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Development and Characterization of 35 SNP Markers in the Fat Greenling <i>Hexagrammos otakii</i>
Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
Dalian Eco-Environmental Monitoring Center of Liaoning Province, Dalian, China
- 1 Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
- 2 Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
- 3 Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Institute, Dalian, China
- 4 Dalian Eco-Environmental Monitoring Center of Liaoning Province, Dalian, China
Open Journal of Marine Science·Volume 13 (2022)·Pages 1–6·Published 5 December 2022·DOI10.4236/ojms.2023.131001
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Abstract
Hexagrammos otakii is an important kind of economic fish species in East Asia. However, wild H. otakii resources have declined sharply in recent years as a result of human disturbance and habitat destruction. Thus, it is crucial to protect the current resources of H. otakii . In this study, 35 novel single nucleotide polymorphism (SNP) markers were developed based on restriction-site associated DNA sequencing. The results showed that the observed heterozygosity and expected heterozygosity ranged from 0.1875 to 0.6562 and 0.2679 to 0.5079, respectively. The minor allele frequency ranged from 0.1875 to 0.4375. Polymorphic information content ranged from 0.229 to 0.375. Six SNPs were found to be deviated significantly from the HWE (P < 0.05). These SNP markers will serve as a useful tool for genetic studies and population evaluation aimed at the conservation of H. otakii .
Keywords<i>Hexagrammos otakii</i>SNPRADGenetic Diversity
- Ren, G., Liu, Q., Gao, T. and Yanagimoto, T. (2013) Population Demography and Genetic Structure of the Fat Greenling (Hexagrammos otakii) Inferred from mtDNA Control Region Sequence Analyses. Biochemical Systematics and Ecology, 47, 156-163. https://doi.org/10.1016/j.bse.2012.09.026
- Kang, B. and Wu, Y.F. (1999) Nutritional Composition Analyses of Hexagrammos otakii. Marine Science, 6, 23-24.
- Shen, Z., Wang, B., Hu, F., Liu, H., Guan, H. and Zheng, F. (2019) Isolation and Characterization of Microsatellite Loci in Hexagrammos otakii based on 2b-RAD Method. Journal of Applied Ichthyology, 36, 55-61. https://doi.org/10.1111/jai.13988
- F.A.O. (1993) Report of the Expert Consultation on Utilization and Conservation of Aquatic Genetic Resources. FAO Fisheries Report, No. 491, 58 p.
- Khandaker, L., Akond, M., Liu, S., Kantartzi, S., Meksem, K., Bellaloui, N., Lightfoot, D. and Kassem, M. (2015) Mapping of QTL Associated with Seed Amino Acids Content in “MD96-5722” by “Spencer” RIL Population of Soybean Using SNP Markers. Food and Nutrition Sciences, 6, 974-984. https://doi:10.4236/fns.2015.611101
- Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M. and Blaxter, M.L. (2011) Genome-Wide Genetic Marker Discovery and Genotyping Using Next-Generation Sequencing. Nature Reviews Genetics, 12, 499-510. https://doi.org/10.1038/nrg3012
- Gao, X.G., Bao, X.B., Sun, W., Li, Y.F., Liu, Z.Y. and Liu, W.D. (2021) Isolation and Characterization of 38 SNP Markers for the Black Rockfish, Sebastes schlegelii by Next-Generation Sequencing. Conservation Genetics Resources, 13, 413-416. https://doi.org/10.1007/s12686-021-01226-3
- Yang, J.P., Li, X.H., Li, Y.F., Zhu, S.L., Chen, W.T. and Li, J. (2020) Isolation and Characterization of 30 SNP Markers in Guangdong Bream (Megalobrama terminalis) by Next-Generation Sequencing. Conservation Genetics Resources, 12, 399-402. https://doi.org/10.1007/s12686-020-01131-1
- Yu, A.Q., Shi, Y.H. and Yan, Y.L. (2019) Development and Characterization of 50 snp Markers in Coilia ectenes. Conservation Genetics Resources, 12, 177-181. https://doi.org/10.1007/s12686-019-01086-y
- Martin, M. (2011) Cutadapt Removes Adapter Sequences from High Throughput Sequencing Reads. EMBnet Journal, 17, 10-12. https://doi.org/10.14806/ej.17.1.200
- Kalinowski, S.T., Taper, M.L. and Marshall, T.C. (2007) Revising How the Computer Program CERVUS Accommodates Genotyping Error Increases Success in Paternity Assignment. Molecular Ecology, 16, 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x