Abstract
Harpadon nehereus is a widespread economical fish found in the coastal seas of China and has important ecological value in the marine ecosystem. However, its germplasm resources have been seriously degraded due to natural factors and anthropogenic activities. In this study, high-throughput sequencing was applied to search for microsatellite loci in H. nehereus transcriptome to provide references for its resource conservation and utilization. Polymorphic loci were developed by non-denaturing polyacrylamide gel electrophoresis, and their cross-species amplified ability was detected in three related species. A total of 5652 microsatellites were identified from 16974320 unigenes. Among the primer pairs designed for 100 SSRs for PCR amplification, 80% were successfully amplified, and 26 loci were polymorphic with a high number of alleles from 3 to 11 each. The expected (He) and observed (Ho) heterozygosities were 0.355–0.885 and 0.375–0.958, respectively. Most of the loci were highly polymorphic (polymorphism information content: 0.316–0.852; mean: 0.713), and these markers can be applied in the population genetic diversity research of H. nehereus. However, the transferability of these primers was low, probably because of the close relation of the collected species. In follow-up work, simple sequence repeats will be excavated with genome-based technologies, and related species will be gathered to address the present inadequacies.
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Acknowledgements
This research was supported by the Scientific Research Projects of Department of Education of Zhejiang Province (No. Y201942611), the Science and Technology Innovation Project of College Students in Zhejiang Province (No. 2021R411008), and the Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang Province.
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Huang, X., Ning, Z. & Yang, T. Development and Characterization of Microsatellite Markers for Harpadon nehereus Based on High-Throughput Sequencing and Cross-Species Amplification in Three Myctophiformes Fishes. J. Ocean Univ. China 22, 181–188 (2023). https://doi.org/10.1007/s11802-023-5089-4
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DOI: https://doi.org/10.1007/s11802-023-5089-4