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Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea)

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Abstract

Large yellow croaker is an important marine culture species in China. Recently, the large yellow croaker industry is threatened by various disease problems, especially for the white spot disease, which is caused by parasite Cryptocaryon irritans. In the current study, we conducted a genome-wide association study (GWAS) for C. irritans resistance in two large yellow croaker populations (n = 264 and n = 480, respectively). We identified 15 QTL with explained genetic variance ranging from 1 to 8% in the two populations. One QTL on chromosome 23 was shared by the two populations, and three QTL had been reported in the previous study. We identified a lot of biological pathways associated with C. irritans resistance, such as hormone transport, response to bacterium, apoptotic process, acute inflammatory response to antigenic stimulus, and NF-kappa B signaling pathway. The genes casp8 and traf6 involved in regulatory network for apoptosis and inflammation were identified to be candidate genes for C. irritans resistance. Our results showed the complex polygenic architecture of resistance of large yellow croaker against C. irritans. These results would be helpful for the researches of the molecular mechanism of C. irritans resistance and genome-assisted breeding of large yellow croaker.

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Data Availability

We agree to archive the sequence data associated with this manuscript on the NCBI should the manuscript be accepted.

Code Availability

The code used during the current study to analyze the datasets is available from the corresponding author on reasonable request.

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Acknowledgments

We thank Dr. Biao Jiang (Sun Yat-sen University) for his assistance on the C. irritans challenge experiment.

Funding

We acknowledge financial support from Science and Technology Major Project of Fujian Province (2020NZ08003), Industry-University Collaboration Project of Fujian Province (2019N5001), Open Research Fund Project of State Key Laboratory of Large Yellow Croaker Breeding ( LYC2019RS02 and LYC2019RS03), Independent Research Project for State Key Laboratory of Large Yellow Croaker Breeding (LYC2017ZY01), the Fundamental Research Funds for the Central Universities (No. 20720200110), the Project of Industry-College-Institute Cooperation between Ningde City and Xiamen University (No. 2019C002), the Special Project of Local Science and Technology Development Guided by the Central Government (2019L3032), the National Key Research and Development Program of China (2018YFC1406306,) and the Foreign Cooperation Project of Fujian Province (No. 2019I1008).

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Author notes

  1. Ji Zhao and Tao Zhou equally contributed to this work.

Authors and Affiliations

  1. State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China

    Ji Zhao & Peng Xu

  2. Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China

    Ji Zhao, Tao Zhou, Huaqiang Bai, Qiaozhen Ke, Bijun Li, Zhixiong Zhou, Fei Pu & Peng Xu

  3. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China

    Qiaozhen Ke, Weiqiang Zheng & Peng Xu

  4. Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China

    Mindong Bai

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  1. Ji Zhao
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  2. Tao Zhou
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Contributions

PX conceived the project. JZ, HB, MB, and QK conducted the C. irritans challenge experiments and collected the sample. JZ, ZZ, and FP contributed the construction of ddRAD libraries. JZ prepared the data, conducted the data analysis, designed the charts and tables and wrote the manuscript. PX, TZ, MB, WZ, and BL revised the manuscript. All authors read and validated the manuscript.

Corresponding author

Correspondence to Peng Xu.

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Ethics Approval

The study was approved by the Laboratory Animal Management and Ethics Committee, College of Ocean and Earth Sciences, Xiamen University. All experimental procedures involving large yellow croaker were performed according to the Regulations for the Administration of Affairs Concerning Experimental Animals (College of Ocean and Earth Sciences, Xiamen University).

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The authors declare that they have no competing interests.

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Zhao, J., Zhou, T., Bai, H. et al. Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea). Mar Biotechnol 23, 242–254 (2021). https://doi.org/10.1007/s10126-021-10019-6

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