Marine Biotechnology

, Volume 21, Issue 2, pp 250–261 | Cite as

Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq

  • Dan Li Jiang
  • Xiao Hui Gu
  • Bi Jun Li
  • Zong Xian Zhu
  • Hui Qin
  • Zi ning Meng
  • Hao Ran Lin
  • Jun Hong XiaEmail author
Original Article


Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.


Nile tilapia Red tilapia Genome-wide association study Salt tolerance QTL-seq 


Authors’ Contributions

JHX and HRL contributed to project conception. Experiments and data analysis were conducted by DLJ, XHG, BJL, ZXZ, ZNM, and HQ. The manuscript was prepared by JHX and DLJ. All the authors read and approved the final manuscript.

Funding Information

This work was supported by the Science and Technology Program of Guangzhou, China (No. 201804020013, 201803020043), Science and Technology Planning Project of Guangdong Province, China (2017A030303008), and National Natural Science Foundation of China (No. 31572612).

Compliance with Ethical Standards

All experiments in this study were approved by the Animal Care and Use Committee of the School of Life Science at Sun Yat-Sen University and were performed according to the regulations and guidelines established by this committee.

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

10126_2019_9877_Fig5_ESM.png (162 kb)
Supplementary Fig.1

Gene expression of candidate genes (Dennd4c and PLAA) in Nile tilapia post 24 h challenges of 20 ppt salinity. The expression level was normalized with the expression level in brain (0 ppt). (PNG 161 kb)

10126_2019_9877_MOESM1_ESM.tif (12.4 mb)
High Resolution Image (TIF 12683 kb)
10126_2019_9877_MOESM2_ESM.docx (15 kb)
Supplementary Table 1 Summary of primer sequences used in this study. (DOCX 14 kb)
10126_2019_9877_MOESM3_ESM.xlsx (161 kb)
Supplementary Table 2 QTL-seq statistics for chrLG18 of red tilapia (XLSX 161 kb)


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Authors and Affiliations

  1. 1.State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China

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