Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Authors: DANZMANN, ROY - University Of Guelph; KOCMAREK, ANDREA - University Of Guelph; NOTMAN, JOSEPH - University Of Guelph; Rexroad, Caird; Palti, Yniv

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2016
Publication Date: 1/15/2016
Publication URL: http://handle.nal.usda.gov/10113/61849
Citation: Danzmann, R., Kocmarek, A., Notman, J., Rexroad III, C.E., Palti, Y. 2016. Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients. Biomed Central (BMC) Genomics. 17:1-18. doi: 10.1186/s12864-016-2363-5.

Interpretive Summary: Maximizing growth rate on the farm is a major goal for all aquaculture breeding programs as faster growing fish require shorter amount of time to reach market size and hence reducing the cost of farming. Increasing day light hours or photoperiod regime can increase growth rate in rainbow trout even at constant temperature. Therefore, in order to understand the dynamics of growth in fish it is important to consider the background influence of photoperiod regime on gene expression differences. This study examined the influence of a declining photoperiod regime (winter solstice) compared to an increasing photoperiod regime (spring equinox) on white muscle gene expression profiles in fast and slow-growing rainbow trout from a commercial North American aquaculture strain. Genetic markers information from the fast and slow-growing fish was used to identify chromosome regions that likely harbor genes that impact growth in rainbow trout. Taken together the results from this study help us in identifying genes and biological pathways that affect growth rate of rainbow trout in the aquaculture production environment and better understand how changes in water temperature and length of day light interact with the genetic background of the fish and impact how fast they can grow to market size.

Technical Abstract: Background: Circannual rhythms in vertebrates can influence a wide variety of physiological processes. Some notable examples include annual reproductive cycles and for poikilotherms, seasonal changes modulating growth. Increasing water temperature elevates growth rates in fishes, but increases in photoperiod regime can have similar influences even at constant temperature. Therefore, in order to understand the dynamics of growth in fish it is important to consider the background influence of photoperiod regime on gene expression differences. This study examined the influence of a declining photoperiod regime (winter solstice) compared to an increasing photoperiod regime (spring equinox) on white muscle gene expression profiles in fast and slow-growing rainbow trout from a commercial aquaculture strain. Results: Slow-growing fish could be characterized as possessing gene expression profiles that conform in many respects to an endurance training regime in humans . They have elevated mitochondrial and cytosolic creatine kinase expression levels and appear to suppress mTOR-signaling as evidenced by elevated TSC2 expression, and they also have elevated p53 levels. Large fish display a physiological repertoire that may be consistent with strength/resistance physiology having elevated cytoskeletal gene component expression and glycogen metabolism cycling along with higher PI3K levels. In many respects small vs. large fish match eccentric vs. concentric muscle expression patterns, respectively. Lipogenic genes are also more elevated in larger fish, the most notable being the G0S2 switch gene. M and Z-line sarcomere remodelling appears to be more prevalent in large fish as evidenced by higher MuRF1 levels along with several other genes. Twenty-three out of 26 gene families with previously reported significant SNP-based growth differences were detected as having significant expression differences. Conclusions: Larger fish display a broader array of genes showing upregulation in expression, and their profiles are more similar to those observed in December lot fish (i.e., an accelerated growth period). Conversely, small fish display gene profiles more similar to seasonal growth decline phases (i.e., September lot fish). Metabolism class genes are more upregulated in small fish and they possess many upregulated genes related to nucleobase turnover and RNA processing and enhanced catabolism. Large fish display higher cellular turnover components (i.e., cell death, apoptosis) and have elevated expression for stress response, signal transduction, and cell-cell signaling genes.