Development of SNP markers in Leiocassis longirostris Günther using high-throughput sequencing
- 30 Downloads
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.
KeywordsLeiocassis 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.
- Chu XL, Zheng BS, Dai DY (1999) Fauna sinica Osteichthyes: Siluriforme. Beijing Scientific & Technical Publishers, Beijing of China, pp 44–45Google Scholar
- Clarke KR, Gorley RN (2001) PRIMER v5: user manual/tutorial. PRIMER-E, PlymouthGoogle Scholar
- 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
- 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
- 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