Abstract
The bighead carp (Hypophthalmichthys nobilis) is a native freshwater fish species in China. However, the wild fishery resources of H. nobilis have recently suffered a drastic decline. In this study, a total of 106,657 putative SNP loci were identified from the assembled transcripts of H. nobilis. Thirty-seven polymorphic loci were characterized from 60 SNP loci randomly selected for validation by using 36 fin clips of H. nobilis from the Yangtze River. The observed heterozygosity, expected heterozygosity, and polymorphic information content of the 37 SNP loci ranged from 0.171 to 1.000, 0.159 to 0.509, and 0.144 to 0.375, respectively, and 13 SNP loci significantly deviated from the Hardy–Weinberg equilibrium (P < 0.01). The SNP loci identified and validated in this study will be useful for the genetic research of H. nobilis.
References
Beuzen ND, Stear MJ, Chang KC (2000) Molecular markers and their use in animal breeding. Vet J 160(1):42–52. https://doi.org/10.1053/tvjl.2000.0468
Chen D, Li S, Wang K (2012) Enhancement and conservation of inland fisheries resources in China. Environ Biol Fish 93(4):531–545. https://doi.org/10.1007/s10641-011-9948-2
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Fu B, Liu H, Yu X, Tong J (2016) A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis). Sci Rep 6:28679. https://doi.org/10.1038/srep28679
Fu J, Zhu W, Wang L, Luo M, Song F, Dong Z (2019) Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis). BMC Genom 20:781. https://doi.org/10.1186/s12864-019-6181-4
Hu M, Hua Q, Zhou H, Wu Z, Wu X (2015) The effect of dams on the larval abundance and composition of four carp species in key river systems in China. Environ Biol Fish 98(4):1201–1205. https://doi.org/10.1007/s10641-014-0342-8
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16(5):1099–1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Ke ZX, Xie P, Guo LG (2009) Impacts of two biomanipulation fishes stocked in a large pen on the plankton abundance and water quality during a period of phytoplankton seasonal succession. Ecol Eng 35(11):1610–1618. https://doi.org/10.1016/j.ecoleng.2008.01.006
Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21):2987–2993. https://doi.org/10.1093/bioinformatics/btr509
Liu S, Qiu S, Chen D, Huang M (1997) Protection and rational utilization of the germplasm resources of the four major Chinese carps in the Yangtze River system. Resour Environ Yangtze Valley 6(2):127–131 (in Chinese)
Mastrochirico-Filho VA, Hata ME, Sato LS, Jorge PH, Foresti F, Rodriguez MV, Martínez P, Porto-Foresti F, Hashimoto DT (2016) SNP discovery from liver transcriptome in the fish Piaractus mesopotamicus. Conserv Genet Resour 8(2):109–114. https://doi.org/10.1007/s12686-016-0521-3
Miller JJ, Eackles MS, Stauffer JR, King TL (2015) Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection. Conserv Genet Resour 7(1):9–11. https://doi.org/10.1007/s12686-014-0296-3
Peng X, Zhao L, Liu J, Guo X (2018) Development of SNP markers for Xenocypris argentea based on transcriptomics. Conserv Genet Resour 10(4):679–684. https://doi.org/10.1007/s12686-017-0900-4
Wang C, Zhao L, Su C, Liu Q (2018) Isolation and characterization of SNPs in bighead carp. Conserv Genet Resour 10(2):149–152. https://doi.org/10.1007/s12686-017-0783-4
Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS (2019) Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. 3 Biotech 9:292. https://doi.org/10.1007/s13205-019-1823-4
Xiao M, Hu Q, Zhao Y, Bao F, Cui F, Zheng R (2018) Development of 36 SNP markers in Ophiocephalus argus Cantor base on high-throughput sequencing. Conserv Genet Resour 10(1):35–38. https://doi.org/10.1007/s12686-017-0757-6
Acknowledgements
This study was financially supported by the Central Public-Interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS (No. 2017JBFR01); Chinese Earmarked Fund for Modern Agro-Industry Technology Research System (No. CARS-45-05); and Natural Science Foundation of Jiangsu Province (CN) (No. BK20160205).
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
An, R., Fu, J., Jiang, B. et al. Development of SNP markers for the bighead carp (Hypophthalmichthys nobilis) by using transcriptomic sequences. Conservation Genet Resour 12, 409–412 (2020). https://doi.org/10.1007/s12686-020-01133-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-020-01133-z