Transcriptomic studies of Atlantic salmon responses to dietary omega-3 long-chain polyunsaturated fatty acids, Piscirickettsia salmonis infection, immunogens, and functional feed

Xue, Xi (2022) Transcriptomic studies of Atlantic salmon responses to dietary omega-3 long-chain polyunsaturated fatty acids, Piscirickettsia salmonis infection, immunogens, and functional feed. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Atlantic salmon farming faces several issues and challenges such as disease outbreaks and the limited supply of fish oil, affecting the sustainability of the industry. The current thesis aimed to gain a better understanding of the dietary requirement of omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA; i.e. DHA+EPA), immune responses against Piscirickettsia salmonis or immunogens, and the immune-modulating properties of a functional feed in Atlantic salmon. In Chapter 2, I studied the impact of varying levels of DHA and EPA (0, 1.0, and 1.4% of the diet) on the hepatic transcriptome. My data suggested that ~1.0% of dietary ω3 LC-PUFA is sufficient to sustain the optimal growth performance of Atlantic salmon, but may not be enough to maintain good health and survival compared with fish fed diets containing a higher amount of DHA and EPA. In Chapter 3, Atlantic salmon parr were infected with an EM-90-like isolate of Piscirickettsia salmonis through intraperitoneal injection. I used microarray and qPCR analyses to study the head kidney transcriptomic differences between high and low infection individuals at 21 days post-injection (DPI). Many innate and adaptive immune processes were dysregulated in P. salmonis-infected Atlantic salmon. In contrast, a small number of general physiological processes was affected. Furthermore, the comparison of individuals with differing infection levels has provided insights into the biological processes possibly involved in natural resistance against P. salmonis. In Chapter 4, I used small RNA deep sequencing and qPCR analyses to characterize Atlantic salmon head kidney miRNA expression responses to polyriboinosinic polyribocytidylic acid [pIC; a synthetic double- stranded RNA (dsRNA) analogue, to elicit antiviral-like responses] and formalin-killed typical Aeromonas salmonicida (a bacterin, to elicit antibacterial responses) stimulations. I identified and qPCR confirmed nine miRNA biomarkers of Atlantic salmon response to pIC and/or bacterin stimulations. I also found that dietary CpG ODN 1668 may be helpful in modulating the bacterin-triggered antibacterial immune response. In Chapter 5, as a follow-up study to Chapter 4, I found that pIC and/or bacterin stimulations significantly modulated the expression of many immune-relevant predicted target genes of previously identified miRNAs. Significant down-regulation of immune-relevant transcripts (e.g. tlr9, irf5, il1r1, hsp90ab1, itgb2) by dietary CpG ODN 1668 were evident, especially among pre-injection and PBS-injected fish. Significant correlations between the changes in mRNA and miRNA expression representing putative miRNA-target pairs provided insights into how miRNAs might fine-tune the expression of immune-relevant mRNAs. Overall, this thesis has provided new insights into the dietary requirement of ω3 LC-PUFA, immune responses against P. salmonis infection and immunogens, and the immunomodulatory functions of dietary CpG in Atlantic salmon. The novel results and molecular biomarkers generated by this thesis will be valuable in future research aimed at improving aquaculture sustainability.

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