The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon

• Published in: Genomics (San Diego, Calif.) Vol. 113; no. 6; pp. 3842 - 3850
• Main Authors: Pavelin, Jon, Jin, Ye Hwa, Gratacap, Remi L., Taggart, John B., Hamilton, Alastair, Verner-Jeffreys, David W., Paley, Richard K., Rubin, Carl-johan, Bishop, Stephen C., Bron, James E., Robledo, Diego, Houston, Ross D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-11-2021; Academic Press
• Subjects: Animals; Aquaculture; CRISPR; Disease resistance; Fish Diseases - genetics; Gene expression; Genetic Markers; Infectious pancreatic necrosis virus; QTL; Quantitative Trait Loci; Salmo salar - genetics; Whole genome resequencing; QTL; Whole genome resequencing; Disease resistance; CRISPR; Gene expression; Aquaculture
• ISSN: 0888-7543; 1089-8646; 1089-8646
• DOI: 10.1016/j.ygeno.2021.09.012

Genetic resistance to infectious pancreatic necrosis virus (IPNV) in Atlantic salmon is a rare example of a trait where a single locus (QTL) explains almost all of the genetic variation. Genetic marker tests based on this QTL on salmon chromosome 26 have been widely applied in selective breeding to markedly reduce the incidence of the disease. In the current study, whole genome sequencing and functional annotation approaches were applied to characterise genes and variants in the QTL region. This was complemented by an analysis of differential expression between salmon fry of homozygous resistant and homozygous susceptible genotypes challenged with IPNV. These analyses pointed to the NEDD-8 activating enzyme 1 (nae1) gene as a putative functional candidate underlying the QTL effect. The role of nae1 in IPN resistance was further assessed via CRISPR-Cas9 knockout of the nae1 gene and chemical inhibition of the nae1 protein activity in Atlantic salmon cell lines, both of which resulted in highly significant reduction in productive IPNV replication. In contrast, CRISPR-Cas9 knockout of a candidate gene previously purported to be a cellular receptor for the virus (cdh1) did not have a major impact on productive IPNV replication. These results suggest that nae1 is the causative gene underlying the major QTL affecting resistance to IPNV in salmon, provide further evidence for the critical role of neddylation in host-pathogen interactions, and highlight the value in combining high-throughput genomics approaches with targeted genome editing to understand the genetic basis of disease resistance.
•Whole genome sequencing and functional annotation were used to characterise the major IPNV resistance QTL in Atlantic salmon.•Gene expression analyses pointed to NEDD-8 activating enzyme 1 (nae1) as a putative functional candidate underlying the QTL.•CRISPR-Cas9 knockout and chemical inhibition of nae1 in cell lines resulted in significant reduction in IPNV replication.•CRISPR-Cas9 knockout of a previously suggested candidate gene (cdh1) did not have an impact on productive IPNV replication.•These results suggest that nae1 is the causative gene underlying the major QTL affecting resistance to IPNV in salmon.