Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR.

G3 : Genes - Genomes - Genetics
Arash AkbarzadehKristina M Miller

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° 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 an...Continue Reading

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Citations

Jun 1, 2021·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Ken M JeffriesKristina M Miller

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Methods Mentioned

BETA
RNA-seq
PCR
PCA
MDS
Assay
amidation

Software Mentioned

factoextra R package
Time PCR Analysis
prepDE
Fluidigm
FastQC
GitHub
systemPipeR
NormFinder
edgeR
Trimmomatic

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