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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00068

Genomic and transcriptomic analysis of amoebic gill disease resistance in Atlantic salmon (Salmo salar L.)

  • 1Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima), Norway
  • 2SalmoBreed AS, Norway
  • 3Norwegian Veterinary Institute, Norway

Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated. In this study, to identify the genetic mechanisms of AGD resistance, we first investigated the molecular signatures of AGD infection in Atlantic salmon through a challenge model, where we compared the transcriptome profiles of the naïve and infected animals. We then conducted a genome-wide association analysis with 1333 challenged tested fish to map the AGD resistance genomic regions, supported by the results from the transcriptomic data. Further, we investigated the potential of incorporating gene expression analysis results in genomic prediction to improve prediction accuracy. Our data suggest thousands of genes have modified their expression following infection, with a significant increase in the transcription of genes with functional properties in cell adhesion and a sharp decline in the abundance of various components of the immune system genes. From the genome-wide association analysis, QTL regions on chromosomes ssa04, ssa09 and ssa13 were detected to be linked with AGD resistance. In particular, we found that QTL region on ssa04 harbours members of the cadherin gene family. These genes play a critical role in target recognition and cell adhesion. The QTL region on ssa09 also is associated with another member of the cadherin gene family, protocadherin Fat 4. The associated genetic markers on ssa13 span a large genomic region that includes interleukin-18-binding protein, a gene with function essential in inhibiting the proinflammatory effect of cytokine IL18. Incorporating gene expression information through a weighted genomic relationship matrix approach decreased genomic prediction accuracy and increased bias of prediction. Together, these findings help to improve our breeding programs and animal welfare against AGD and advance our knowledge of the genetic basis of host-pathogen interactions.

Keywords: Atlantic salmon, Amoebic gill disease, Transcriptome, GWAS, Genomic prediction

Received: 29 Jun 2018; Accepted: 28 Jan 2019.

Edited by:

Haja N. Kadarmideen, Technical University of Denmark, Denmark

Reviewed by:

Yniv Palti, Cool and Cold Water Aquaculture Research (USDA-ARS), United States
Chuanju Dong, Henan Normal University, China
Xiaoping He, Department of Fisheries and Oceans (Canada), Canada  

Copyright: © 2019 Boison, Gjerde, Hillestad, Makvandi-Nejad and Moghadam. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Hooman Moghadam, SalmoBreed AS, Bergen, 5035, Hordaland, Norway, hooman@salmobreed.no