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PreprintCited by 40Environmental Toxicology and EcotoxicologyPhysiological and biochemical adaptationsAquaculture disease management and microbiota

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Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR

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Akbarzadeh, Arash, Houde, Aimee Lee S., Sutherland, Ben J.G., Günther, Oliver P., Miller, Kristina M.·2020·G3 Genes Genomes Genetics
DOI 10.1101/2020.05.14.086090PMC PMC7466982

Preprint — published as 10.1534/g3.120.401487 · Paper page

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Abstract

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon ( Oncorhynchus tshawytscha ), held in normoxia [dissolved oxygen (DO) > 8 mg L −1 ] and hypoxia (DO = 4□5 mg L −1 ) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.

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Metadata

Authors
Akbarzadeh, A., Houde, A. L. S., Sutherland, B. J. G., Günther, O. P., & Miller, K. M.
Affiliations
Fisheries and Oceans Canada (CA)
Corresponding author
  • Akbarzadeh, Arash
  • Miller, Kristina M.
ORCID
Venue
G3 Genes Genomes Genetics
Publisher
openRxiv
Published
2020-05-16
Volume
10
Issue
9
Pages
3321-3336
ISSN
2160-1836 (ISSN-L)
DOI
10.1101/2020.05.14.086090
PMC
PMC7466982
OpenAlex
W3044719851
Cited by
40
References
1
Citations by year
2026: 8 · 2025: 9 · 2024: 10 · 2023: 4 · 2022: 5 · 2021: 4
FWCI
1.30
Type
journal article
Language
en
Open access
Licence
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (cc-by)
Funders
Pacific Salmon Foundation
Topics
  • Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Environmental Toxicology and Ecotoxicology
  • Physical Sciences › Environmental Science › Ecology › Physiological and biochemical adaptations
  • Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
Keywords
hypoxia, hypoxia markers, Oncorhynchus tshawytscha, gill gene expression, dissolved oxygen, differentially expressed genes, cell cycle, cell proliferation, qPCR assay validation, water salinity, stressor identification
MeSH terms
Animals, Hypoxia, RNA, Salmonidae, Biomarkers, Sequence Analysis, RNA

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