Abstract
Ocellated icefish (Chionodraco rastrospinosus, C. rastrospinosu), plays an essential role in the Antarctic food web, and is mainly distributed at depths of 200-1,000 m in the Southern Ocean. The abundance of this species has been drastically reduced due to various impacts, including overfishing and climate change. Therefore, in order to develop, sustainably exploit and protect this species, it is urgent to understand the state of its population resources. However, there is little information available regarding its genetic structure and a lack of effective molecular markers of this species. In this study, 105 novel single nucleotide polymorphism (SNP) markers were developed using double digest restriction site-associated DNA sequencing (ddRAD-Seq). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0 to 1 and 0.2188 to 0.5, respectively. The polymorphism information content (PIC) value ranged from 0.194824 to 0.375. After Bonferroni correction, none of the loci deviated significantly from Hardy-Weinberg equilibrium (p > 0.05). The development of these SNP markers will be useful for the genetic analysis and scientific management of C. rastrospinosus.
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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, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4(1):s13742–s13015. https://doi.org/10.1186/s13742-015-0047-8
Duan M, Zhang C, Liu Y, Ye Z, Liu C, Tian Y, He J (2022) Early-life history traits of two icefishes, spiny icefish Chaenodraco wilsoni and ocellated icefish Chionodraco rastrospinosus, in the Ross Sea revealed by otolith microstructure. Polar Biol 45(3):427–436. https://doi.org/10.1007/s00300-021-03002-3
Kock KH (2005) Antarctic icefishes (Channichthyidae): a unique family of fishes. A review, part I. 28(11):862–895. Polar biologyhttps://doi.org/10.1007/s00300-005-0019-z
Kock KH, Gage JD, Tyler PA (1993) Antarctic fish and fisheries. J Mar Biol Assoc UK 73:252–359. https://doi.org/10.1017/S0025315400032835
Kuhn KL, Gaffney PM (2006) Preliminary assessment of population structure in the mackerel icefish (Champsocephalus gunnari). Polar Biol 29:927–935. https://doi.org/10.1007/s00300-006-0134-5
Kuhn KL, Gaffney PM (2008) Population subdivision in the Antarctic toothfish (Dissostichus mawsoni) revealed by mitochondrial and nuclear single nucleotide polymorphisms (SNPs). Antarct Sci 20(4):327–338. https://doi.org/10.1017/S0954102008000965
La Mesa M, Catalano B, Jones CD (2013) Early life history of the ocellated icefish, Chionodraco rastrospinosus, off the Antarctic Peninsula. Antarct Sci 25(3):373–380. https://doi.org/10.1017/S0954102012001095
La Mesa M, Guicciardi S, Donato F, Riginella E, Schiavon L, Papetti C (2020) Comparative analysis of otolith morphology in icefishes (Channichthyidae) applying different statistical classification methods. Fish Res 230:105668. https://doi.org/10.1016/j.fishres.2020.105668
Li XL, Hu XX, Lu HJ, Liu Y, Wang CC (2021) Development and validation of 107 SNP markers in Todarodes pacificus (Ommastrephidae). Conserv Genet Resour 13(4):417–424. https://doi.org/10.1007/s12686-021-01227-2
Liu K, Muse SV (2005) Power marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129. https://doi.org/10.1093/bioinformatics/bti282
Marschoff ER, Barrera-Oro ER, Alescio NS, Ainley DG (2012) Slow recovery of previously depleted demersal fish at the South Shetland Islands, 1983–2010. Fish Res 125:206–213. https://doi.org/10.1016/j.fishres.2012.02.017
Miao GD, Wang F, Guo JH, Zhang P, Ma HY (2022) Development of 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD approach. Conserv Genet Resour 14(1):19–26. https://doi.org/10.1007/s12686-021-01236-1
Papetti C, Zane L, Patarnello T (2006) Isolation and characterization of microsatellite loci in the icefish Chionodraco rastrospinosus (Perciformes, Notothenioidea, Channichthyidae). Mol Ecol Notes 6:207–209. https://doi.org/10.1111/j.1471-8286.2005.01194.x
Russell D, Sambrook J (2001) Molecular Cloning: A Laboratory Manual
Schiavon L, Dulière V, La Mesa M, Marino IAM, Codogno G, Boscari E, Riginella E, Battistotti A, Lucassen M, Zane L, Papetti C (2021) Species distribution, hybridization and connectivity in the genus Chionodraco: unveiling unknown icefish diversity in antarctica. Divers Distrib 27:766–783. https://doi.org/10.1111/ddi.13249
Shen Y, Zhu GP (2022) First report on the burden and distribution of Cu, Zn, Pb, and cd in the Ocellated icefish (Chionodraco rastrospinosus) of northern Antarctic Peninsula. Mar Pollut Bull 182:113963. https://doi.org/10.1016/j.marpolbul.2022.113963
Wei XY, Zhu GP (2022) Shape and ontogenetic changes in otolith of the ocellated icefish (Chionodraco rastrospinosus) from the Bransfield Strait. Antarct Zool 153:126025. https://doi.org/10.1016/j.zool.2022.126025
Xu H, Wang CC, Liu Y, Liu BL, Li G (2021) Development and characterization of 101 SNP markers in jumbo flying squid, Dosidicus gigas. Conserv Genet Resour 13(1):13–20. https://doi.org/10.1007/s12686-020-01177-1
Zhang J, Yang JJ, Zhang LK, Luo J, Zhao H, Zhang JN, Wen CL (2020) A new SNP genotyping technology target SNP-seq and its application in genetic analysis of cucumber varieties. Sci Rep 10(1):1–11. https://doi.org/10.1038/s41598-020-62518-6
Zhao Y, Wang CC, Liu BL, Li G, Xu H (2021) Development And Identification of 131 SNP Markers in Sthenoteuthis Pteropus (Steenstrup). Conservation Genet Resources 14, 371–380 (2022). https://doi.org/10.1007/s12686-022-01293-0
Funding
This research was supported by the International Science and Technology Cooperation Key Special Project of the National Key Research and Development Program (grant no 2023YFE0104500); the National Natural Science Foundation of China (Grant No. 31702312); the National Natural Science Foundation of China (Grant No. 41776185); the National Key R&D Program of China (Grant No. 2018YFC1406801); China Scholarship Council (Grant No. 2021 − 109).
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Yewei Yu carried out all the experiments; Congcong Wang and Yang Liu designed the methods and experiments, interpreted the results and finished the discussion. Guoping Zhu was responsible for overall supervision and participated in coordination. All authors read and approved the final manuscript.
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Yu, Y., Liu, Y., Zhu, G. et al. Development and validation of 105 SNP markers in Chionodraco rastrospinosus. Conservation Genet Resour 15, 205–213 (2023). https://doi.org/10.1007/s12686-023-01318-2
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DOI: https://doi.org/10.1007/s12686-023-01318-2