Marine Biotechnology

, Volume 21, Issue 3, pp 348–358 | Cite as

Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus)

  • Le Wang
  • Nan Xie
  • Yubang Shen
  • Baoqing Ye
  • Gen Hua YueEmail author
  • Xiaoyu FengEmail author
Original Article


High-density genetic maps are essential for mapping QTL, improving genome assembly, comparative genomics, and studying sex chromosome evolution. The northern snakehead (Channa argus) is an economically important foodfish species with significant sexual dimorphism, where the males grow much faster and bigger than the females. However, to date, the sex determination pattern is still not clear, limiting identification of sex chromosomes, even sex determination genes and development of monosex populations that are valuable for both sex evolution of vertebrates and aquaculture practices. Here, a sex-averaged map and two sex-specific genetic maps were constructed with 2974, 2323, and 2338 SNPs, respectively. Little difference was observed in the pattern of sex-specific recombination between female- and male-specific genetic maps. Genome scan identified a major locus for sex determination at LG16. Females and males are, respectively, homogametic and heterogametic, suggesting an XY sex determination system for this species. By resequencing genomes, InDels in the sex-associated QTL region were discovered and used for developing sex-specific PCR assays for fast sexing of snakehead. These high-density genetic maps provide useful resources for future genomic studies in snakehead and its related species. The PCR assays for sexing are of importance in developing all male populations for aquaculture.


Snakehead Genetic map Sex determination Molecular sexing 


Authors’ Contributions

XYF and NX initiated the project for genetic improvement of Northern snakehead. LW, XYF, NX, and GHY designed the experiments. XF and NX set up the cross and collected samples. LW, NX, YS, and BY conducted the lab experiments. LW analyzed the data. LW and GHY drafted the manuscript. All authors read and approved the final manuscript.

Funding Information

This research is supported by the internal fund of the Institute of Fisheries, Hangzhou Academy of Agricultural Science.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Consent for Publication

Not applicable

Ethics Approval and Consent to Participate

Not applicable

Supplementary material

10126_2019_9884_MOESM1_ESM.xlsx (293 kb)
Table S1 Detailed SNPs and map information for genetic maps of the snakehead (XLSX 292 kb)
10126_2019_9884_MOESM2_ESM.xlsx (11 kb)
Table S2 (XLSX 10 kb)
10126_2019_9884_MOESM3_ESM.xlsx (23 kb)
Table S3 (XLSX 23 kb)
10126_2019_9884_MOESM4_ESM.xlsx (10 kb)
Table S4 (XLSX 10 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingaporeRepublic of Singapore
  2. 2.Institute of Fishery ScienceHangzhou Academy of Agriculture SciencesHangzhouChina
  3. 3.Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of EducationShanghai Ocean UniversityShanghaiChina
  4. 4.Department of Biological SciencesNational University of SingaporeSingaporeRepublic of Singapore
  5. 5.School of Biological SciencesNanyang Technological UniversitySingaporeRepublic of Singapore

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