Abstract
Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr–smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.
Highlights
Beyond their cultural importance, salmonids can provide over a billion dollars annually to the economies of countries with recreational and commercial fisheries (e.g. Canada, Pinfold, 2011)
used the Fluidigm BioMark HD platform for measuring gene expression, a high throughput microfluidics-based technology that can individually quantify 96 assays across 96 samples at once. We focused on these four groups because of their population declines in Southern British Columbia (BC), Canada and subsequent hatchery supplementation (DFO 2013; Beamish et al, 2009; Noakes et al, 2000)
Combining the Sockeye salmon and Rainbow trout signatures using sparse independent principal component analysis (sIPCA) to identify the top 100 features, there were 53 upregulated and 23 downregulated features that were significant for the Sockeye salmon limma analysis (Table S1)
Summary
Salmonids can provide over a billion dollars annually to the economies of countries with recreational and commercial fisheries (e.g. Canada, Pinfold, 2011). To increase salmonid populations and augment fisheries, hatchery breeding programs are used (Fraser, 2008). Aquaculture is used to alleviate some of the fishing pressure on wild populations (Naylor et al, 2000) and provide additional economic opportunities (Bostock et al, 2010). The success of both hatcheries and aquaculture is known to be limited by the physiological condition of the smolt life stage during the transition from freshwater to seawater Tools to measure the physiological condition of smolts are routinely used and improvements in them sought to inform culture and decisions for optimizing smolt performance
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