High-density SNP mapping, QTL analysis and transcriptome assessment for resistance to Pancreas disease in Atlantic Salmon

Hooman Moghadama*, Anna Sonessona, Matthew Baranskia, Aleksei Krasnova, Ashie Norrisb and Håvard Bakkec
 
aNofima, P.O. Box 210, N-1431 Ås, Norway
bMarine Harvest, Rinmore, Fanad, Letterkenny, Ireland
cSalmo Breed AS, Bergen, Norway
 
*E-mail: hooman.moghadam@nofima.no <mailto:>

Introduction

Pancreas disease (PD) is a contagious disease caused by salmonid alphavirus (SAV) with major economic and welfare impacts on salmon farming. Previous work has shown that PD resistance has significant underlying additive genetic components and can potentially be improved through selective breeding1. The aim of this study is to further identify and characterize genes and genomic regions that control PD resistance in Atlantic salmon.

Material and Methods

In this study we investigated the genetic basis of PD resistance in two different populations of Atlantic salmon. The first population consisted of 1,496 fry from 59 full-sibling families of the Marine Harvest Norway breeding program - the Mowi strain. These fish were challenged (50 days post hatch with an average weight of 0.5g) with the SAV3 strain of salmonid alphavirus. All individuals were genotyped on a 37K Affymetrix Axiom SNP array. Through GWAS analysis, we setup a genomic (G) relationship matrix2 using 30,363 detected SNPs. The effect of each SNP was then analysed using ASReml. F-statistics was used to test the significance of the genotype effect.

In the second population, we used Illumina platform to sequence and compare the transcriptome profiles from the heart muscle of 40 post-smolt individuals, representing 32 different families. These fish were selected from approximately 5,300 Salmobreed fish that were challenged with the SAV3 strain and exhibited various degrees of resistance against the disease. For both challenge tests, mortalities were removed from the tanks on a daily bases, whereas survivors were collected and euthanized at the end of the experiment.

Results

We identified 86 SNPs to be significantly associated with resistance to PD. The SNPs are located on 26 different linkage groups and distributed across 73 different genes. The analysis of gene expression data further revealed vast differences in the abundance and regulation of a large number of transcripts between the resistant and the susceptible individuals. In particular, fish that survived the challenge had significantly higher expression of genes with functions in immunity, response to inflammation, stress and defense. On the other hand, susceptible fish showed a marked alteration in the expression of genes involved in lipid metabolism, cardiac physiology and development. Although the two fish stock investigated in this study represent individuals with different genetic backgrounds and developmental stages, more than 30% of the genes that were identified through our GWAS investigation were also exhibited significant differences in their profiles of transcript expression.

Conclusion

Through integration of genome-wide SNP analysis and transcriptome profiling, we have identified candidate genes and genomic regions that seem to be associated to PD resistance in Atlantic salmon.

1      Norris, A. et al. J Fish Dis 31, 913-920, (2008).

2      VanRaden, P. M. et al. J Dairy Sci 90, 2434-2441, (2007).

3      Lemstrova, R. et al. Pharmacogenomics 15, 1133-1145, (2014).