Development of multi-species qPCR assays for a nanofluidic transcriptional profiling chip to assess responses of salmonids to changing environments

Ecologically and socio-economically important salmonid fishes in Canada are threatened by diverse environmental stressors. Using a prototype for a custom-designed nanofluidic stress transcriptional profiling chip (STP-Chip), we designed and tested 112 multi-species Taqman qPCR assays using gill, liver, and muscle tissue from eight species of salmonids across four genera. Of the tested 112 assays, 69 assays showed amplification in gill, 64 in liver, and 67 in muscle across all eight salmonid species. In general, the assays performed better in Salmo, Oncorhynchus, and Salvelinus species than in Coregonus species. Not surprisingly, we observed tissue-specific variation among qPCR amplification patterns. Stress, circadian rhythm, apoptosis, growth-metabolism, and detoxification-relevant assays showed high success rates for amplification across all salmonid species for all three tissues. In contrast, neural plasticity, appetite regulation, osmoregulation, immune function, endocrine disruption, and hypoxia-relevant assays showed poorer amplification, potentially due to the tissues being tested. These qPCR assays can be used to design custom STP-Chips for quantifying stress in salmonid fishes and monitoring physiological responses to rapid environmental changes regionally and globally.