QTL Fine Mapping for Sex Determination Region in Bighead Carp (Hypophthalmichthys nobilis) and Comparison with Silver Carp (Hypophthalmichthys molitrix)

  • Ying Zhou
  • Haiyang Liu
  • Xinhua Wang
  • Beide Fu
  • Xiaomu Yu
  • Jingou TongEmail author
Original Article


Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are genetically close aquaculture fish in the Cyprinidae, which have been confirmed to hold XX/XY sex determination. However, genomic locations of potential sex-related loci in these two fishes are still unknown. In this study, a high-resolution genetic linkage map was constructed by using 2976 SNP and 924 microsatellite markers in a F1 full-sib family of bighead carp, the length of which spanned 2022.34 cM with an average inter-marker distance of 0.52 cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish as well as grass carp. QTL fine mapping for sex trait was performed based on this linkage map of bighead carp and an unpublished linkage map of silver carp. A map distance of 3.863 cM (69.787–73.650 cM) on LG19 of bighead carp and 4.705 cM (79.096–83.801 cM) on LG21 of silver carp was significantly associated with sex phenotypes, and these two LGs are homologous between two fish species. Fourteen markers harboring in these regions were in strong linkage disequilibrium with the sex phenotype variance explained (PVE) varying from 89 to 100%. Two common markers were mapped on the QTL regions of bighead carp and silver carp, suggesting that these two carp species may have similar genetic bases for sex determination. Eleven potentially sex-related genes were identified within or near the sex QTL markers in two species. This study provided insights into elucidating mechanisms and evolution of sex determination in cyprinid fishes.


QTL Sex determination region Comparative mapping Bighead carp Silver carp Sex-related genes 



We would like to thank all colleagues of our lab (Meixia Pang, Xueli Liu, Baojiang Gan) for sample preparation and laboratory technical assistance.

Authors’ Contributions

JT conceived this study and guided the experiments. YZ and HL carried out the experiments and wrote the manuscript. BF performed bioinformatic analysis. XW and XY performed experiments and prepared mapping animals. All authors read and approved the final manuscript.

Funding Information

This research was supported by the National Key Research and Development Program (No. 2018YFD009102) and State Key Laboratory of Freshwater Ecology and Biotechnology (2019FBZ04).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

10126_2019_9929_MOESM1_ESM.xls (20 kb)
Table S1 The information of primers used for qPCR in this study (XLS 20 kb)
10126_2019_9929_MOESM2_ESM.xlsx (358 kb)
Table S2 The information of 3,900 markers located in the high-density linkage map of bighead carp (XLSX 358 kb)
10126_2019_9929_Fig7_ESM.png (200 kb)
Figure S1

The lengths and marker distributions of 24 linkage groups in the female map of bighead carp (PNG 200 kb)

10126_2019_9929_MOESM3_ESM.tif (779 kb)
High Resolution Image (TIF 778 kb)
10126_2019_9929_Fig8_ESM.png (140 kb)
Figure S2

The lengths and marker distributions of 24 linkage groups in the male map of bighead carp (PNG 140 kb)

10126_2019_9929_MOESM4_ESM.tif (645 kb)
High Resolution Image (TIF 645 kb)
10126_2019_9929_Fig9_ESM.png (528 kb)
Figure S3

The syntenic relationships between female (left) and male (right) linkage groups of bighead carp. The common markers are indicated with lines (PNG 527 kb)

10126_2019_9929_MOESM5_ESM.tif (1.4 mb)
High Resolution Image (TIF 1436 kb)


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Copyright information

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

Authors and Affiliations

  1. 1.State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed DesignChinese Academy of SciencesWuhanChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.College of Animal Science and TechnologyHenan University of Animal Husbandry and EconomyZhengzhouChina

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