conserv Genet Resour. https://doi.org/10.1007/s12686-018-1076-2
Peakall R, Smouse PE (2006) GENALEX 6, genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Rousset F (2008) GENEPOP’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Res 8:103–106
Shen HS, Gu RB, Xu GC, Xu P, Nie ZJ, Hu YC (2015) In-depth transcriptome analysis of Coilia ectenes, an important fish resource in the Yangtze River: de novo assembly, gene annotation. Mar Genom 23:15–17
Wang CD, Zhao LJ, Su CQ, Liu QG (2018) Isolation and characterization of SNPs in bighead carp. Conserv Genet Resour 10(2):1–4
Xiao MS, Hu QS, Zhao Y, Bao FY(2019) Development of SNP markers in Leiocassis longirostris Günther using high-throughput sequencing. Conserv Genet Resour. https://doi.org/10.1007/s12686-019-01084-0
Xu GC, Tang X, Zhang CX, Gu RB, Zheng JL, Xu P, Le GW (2011) First studies of embryonic and larval development of Coilia nasus (Engraulidae) under controlled conditions. Aquac Res 42(4):593–601
Yang JP, Li YF, Zhu SL, Chen WT, Li J, Xue HM, Li XH (2018) Development and characterization of 26 SNP markers in Ochetobius elongatus, based on restriction site-associated DNA sequencing (RAD-seq). Conserv Genet Res. https://doi.org/10.1007/s12686-018-1075-3
Yeh F, Yang R, Boyle T, Ye Z, Xiyan J (2000) POPGENE 32, Microsoft windows-based freeware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton
Acknowledgements
This study is supported by Shanghai Key Scientific and Technological Project on Agriculture from Shanghai Municipal Agricultural Commission (Grant No. (2016)-6-2-2), Shanghai Commercial Yangtze Estuary Aquatic Breeding Engineering and Technology Research Center Project (Grant No. 13DZ2251800) and Shanghai Key Scientific Technological Project from Shanghai Science and Technology Commission (Grant No. 17391900300).
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Yu, A., Shi, Y. & Yan, Y. Development and characterization of 50 SNP markers in Coilia ectenes. Conservation Genet Resour 12, 177–181 (2020). https://doi.org/10.1007/s12686-019-01086-y
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DOI: https://doi.org/10.1007/s12686-019-01086-y