Development and validation of 98 SNP markers in Japanese anchovy, Engraulis japonicus

IF 0.9 4区环境科学与生态学 Q4 BIODIVERSITY CONSERVATION Conservation Genetics Resources Pub Date : 2023-12-19 DOI:10.1007/s12686-023-01342-2

Chenghui Song, Yang Liu, Congcong Wang

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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.

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日本鳀鱼 98 个 SNP 标记的开发与验证

日本鳀鱼（Engraulis japonicus）是一种重要的经济鱼类，分布于西北太平洋。对日本鳀鱼渔业的有效评估和管理需要有关其种群遗传结构的可靠信息。最近发展起来的双消化限制位点相关 DNA 测序（ddRAD-Seq）方法可能有助于发现 SNPs 和评估遗传结构。在我们的研究中，利用 ddRAD-Seq 开发了 98 个单核苷酸多态性（SNP）标记。观察到的杂合度（Ho）和预期杂合度（He）分别为 0.3333 至 0.8000 和 0.2778 至 0.5000。多态性信息含量（PIC）为 0.239198 至 0.375。所有位点均符合哈代-温伯格平衡。这些新的多态性SNP标记将在日本鳗鲡遗传研究中发挥重要作用，有利于日本鳗鲡资源的开发和利用。本研究旨在通过SNP标记的开发，为日本鳗鲡种群遗传多样性研究提供技术支持。

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来源期刊

Conservation Genetics Resources BIODIVERSITY CONSERVATION-GENETICS & HEREDITY

CiteScore

2.90

自引率

9.10%

发文量

审稿时长

3-6 weeks

期刊介绍： Conservation Genetics Resources promotes the conservation of genetic diversity and advances the study of conservation genetics by providing rapid publication of technical papers and reviews on methodological innovations or improvements, computer programs, and genomic resources, as well as on the practical application of these resources towards the development of effective conservation policy and practice.