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Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish

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Abstract

Hypoxic condition is common in aquaculture, leading to major economic losses. Genetic analysis of hypoxia tolerance, therefore, is not only scientifically significant, but also economically important. Catfish is generally regarded as being highly tolerant to low dissolved oxygen, but variations exist among various populations, strains, and species. In this study, we conducted a genome-wide association study (GWAS) using the catfish 250 K SNP array to identify quantitative trait locus (QTL) associated with tolerance to low dissolved oxygen in the channel catfish × blue catfish interspecific system. Four linkage groups (LG2, LG4, LG23, and LG29) were found to be associated with low oxygen tolerance in hybrid catfish. Multiple significant SNPs were found to be physically linked in genomic regions containing significant QTL for low oxygen tolerance on LG2 and LG23, and in those regions containing suggestively significant QTL on LG2, LG4, LG23, and LG29, suggesting that the physically linked SNPs were genuinely segregating and related with low oxygen tolerance. Analysis of genes within the associated genomic regions suggested that many of these genes were involved in VEGF, MAPK, mTOR, PI3K-Akt, P53-mediated apoptosis, and DNA damage checkpoint pathways. Comparative analysis indicated that most of the QTL at the species level, as analyzed by using the interspecific system, did not overlap with those identified from six strains of channel catfish, confirming the complexity of the genetic architecture of hypoxia tolerance in catfish.

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Acknowledgements

The authors thank Jun Yao, Yun Li, Sen Gao, and Qiang Fu for help with hypoxia challenge and sample collection. Thanks are given to Ludmilla Kaltenboeck and Huseyin Kucuktas for their technical assistance. Xiaoxiao Zhong was supported by scholarships from the China Scholarship Council (CSC).

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Authors and Affiliations

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

    Xiaoxiao Zhong, Xiaozhu Wang, Tao Zhou, Yulin Jin, Suxu Tan, Chen Jiang, Xin Geng, Ning Li, Huitong Shi, Qifan Zeng, Yujia Yang, Zihao Yuan, Lisui Bao, Shikai Liu, Changxu Tian, Eric Peatman & Zhanjiang Liu

  2. Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, 266003, China

    Xiaoxiao Zhong & Qi Li

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  1. Xiaoxiao Zhong
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  2. Xiaozhu Wang
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  3. Tao Zhou
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  17. Qi Li
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Correspondence to Zhanjiang Liu.

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Funding

This project was supported by USDA Aquaculture Research Program Competitive Grant no. 2014-70007-22395, and by Agriculture and Food Research Initiative Competitive Grant no. 2015-67015-22975 from Animal Disease Program, and 2015-67015-22907 from the Tools and Resources - Animal Breeding, Genetics and Genomics Program of the USDA National Institute of Food and Agriculture (NIFA).

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The authors declare that they have no conflict of interest.

Ethical Approval

The experiment was undertaken with the approval of the Institutional Animal Care and Use Committee (IACUC) at Auburn University. Blood samples were collected after euthanasia. All animal procedures were carried out according to the Guide for the Care and Use of Laboratory Animals and the Animal Welfare Act in the United States.

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Zhong, X., Wang, X., Zhou, T. et al. Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish. Mar Biotechnol 19, 379–390 (2017). https://doi.org/10.1007/s10126-017-9757-5

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