Transcriptomic analysis of spleen infected with infectious salmon anemia virus reveals distinct pattern of viral replication on resistant and susceptible Atlantic salmon ( Salmo salar )

Dettleff, Phillip; Moen, Thomas; Santi, Nina; Martı́nez, Vı́ctor

doi:10.1016/j.fsi.2017.01.005

Cited by 36 publications

(23 citation statements)

References 58 publications

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“…Dettleff, Moen, Santi, and Martinez () used RNAseq to compare gene expression between pools of DNA from challenged families that were genetically resistant and pools from families that were susceptible to ISA. They found decreased expression of upregulated transcripts of interleukin‐10‐like ( il10 ), interleukin‐10 receptor subunit beta‐like ( il10rb ) and interleukin‐13 receptor ( il13ra2 ) in resistant families.…”

Section: Discussionmentioning

confidence: 99%

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

et al. 2019

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Infectious salmon anaemia (ISA) is a highly virulent viral disease of Atlantic salmon that causes massive economic losses to infected aquaculture operations. Our goal was to detect and map quantitative trait loci (QTL) that confer resistance to ISA in an admixed commercial strain of Atlantic salmon that was largely founded from the Saint John River (SJR) in North America. Full‐sibling families were challenged with a virulent strain of ISA virus. Mortality was tracked during two annual trials with individual fish that survived to the end of the trial being classified as ‘resistant’, and those that died were classified as ‘susceptible’. Ten families with intermediate levels of mortality and an average size of 54.2 individuals were chosen for genotyping with a 50K SNP array designed for the SJR strain. Single nucleotide polymorphisms that were segregating within families were first used to make a composite 11K female linkage map that was then used to find the positions of QTL for ISA resistance using a half‐sib model. The dam‐based HS model detected a total of three QTL for ISA resistance including an experiment‐wide significant QTL on Ssa25 that accounted for 8.3% of the phenotypic variance and chromosome‐wide significant QTL on Ssa03 and on Ssa04 that accounted for 6.0% and 6.6% respectively. We conclude that classic linkage mapping within families continues to be an important method of detecting QTL for oligogenic traits in strains founded from multiple populations. Single nucleotide polymorphisms with moderate trait effects are being used to select within families for more ISA‐resistant strains of Atlantic salmon.

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Section: Discussionmentioning

confidence: 99%

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

et al. 2019

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“…The dataset adds to the increasing volume of RNA-Seq information being made available by the research community. The majority of existing Atlantic salmon RNA-Seq datasets have been generated to address specific biological questions, including host response to disease challenge (Dettleff et al, 2017 ; Valenzuela-Muñoz et al, 2017 ; Rozas-Serri et al, 2018 ), developmental progression (Wang et al, 2014 ) or nutritional requirements (Jin et al, 2018 ). The consequence is a paucity of transcriptomic profiling of animals not subject to an experimental regime designed to elicit specific responses or that characterize a biological extreme.…”

Section: Discussionmentioning

confidence: 99%

Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon

et al. 2018

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The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to homeobox and bhlh families were identified for pituitary gland, pou and zf-c2h2 families for brain, arid, and zf-c2h2 for ovary and rxr-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.

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“…A few studies comparing between susceptible and resistant fish identified differences in their type-I IFN mediated antiviral responses. Higher IFN response in susceptible fish was found also for Atlantic salmon at day 7 and 21 post infection with IPNV [41] and for late stage of ISAV infection [40]. These studies potentially suggested that an earlier activation of the IFN response could improve resistance.…”

Section: Anti-viral Immune Response In Susceptible Fishmentioning

confidence: 61%

Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance

Tadmor-Levi

Doron‐Faigenboim

Marcos-Haddad

et al. 2019

Preprint

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Background Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp ( Cyprinus carpio ), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection. Results In susceptible fish, over four times more differentially expressed genes were up-regulated between day 0 and 4 compared to resistant fish. Susceptible and resistant fish responded distinctively to infection as only 55 (9%) of the up-regulated genes were shared by these two fish types. Susceptible fish elicited a typical anti-viral response, involving interferon and interferon responsive genes, earlier than resistant fish did. Furthermore, chemokine profiles indicated that the two fish types elicited different cellular immunity responses. A comparative phylogenetic approach assisted in chemokine copies annotation pointing to different orthologous copies common to bony-fishes and even carp-specific paralogs that were differentially regulated and contributed to the different response of these two fish types. Susceptible fish up-regulated more ccl19 chemokines, which attract T-cells and macrophages, the anti-viral role of which is established, whereas resistant fish up-regulated more cxcl8/il8 chemokines, which attract neutrophils, the antiviral role of which is unfamiliar. Conclusions Taken together, by pointing out transcriptional differences between susceptible and resistant fish in response to CyHV-3 infection, this study unraveled possible genes and pathways that take part in disease resistance mechanisms in fish and thus, enhances our understanding of fish immunogenetics and supports the development of sustainable and safe aquaculture.

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Transcriptomic analysis of spleen infected with infectious salmon anemia virus reveals distinct pattern of viral replication on resistant and susceptible Atlantic salmon ( Salmo salar )

Cited by 36 publications

References 58 publications

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon

Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance

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