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Effects of rrm1 on NNV Resistance Revealed by RNA-seq and Gene Editing

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Abstract

Viral nervous necrosis (VNN) disease caused by the nervous necrosis virus (NNV) is a major disease, leading to a huge economic loss in aquaculture. Previous GWAS and QTL mapping have identified a major QTL for NNV resistance in linkage group 20 in Asian seabass. However, no causative gene for NNV resistance has been identified. In this study, RNA-seq from brains of Asian seabass fingerlings challenged with NNV at four time points (5, 10, 15 and 20 days post-challenge) identified 1228, 245, 189 and 134 DEGs, respectively. Eight DEGs, including rrm1, were located in the major QTL for NNV resistance. An association study in 445 survived and 608 dead fingerlings after NNV challenge revealed that the SNP in rrm1 were significantly associated with NNV resistance. Therefore, rrm1 was selected for functional analysis, as a candidate gene for NNV resistance. The expression of rrm1 was significantly increased in the gill, liver, spleen and muscle, and was suppressed in the brain, gut and skin after NNV challenge. The rrm1 protein was localized in the nuclear membrane. Over-expression of rrm1 significantly decreased viral RNA and titer in NNV-infected Asian seabass cells, whereas knock-down of rrm1 significantly increased viral RNA and titer in NNV-infected Asian seabass cells. The rrm1 knockout heterozygous zebrafish was more susceptible to NNV infection. Our study suggests that rrm1 is one of the causative genes for NNV resistance and the SNP in the gene may be applied for accelerating genetic improvement for NNV resistance.

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Data Availability

Raw sequence data for the study has been deposited into the DDBJ Sequence Read Archive database with Bioproject no. PRJDB11816.

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Acknowledgements

We thank our lab members Mr Hongyan Pang and Yanfei Wen for assistance in spawning, egg collection, larval and juvenile culture. Zituo Yang is supported by a graduate research scholarship from Tropical Marine Science Institute, National University of Singapore

Funding

This research was supported by the internal fund of Temasek Life Sciences Laboratory, Singapore.

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Authors and Affiliations

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

    Zituo Yang, Sek Man Wong & Gen Hua Yue

  2. Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore

    Zituo Yang, Sek Man Wong & Gen Hua Yue

  3. National University of Singapore Suzhou Research Institute, Suzhou, 215123, Jiangsu, China

    Sek Man Wong

  4. School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore

    Gen Hua Yue

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  1. Zituo Yang
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Contributions

This manuscript is a part of the PhD thesis of ZTY. GHY initiated the selective breeding program of the Asian seabass in 2003. ZTY, SMW and GHY designed the study. ZTY cultured fish, conducted challenge experiments and collected samples. ZTY constructed all experiments, analyzed the data and drafted the manuscript. SMW and GHY supervised the PhD thesis of ZTY. All authors read and approved the final manuscript for publication.

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Correspondence to Sek Man Wong or Gen Hua Yue.

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Yang, Z., Wong, S.M. & Yue, G.H. Effects of rrm1 on NNV Resistance Revealed by RNA-seq and Gene Editing. Mar Biotechnol 23, 854–869 (2021). https://doi.org/10.1007/s10126-021-10068-x

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