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

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Abstract

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.

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Acknowledgements

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

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Authors and Affiliations

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA

    Ning Li, Tao Zhou, Xin Geng, Yulin Jin, Xiaozhu Wang, Shikai Liu, Xiaoyan Xu & Dongya Gao

  2. Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, China

    Xiaoyan Xu

  3. The Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China

    Qi Li

  4. Department of Biology, Syracuse University, Syracuse, NY, 13244, USA

    Zhanjiang Liu

Authors
  1. Ning Li
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  2. Tao Zhou
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  3. Xin Geng
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  4. Yulin Jin
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  5. Xiaozhu Wang
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  6. Shikai Liu
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  7. Xiaoyan Xu
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  8. Dongya Gao
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  9. Qi Li
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  10. Zhanjiang Liu
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Corresponding author

Correspondence to Zhanjiang Liu.

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Funding

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.

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Communicated by S. Hohmann.

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Li, N., Zhou, T., Geng, X. et al. Identification of novel genes significantly affecting growth in catfish through GWAS analysis. Mol Genet Genomics 293, 587–599 (2018). https://doi.org/10.1007/s00438-017-1406-1

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  • DOI: https://doi.org/10.1007/s00438-017-1406-1

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