Development of SNP markers in Leiocassis longirostris Günther using high-throughput sequencing

  • Mingsong XiaoEmail author
  • Qinsen Hu
  • Yan Zhao
  • Fangyin Bao
Technical Note


The Chinese longsnout catfish (Leiocassis longirostris Günther) is a semi-migratory freshwater species. Leiocassis longirostris is mainly inhabiting the main stream of the Yangtze River and rarely found in lakes due to over fishing, environmental pollution and other human disturbances. Novel single nucleotide polymorphisms (SNPs) were screened based on high-throughput sequencing in Leiocassis longirostris. In this study, 40 SNP markers were developed successfully with 30 individuals from the Yangtze River segment of Nanjing, China. The observed heterozygosity (Ho) ranged from 0.0003 to 1.0000, while the expected heterozygosity (He) varied from 0.3367 to 0.9390. The minor allele frequency ranged from 0.0167 to 0.2500. Thirty-four SNPs have been confirmed to fit Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.0013). The first set of SNP makers developed from Leiocassis longirostris will provide valuable informating in population genetics and resource conservation.


Leiocassis longirostris SNP Transcriptome Genetic diversity 



This research was supported by the Natural Science Foundation of Anhui Province, China (1708085MC78), Anhui Province Key Research and Development Plan Project, China (1804a07020119).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Ethics approval and consent

The six specimens of Leiocassis longirostris were used for the experiments. Investigations were conducted according to the guiding principles for the use and care of laboratory animals and in compliance with Anhui Science and Technology University regulations on animal welfare. All surgery was performed by MS-222 anesthesia.


  1. Chu XL, Zheng BS, Dai DY (1999) Fauna sinica Osteichthyes: Siluriforme. Beijing Scientific & Technical Publishers, Beijing of China, pp 44–45Google Scholar
  2. Clarke KR, Gorley RN (2001) PRIMER v5: user manual/tutorial. PRIMER-E, PlymouthGoogle Scholar
  3. Dudgeon D (2000) The ecology of tropical Asian rivers and streams in relation to biodiversity conservation. Ann Rev Ecol Syst 31:239–263CrossRefGoogle Scholar
  4. Francis CY, Rong CY, Boyle T (2000) Popgene Microsoft Windows based freeware for population genetic analysis. In: Molecular biology and biotechnology centre. University of Alberta, CanadaGoogle Scholar
  5. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson PK, Ding L (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283–2285CrossRefGoogle Scholar
  6. Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993CrossRefGoogle Scholar
  7. Liang HW, Guo SS, Luo XZ, Li Z, Zou GW (2016) Molecular diagnostic markers of Tachysurus fulvidraco and Leiocassis longirostris and their hybrids. Springer Plus 5:2115CrossRefGoogle Scholar
  8. Liu B, Teng SS, Shao YQ, Chai XL, Xiao GQ, Fang J, Zhang JM (2016) Characterization of 20 SNP markers in the blood clam (Tegillarca granosa) using T m-shift assay. Conserv Genet Resour 8(3):239–242CrossRefGoogle Scholar
  9. Luo M, Jiang LK, Liu Y, Zhan GQ, Xia SZ (2000) Comparative study on isoenzymes in Leiocassis longirostris. Chin J Appl Environ Biol 6:447–451Google Scholar
  10. Meldgaard T, Nielsen EE, Loeschcke V (2003) Fragmentation by weirs in a riverine system: a study of genetic variation in time and space among populations of European grayling (Thymallus thymallus) in a Danish river system. Conserv Genet 4:735–747CrossRefGoogle Scholar
  11. Shen T, He XS, Lei ML, Wang JR, Li XM, Li JM (2014) Cloning and structure of a histocompatibility class IIA gene (Lelo-DAA) in Chinese longsnout catfish (Leiocassis longirostris). Genes Genom 36:745–753CrossRefGoogle Scholar
  12. Wang ZW, Zhou JF, Ye YZ, Wei QW, Wu QJ (2006) Genetic structure and low-genetic diversity suggesting the necessity for conservation of the Chinese longsnout catfish, Leiocassis longirostris (Pisces: Bagriidae). Environ Biol Fish 75:455–463CrossRefGoogle Scholar
  13. Wu CJ (1975) Population ecology of Leiocassis longirostris Gunther (Pisces, Bagridae) with reference to the problem of maximum sustained yield. Acta Hydrobiol Sin 5(3):387–409Google Scholar
  14. Xiao MS, Yang G (2009) Isolation and characterization of 17 microsatellite loci for the Chinese longsnout catfish (Leiocassis longirostris). Mol Ecol Res 9(3):1039–1041CrossRefGoogle Scholar
  15. Xiao MS, Xia HW, Ma YH (2012) Genetic variation of the Chinese longsnout catfish Leiocassis longirostris in the Yangtze River revealed using mitochondrial DNA cytochrome b sequences. Acta Ecol Sin 32:305–314CrossRefGoogle Scholar
  16. Xiao MS, Hu QS, Zhao Y, Bao FY, Cui F, Zheng RQ (2018) Development of 36 SNP markers in Ophiocephalus argus Cantor based on high-throughput sequencing. Conserv Genet Resour 10(1):35–38CrossRefGoogle Scholar
  17. Yang G, Xiao MS, Yu YY, Xu SX (2012) Genetic variation at mtDNA and microsatellite loci in Chinese longsnout catfish (Leiocassis longirostris). Mol Biol Rep 39:4605–4617CrossRefGoogle Scholar
  18. Yu YY, Xiao MS, Chen L, Yang G (2009) Isolation and characterization of microsatellite loci in the longsnout catfish (Leiocassis longirostris). Aquac Res 40:246–248CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.College of Life and Health SciencesAnhui Science and Technology UniversityFengyangChina

Personalised recommendations