Abstract
Triplophysa (Hedinichthys) yarkandensis macroptera is an endemic species in China, that is mainly distributed in Gansu Province. To date, research on this species has been very limited, focusing mainly on its taxonomy, without any available molecular markers. In the present study, we identified 55 SNP markers in T. (Hedinichthys) yarkandensis macroptera. The minor allele frequency ranged from 0.050 to 0.500, and the observed and expected heterozygosity ranged from 0.167 to 1.000 and 0.155 to 0.508, respectively. The polymorphic information content ranged from 0.141 to 0.375. Among these SNP markers, seventeen loci showed significant departures from Hardy-Weinberg equilibrium after Bonferroni correction. These novel SNP markers will be helpful for future studies on genetic management and population conservation in this species.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data Availability
The data and material that support the findings of this study are available from the corresponding author upon reasonable request.
Code Availability
Not applicable.
References
Alzohairy AM (2011) BioEdit: an important software for molecular biology. Gerf Bull Biosci 1:60–61
Blanc-Jolivet C, Kersten B, Daïnou K, Hardy O, Guichoux E, Del-camp A, Degen B (2017) Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia. Conserv Genet Res 9:531–533. https://doi.org/10.1007/s12686-017-0716-2
Chen YY, Chen YF, Liu HZ (1996) Studies on the position of the QingHai-XiZang plateau region in zoogeographic divisions and its eastern demarcation line. Acta Hydrobiol Sin 20:97–103
Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
He DK, Chen YX, Chen YF (2006) Molecular phylogeny and biogeography of the genus Triplophysa. Prog Nat Sci 16:1395–1404
He CL, Song ZB, Zhang E (2011) Triplophysa fishes in China and the status of its taxonomic studies. Sichuan J Zool 30:150–155. https://doi.org/10.3969/j.issn.1000-7083.2011.01.038
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Lalitha S (2000) Primer Premier 5. Biotech Softw Internet Rep 6:270–272. https://doi.org/10.1089/152791600459894
Prokofiev AM (2010) Morphological classification of loaches (Nemacheilinae). J Ichthyol 50:827–913. https://doi.org/10.1134/S0032945210100012
Ren B, Ma YW, Turson, Guo Y, Zhang RM, Au ABD, Liu ZZ J (2004) The study on the biology of Triplophysa (Hedinichthgs) yarkandensis (day) in Akesu River. Chin J Fisheries 17:46–52
Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP an other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305. https://doi.org/10.1186/1297-9686-34-3-275
Wang L, Huang SQ, Xia JH, Liu P, Wan ZY, Yue GH (2015a) Genome-wide discovery of gene-related SNPs in Barramundi Lates calcarifer. Conserv Genet Resour 7:605–608. https://doi.org/10.1007/s12686-015-0444-4
Wang T, Zhang YP, Guan LH, Du YY, Lou ZY, Jiao WL (2015b) Current freshwater fish resources and the application of DNA barcoding in species identification in Gansu Province. Biodivers Sci 23:306–313
Zhao TQ (1983) Numerical Taxonomy and Infraspecific differentiation of the Loach Nemacheilus Yarkandensis Day. Acta Zootaxonomica Sinica 8:438–447
Zhu SQ (1989) The loaches of the subfamily nemacheilinae in China. Jiangsu Science and Technology Publishing House, Nanjing
Acknowledgements
The authors are grateful to Wenqiong Wu and Siyi Zhu for their assistance with the laboratory work.
Funding
This work was supported by grants from the Project of Investigation on Fishery Resources and Environment of Northwest China, the Project of Sichuan Science and Technology Program (2021YFYZ0015).
Author information
Authors and Affiliations
Contributions
Qiang Li wrote the manuscript. Yeyu Chen revised the manuscript. Hongyu Ke, Zhongmeng Zhao and Han Zhao provided a source of this species. Jiansheng Lai, Xiaoyun Wu, Mingjiang Song and Feiyang Li performed the experiments. Ya Liu designed the experiments and provided formal analysis. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Competing Interests
The authors do not have any conflict of interest.
Ethics approval
All fish handling and experimental procedures were approved by Animal Care and Use Committee of the Fishery Institute of the Sichuan Academy of Agricultural Sciences, and all animal collection and use protocols were carried out in accordance with the guidelines and regulations for the care and use of laboratory animals at the Fishery Institute of the Sichuan Academy of Agricultural Sciences.
Consent to participate
The authors provide consent to participate.
Consent for publication
The authors provide consent for publication.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Li, Q., Chen, Y., Ke, H. et al. Isolation and characterization of 55 SNP markers in Triplophysa (Hedinichthys) yarkandensis macroptera. Conservation Genet Resour 16, 127–130 (2024). https://doi.org/10.1007/s12686-023-01345-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-023-01345-z