Molecular Genetics and Genomics

, Volume 293, Issue 3, pp 587–599 | Cite as

Identification of novel genes significantly affecting growth in catfish through GWAS analysis

  • Ning Li
  • Tao Zhou
  • Xin Geng
  • Yulin Jin
  • Xiaozhu Wang
  • Shikai Liu
  • Xiaoyan Xu
  • Dongya Gao
  • Qi Li
  • Zhanjiang LiuEmail author
Original Article


Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was found to be significantly associated with body weight. In addition, four suggestively associated QTL regions were identified on linkage groups 1, 2, 23 and 24. Most candidate genes in the associated regions are known to be involved in muscle growth and bone development, some of which were reported to be associated with obesity in humans and pigs, suggesting that the functions of these genes may be evolutionarily conserved in controlling growth. Additional fine mapping or functional studies should allow identification of the causal genes for fast growth in catfish, and elucidation of molecular mechanisms of regulation of growth in fish.


GWAS QTL Growth Fish Hybrid 



The authors wish to thank Ludmilla Kaltenboeck and Huseyin Kucuktas for their technical assistance.

Compliance with ethical standards


This project was supported by a competitive AFRI grant from the Animal Genomics, Genetics and Breeding Program of the USDA National Institute of Food and Agriculture (#2015-67015-22907). Ning Li, Tao Zhou and Yulin Jin are supported by scholarship from the China Scholarship Council.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

All procedures involving the handling and treatment of fish were approved by the Institutional Animal Care and Use Committee (IACUC) at Auburn University.

Supplementary material

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Supplementary material 1 (DOCX 343 KB)
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Supplementary material 4 (XLSX 9 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Ning Li
    • 1
  • Tao Zhou
    • 1
  • Xin Geng
    • 1
  • Yulin Jin
    • 1
  • Xiaozhu Wang
    • 1
  • Shikai Liu
    • 1
  • Xiaoyan Xu
    • 1
    • 2
  • Dongya Gao
    • 1
  • Qi Li
    • 3
  • Zhanjiang Liu
    • 4
    Email author
  1. 1.The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic SciencesAuburn UniversityAuburnUSA
  2. 2.Key Laboratory of Exploration and Utilization of Aquatic Genetic ResourcesShanghai Ocean UniversityShanghaiChina
  3. 3.The Shellfish Genetics and Breeding Laboratory, Fisheries CollegeOcean University of ChinaQingdaoChina
  4. 4.Department of BiologySyracuse UniversitySyracuseUSA

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