Stress-Response Transcriptional Profiling (STP-Chip) Resources
GEN-FISH greatly adapted from its initial vision of developing one “universal” stress-response transcriptional profiling (STP) chip; when it became clear that the candidate genes were not universally expressed across taxonomic groups, our team pivoted to no fewer than 20 iterative, order-specific STP-Chips. These chips can address and investigate stressors ranging from transport stress to circadian rhythm to osmoregulatory stressors across 6 orders of fishes.
On top of that, there have been multiple chips developed that were not part of the original proposal, including an American Eel chip and a chip that can target genes expressed in mucus, allowing for truly non-lethal and minimally-invasive sample collection. A tremendous amount of time and dedicated work has gone into each version of each STP-Chip.
SAL_CIR1V1_28
SAL_NEU1V1_28
SAL_NEU1V1_28
SAL_NEU1V1_28
SAL_STP2V1_56
PROOF OF CONCEPT STRESSOR TRIALS
These experiments served to verify the effectiveness of the STP-Chips within and across species and stressors. Click each species to learn more.
Arctic Char
Arctic Char + Thermal Stress: PhD student Shayla Larson-Hossack is studying the effects of depleted energy reserves on thermal tolerance in Arctic Char. Using the Salmoniformes General Stress STP-Chip, liver and gill transcriptional profiling will be performed to gain insight into the metabolic and physiological responses associated with fasting and thermal challenges in Arctic Char. The experimental component of this work was performed at the Ontario Aquaculture Research Centre (Agricultural Research and Innovation Ontario). Analyses are ongoing. PI: Dr. Nicholas Bernier, University of Guelph.
Arctic Charr + Immune Stress + Diet Stress: PhD student Shayla Larson-Hossack is studying the effects of depleted energy reserves on immune performance in Arctic char. Using the Salmoniformes General Stress STP-Chip, transcriptional profiling of the liver, spleen, head kidney, and gills will be performed to gain insight into the immune and metabolic responses associated with fasting and immunization with a novel multivalent salmonid vaccine developed by Merck Animal Health Canada, Forte VII. The experimental component of this work was performed at the Ontario Aquaculture Research Centre (Agricultural Research and Innovation Ontario). Analyses are ongoing. PI: Dr. Nicholas Bernier, University of Guelph.
Atlantic Salmon
Atlantic Salmon + Thermal Stress: As part of a collaboration with the Nova Scotia Salmon Association, the Margaree Salmon Association, and the Unamag’i Institute of Natural Resources, we are studying the behavioural transcriptomics of juvenile Atlantic Salmon to temperature stress and predation stress by Smallmouth Bass in the Southwest Margaree River, NS. MSc student Holly Mosco’s study will be validating in-field use of the Salmoniformes Mucus (Nonlethal) General Stress chip (in comparison to the Salmoniformes Osmoregulatory chip), determining whether pulses in Smallmouth Bass movements cause detectable changes in both salmon behavioural and molecular (i.e., transcriptomic) stress responses. We will also be using eDNA to determine relative Smallmouth Bass abundances throughout the season as the fish collectively move upstream and downstream, varying their exposure to juvenile salmon. PI: Dr. Christina Semeniuk, University of Windsor.
Atlantic Sturgeon
Atlantic Sturgeon + Thermal Stress: PhD student Faith Penny performed pioneering work on the transcriptomics of heat stress. She was the first to compare Atlantic Sturgeon (dipliod) and Shortnose Sturgeon (polyploid) and found they had completely different transcriptomic responses to heat stress. PI: Dr. Scott Pavey, University of New Brunswick
Atlantic Sturgeon + Thermal Stress + Diet Stress: HQP Hossein Haghighi and Kye Madden used RNA-sequencing data from Atlantic Sturgeon, Shortnose Sturgeon, and Lake Sturgeon to generate sequence data for designing a 56 gene Acipenser sturgeons STP-Chip. The chip was tested on Lake Sturgeon that were acutely exposed to high temperatures or were fasted. PI: Dr. Ken Jeffries, University of Manitoba.
- Penny, FM, Bugg, WS, Kieffer, JD, Jeffries, KM, Pavey, SA. 2023. Atlantic Sturgeon and Shortnose Sturgeon exhibit highly divergent transcriptomic responses to acute heat stress. Comparative Biochemistry and Physiology – Part D: Genomics and Proteomics 45: 101058.
Black Bass
Black Bass + Anthropogenic Stress: Declan Burton (PhD student), Myra Thapar (PhD student) and Luc LaRochelle (PhD student) have conducted a number of studies in partnership with Parks Canada, OMNR, various lake associations, and tournament organizers to assess different recreational fisheries issues related to Black Bass management. This has included a comparison of transcriptomic profiles of bass inside versus outside fishing sanctuaries, evaluating the state of bass following different types of fishing tournaments, and evaluating livewell care (especially the use of ice to chill fish) practices. PI: Dr. Steven Cooke, Carleton University.
Bloater
Bloater + Anthropogenic Stress: Declan Burton (PhD student) partnered with OMNR, USGS, and USFWS to assess the extent to which Lake Trout and Bloater could be nonlethally sampled. He also used the STP-Chip to assess whether there were differences in the physiological status of fish that died vs fish that survived post stocking. PI: Dr. Steven Cooke, Carleton University.
