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Genome-Wide Association Study Identifies Loci Associated with Resistance to Viral Nervous Necrosis Disease in Asian Seabass

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Abstract

Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), is one major threat to mariculture. Identifying loci and understanding the mechanisms associated with resistance to VNN are important in selective breeding programs. We performed a genome-wide association study (GWAS) using genotyping-by-sequencing (GBS) to study the genomic architecture of resistance to NNV infection in Asian seabass. We genotyped 986 individuals from 43 families produced by 15 founders with 44498 bi-allelic genetic variants using GBS. The GWAS identified three genome-wide significant loci on chromosomes 16, 19, and 20, respectively, and six suggestive loci on chromosomes 1, 8, 14, 15, 21, and 24, respectively, associated with resistance to NNV infection measured as binary and quantitative traits. Using the 500 most significant markers in combination with a training population of 800 samples could reach a genomic prediction accuracy of 0.7. Candidate genes significantly associated with resistance to NNV, including lysine-specific demethylase 2A, beta-defensin 1, and cystatin-B, which play important roles in immune responses against virus infection, were identified. Almost all the candidate genes were differentially expressed in different tissues against NNV infection. The significant genetic variants can be used in genomic selection and help understand the mechanism of resistance to VNN. Future studies should use populations of large effective size and whole genome resequencing to identify more useful genetic variants.

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Acknowledgements

This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore under its Competitive Research Program (CRP Award No. NRF-CRP7-2010-01) and TLL’s Innovation Support Fund (TLL-ISF-2015-001).

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  1. Le Wang, Peng Liu and Shuqing Huang contributed equally to this paper

Authors and Affiliations

  1. Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore

    Le Wang, Peng Liu, Shuqing Huang, Baoqing Ye, Elaine Chua, Zi Yi Wan & Gen Hua Yue

  2. Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore

    Peng Liu & Gen Hua Yue

  3. School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore

    Zi Yi Wan & Gen Hua Yue

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  1. Le Wang
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Contributions

LW and GHY designed the experiments. LW, PL, and ZYW performed the virus challenge. LW, SQH, EC, and ZYW conducted the lab experiments. LW and BY analyzed the data. LW and GHY drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Gen Hua Yue.

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The authors declare that they have no conflict of interests.

Sequence Data Accession

Raw sequence data for the study has been deposited into the DDBJ Sequence Read Archive database with Bioproject no. PRJDB5163.

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Wang, L., Liu, P., Huang, S. et al. Genome-Wide Association Study Identifies Loci Associated with Resistance to Viral Nervous Necrosis Disease in Asian Seabass. Mar Biotechnol 19, 255–265 (2017). https://doi.org/10.1007/s10126-017-9747-7

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