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中国农学通报

中国农学通报 ›› 2026, Vol. 42 ›› Issue (18): 180-189.doi: 10.11924/j.issn.1000-6850.casb2026-0501

• 水产·渔业 • 上一篇    下一篇

黄魟基因组分子标记开发及统计分析

刘晓茹1(), 邢琬聆1, 李明僧1, 张耀仁1, 李鹏飞2, 徐胜勇1,3(), 徐开达2()   

  1. 1 浙江海洋大学水产学院， 浙江舟山 316022
    2 浙江省海洋水产研究所， 浙江舟山 316021
    3 全省深远海适养种质发掘与高效牧养技术重点实验室/浙江海洋大学， 浙江舟山 316022
  • 收稿日期:2026-06-18 修回日期:2026-07-17 出版日期:2026-09-25 发布日期:2026-09-24
  • 通讯作者:
    徐胜勇，男，1989年出生，山东青岛人，副研究员，博士，主要从事海洋鱼类基因组学研究；通信地址：316022 浙江省舟山市浙江海洋大学新城校区 浙江海洋大学水产学院，Tel：0580-2556416，E-mail：；
    徐开达，男，1981年出生，浙江舟山人，正高级工程师，主要从事渔业资源养护和合理利用、增殖修复放流技术研究。通信地址：316021 浙江省舟山市定海区临城街道体育路28号 浙江省海洋水产研究所，E-mail：。
  • 作者简介:

    刘晓茹，女，2002年出生，四川雅安人，在读硕士研究生，研究方向：海洋鱼类基因组学。通信地址：316022 浙江省舟山市浙江海洋大学新城校区 浙江海洋大学水产学院，E-mail：。

  • 基金资助:
    国家重点研发计划项目“东海渔业资源一体化修复与海洋牧场构建技术”(2023YFD2401901); 国家重点研发计划项目“近海渔业资源评估与生态渔业技术”(2024YDF2400403); 国家自然科学基金项目“基于群体基因组学的条纹斑竹鲨种群遗传格局及生态适应研究”(32200413)

Development and Statistical Analysis of Genomic Molecular Markers of Hemitrygon bennettii

LIU Xiaoru1(), XING Wanling1, LI Mingseng1, ZHANG Yaoren1, LI Pengfei2, XU Shengyong1,3(), XU Kaida2()   

  1. 1 College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang 316022
    2 Zhejiang Marine Fisheries Research Institute, Zhoushan, Zhejiang 316021
    3 Provincial Key Laboratory of Germplasm Exploration and Efficient Ranching Technology for Deep-Sea Aquaculture/ Zhejiang Ocean University, Zhoushan, Zhejiang 316022
  • Received:2026-06-18 Revised:2026-07-17 Published:2026-09-25 Online:2026-09-24

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摘要：

针对黄魟(Hemitrygon bennettii)种质识别缺乏有效分子标记、遗传多样性特征尚不明确的问题，为其种质鉴定、种群遗传多样性评估提供基础资料，同时为黄魟系统发育、遗传多样性保护及资源管理提供分子支撑，推动其保护遗传学相关研究的深入开展。采用高通量测序数据结合生物信息学分析方法，筛选全基因组单核苷酸多态(SNP)标记并开展种群历史动态分析；识别基因组微卫星位点，筛选高质量位点并设计特异性引物，同时对比分析黄魟与赤魟(H. akajei)的种间微卫星差异；组装线粒体基因组全序列并分析其结构与变异特征。共筛选并注释16150339个SNP位点，基于全基因SNP位点的种群历史动态分析结果显示，黄魟种群在约200万~400万年前经历了两次扩张事件，并在10万~180万年前经历了一次收缩事件；识别出521449个基因组微卫星位点，分布频率为163.02个/Mb，经筛选后获得116个高质量微卫星位点并设计特异性引物，同时筛选到19个黄魟-赤魟种间共有且高异质性的微卫星位点；组装的黄魟线粒体基因组全长17724 bp，比较分析共检测到49个变异位点，且发现黄魟线粒体基因组存在种内长度异质性。本研究筛选的SNP位点、微卫星位点及线粒体基因组全序列，可直接应用于黄魟的种群遗传学分析、种质鉴定、系统发育研究、遗传多样性评估及种质资源科学管理。

关键词: 黄魟, 分子标记, 单核苷酸多态, 微卫星, 线粒体基因组

Abstract:

The lack of effective molecular markers for germplasm identification and ambiguous genetic diversity characteristics severely restrict the research progress of Hemitrygon bennettii. This study aimed to establish fundamental data for germplasm identification and population genetic diversity evaluation of H. bennettii, and to provide molecular evidence for its phylogenetic analysis, genetic diversity conservation, and fishery resource management. The findings are expected to further promote the in-depth development of conservation genetics research on this species. High-throughput sequencing data and bioinformatics approaches were applied to screen genome-wide single nucleotide polymorphism (SNP) markers and analyze the population demographic history of H. bennettii. Genome-wide microsatellite loci were identified, and high-quality loci were screened for specific primer design. Furthermore, interspecific microsatellite variations between H. bennettii and H. akajei were comparatively analyzed. In addition, the complete mitochondrial genome of H. bennettii was assembled, and its genomic structure and variation characteristics were systematically analyzed. A total of 16150339 SNP loci were screened and annotated. Population demographic analysis based on genome-wide SNPs indicated that the H. bennettii population had experienced two expansion events and one bottleneck contraction event. In total, 521449 microsatellite loci were identified in the genome, with a distribution frequency of 163.02 loci per Mb. After strict screening, 116 high-quality microsatellite loci were obtained with specific primers successfully designed. Meanwhile, 19 microsatellite loci shared by H. bennettii and H. akajei with high interspecific heterogeneity were screened out. The total length of the assembled mitochondrial genome of H. bennettii was 17724 bp. A total of 49 variable sites were detected, and obvious intraspecific length heterogeneity was found in its mitochondrial genome. The SNP markers, microsatellite loci, and complete mitochondrial genome sequence obtained in this study can be effectively applied to subsequent population genetic analysis and germplasm identification of H. bennettii. This study provides reliable molecular baseline data for phylogenetic research, genetic diversity assessment, and scientific conservation and management of H. bennettii germplasm resources.

Key words: Hemitrygon bennettii, molecular marker, single nucleotide polymorphism (SNP), microsatellite, mitochondrial genome

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