Developing specific molecular biomarkers for thermal stress in salmonids

Abstract

Background: Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue.

Results: Candidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon (O. nerka) and Chinook salmon (O. tshawytscha) (cool, 13-14 °C and warm temperatures 18-19 °C) over 5-7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies.

Conclusions: The results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon.

Keywords: Biomarker; Gene expression; Pacific salmon; Salmon FIT-CHIPs; Thermal stress.

Fig. 1

The Venn diagram on the left compares three signatures that were returned by robust limma analysis with an FDR threshold of 0.01 for the 2007 sockeye, 2008 sockeye and 2009 pink salmon data sets (corresponding to signatures DS0101, DS0102 and DS0103 in Table 6). The right plot shows PCA results for 98 samples and 139 EST identifiers returned as significant by all three robust limma analyses

Fig. 2

Gene expression box plots of thermal stress biomarkers for adult sockeye salmon held at cool and warm temperature conducted in 2007 and 2008. m = moribund. *P < 0.05; **P < 0.01; ***P < 0.001

Fig. 3

Gene expression box plots of thermal stress biomarkers for juvenile Chinook salmon held at cool and warm temperature conducted in 2017 and 2018. m = moribund. *P < 0.05; **P < 0.01; ***P < 0.001