Abstract
The Japanese anchovy, Engraulis japonicus, is an important economic fish that is distributed in the northwest Pacific Ocean. The effective assessment and management of the Engraulis japonicus fishery requires reliable information regarding its population’s genetic structure. The recent development of double digest restriction-site associated DNA sequencing (ddRAD-Seq) methods may contribute to the discovery of SNPs and the assessment of genetic structure. In our study, 98 single nucleotide polymorphism (SNP) markers were developed using ddRAD-Seq. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.8000 and 0.2778 to 0.5000, respectively. The polymorphism information content (PIC) ranged from 0.239198 to 0.375. All loci have been substantiated to follow the Hardy–Weinberg equilibrium. These novel polymorphic SNP markers will play an important role in the genetic research of E.japonicus, which will be beneficial to the development and utilization of E.japonicus resources. This study aims to provide technical support for the research of genetic diversity of E. japonicus populations through the development of SNP markers.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22(11):3124–3140. https://doi.org/10.1111/mec.12354
Chang CC, Chow CC, Cam TL, Shashaank V, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Giga Sci 4(1):7. https://doi.org/10.1186/s13742-015-0047
Checkley DM, Asch RG, Rykaczewski R (2017) Climate, Anchovy, and Sardine. Annual Rev Mar Sci 9:469–493. https://doi.org/10.1146/annurev-marine-122414-033819
Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89(5):415–426. https://doi.org/10.1093/jhered/89.5.415
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinf (Oxford England) 21(9):2128–2129. https://doi.org/10.1093/bioinformatics/bti282
Okazaki Y, Tadokoro K, Kubota H, Kamimura Y, Hidaka K (2019) Dietary overlap and optimal prey environments of larval and juvenile sardine and anchovy in the mixed water region of the western North Pacific. Mar Ecol Prog Ser 630:149–160. https://doi.org/10.3354/meps13124
Shendure J, Ji HL (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145. https://doi.org/10.1038/nbt1486
Yu ZN, Kong XY, Guo TH, Jiang YY, Zhuang ZM, Jin XS (2005) Mitochondrial DNA sequence variation of Japanese anchovy Engraulis japonicus from the Yellow Sea and East China Sea. Fish Sci 71(2):299–307. https://doi.org/10.1111/j.1444-2906.2005.00964.x
Zhang BD, Li YL, Xue DX, Liu JX (2020) Population Genomics reveals shallow genetic structure in a connected and ecologically important fish from the Northwestern Pacific Ocean. Front Mar Sci 7:374. https://doi.org/10.3389/fmars.2020.00374
Zheng W, Zou l, Han ZQ (2015) Genetic analysis of the populations of Japanese anchovy Engraulis japonicus from the Yellow Sea and East China Sea based on mitochondrial cytochrome b sequence. Biochem Syst Ecol 58:169–177. https://doi.org/10.1016/j.bse.2014.12.007
Funding
This research was supported by Program on the Survey, Monitoring and Assessment of Global Fishery Resources (Comprehensive scientific survey of fisheries resources at the high seas) sponsored by the Ministry of Agriculture and Rural Affairs; the National Natural Science Foundation of China (Grant No. 31702312).
Author information
Authors and Affiliations
Contributions
Chenghui Song and Yang Liu carried out all the experiments; Congcong Wang and Yang Liu designed the methods and experiments, interpreted the results and finished the discussion. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Declarations
Experimental protocols involving live animals were approved by the Ethics Committee for the Use of Animal Subjects of Shanghai Ocean University.
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Song, C., Liu, Y. & Wang, C. Development and validation of 98 SNP markers in Japanese anchovy, Engraulis japonicus. Conservation Genet Resour 16, 117–125 (2024). https://doi.org/10.1007/s12686-023-01342-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-023-01342-2