Brook Trout
Brook Trout + Thermal Stress: HQP Matt Thorstensen and Theresa Mackey partnering with DFO used transcriptional profiling for assessing the effects of acute thermal stress on Brook Trout. We showed that the behavioural avoidance response occurs at the same time that the transcriptional response begins to change in gill and liver tissue. PI: Dr. Ken Jeffries, University of Manitoba.
- Durhack, T.C., Thorstensen, M.J., Mackey, T.E., Aminot, M., Lawrence, M.J., Audet, C., Enders, E.C. and Jeffries, K.M., 2025. Behavioural responses to acute warming precede critical shifts in the cellular and physiological thermal stress responses in a salmonid fish (brook trout, Salvelinus fontinalis). Journal of Experimental Biology, 228(3), p.JEB249964.
Brook Trout + Thermal Stress: PhD student Ghizlane Banousse studied epigenetic effects related to temperature conditions experienced by breeders at the time of gonad maturation using transcriptomes (Banousse et al. 2024) and Salmoniformes Neuroplasticity STP-Chips (Banousse et al. 2025). PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski; Dr. Christina Semeniuk, University of Windsor.
- Banousse, G., E. Normandeau, C. Semeniuk, L. Bernatchez et C. Audet. 2024. Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study. G3: Genes|Genomes|Genetics. 14: jkae051. https://doi.org/10.1093/g3journal/jkae051. Data depository : DFDR – https://doi.org/10.20383/103.0894
- Banousse, G., C. Semeniuk, D. Garant, J. Jeffrey, SK. S. Islam, N. Bernier, K. Jeffries et C. Audet. 2025. Genetic and environmental basis of transcriptional thermal plasticity of brook charr (Salvelinus fontinalis) fry. Canadian Journal of Fisheries and Aquatic Sciences, 82: 1-15. http://dx.doi.org/10.1139/cjfas-2024-0205. Data depository: Figshare – https://doi.org/10.6084/m9.figshare.26298964.v1
Brook Trout + Thermal Stress: MSc student Christophe Jourdain-Bonneau studied the effect of a thermal chronic stress on juvenile Brook Trout and compared these effects according to the presence or not of a selection process. Data is analyzed, writing is ongoing. PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
Brook Trout + Water Quality Stress + Hypoxia Stress: In an OMNR aquaculture context, PhD student Ghizlane Banousse and MSc student Angelina Lagneau compared the effect of generation time spent in captivity on Brook Trout juvenile performance and on brain activity (Salmoniformes Neuroplasticity STP-Chip). PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski; Dr. Christina Semeniuk, University of Windsor.
- Banousse, G., C. Audet, A. Lagneau, A. Wilder, C.C. Wilson, C.A.D. Semeniuk. Influence of generations in captivity, life stage and temperature on gene expression in brain tissue of juvenile brook charr (Salvelinus fontinalis). Data depository: Figshare – https://figshare.com/s/f4a0762e23b43f7085af
Brook Trout + Water Quality Stress + Hypoxia Stress: Post-doc Maria Martinez-Silva compared anadromous and resident Brookt Trout using Salmoniformes STP-Chips sampled on 5 different sites from the Sainte-Marguerite River (Qué.) and will combine transcriptomics to behaviour and metabolic data obtained by partners on the project (Réseau Québec Maritime, Ministère de l’Environnement, de la Lutte contre les Changements Climatiques, de la Faune et des Parcs du Québec). PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
Brook Trout + Anthropogenic Stress: PhD student Julie Viana together with partnering Institut France-Québec pour la coopération scientifique en appui au secteur maritime (IFQM) and Fondation de France studied the genetics of small Brook Trout populations inhabiting the St-Pierre-and-Miquelon archipelago. Population genetics showed differences among the three main islands (St-Pierre, Langlande, Miquelon) and among hydrosystems present on the three islands. STP-Chips were used to see whether or not the genetic landscape was associated to a phenotypic landscape.
- Viana, J., G. Evanno, C. Audet et F. Teletchea. 2025. Fine-scale genetic structure of small fish populations in islands: the case of brook charr Salvelinus fontinalis (Mitchill, 1814) in Saint-Pierre and Miquelon (France). Evolutionary Applications 2025: 18:e70041. https://doi.org/10.1111/eva.70041.
Brook Trout + Anthropogenic Stress: Partnering with Pourvoirie des Bouleaux Blancs, Forestville (Qué.) in a field context, PhD student Ghizlane Banousse and MSc student Angelina Lagneau compared Brook Trout from 7 different lakes administered by the same outfitter who found performance differences among his lakes. PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski; Dr. Christina Semeniuk, University of Windsor.
Brook Trout + Anthropogenic Stress: HQP Riley Beach, Grace Dycha, Alex Wilder and Sarah Al-Zaher examined the effects of sound stressors on neural plasticity and brain expression of critical genes for neural development in Brook Trout and found differential regulation of many genes in this axis. The development of this Salmoniformes Neuroplasticity STP-Chip now opens the way for additional work understanding how environmental stressors can have critical influences on neural development. PI: Dr. Dennis Higgs, University of Windsor.
- Riley K. Beach, Grace M. Dycha, Alex Wilder, Christina A.D. Semeniuk, Daniel D. Heath & Dennis M. Higgs. No trout about it: behavioural and transcriptional effects of long-term noise exposure in brook trout (Salvelinus fontinalis). Published Can J Fish Aq Sci 2025.
Brook Trout + Anthropogenic Stress: Declan Burton (PhD student) worked with Kenauk Nature to assess the effects of stocking Brook Trout on survival across a range of temperatures. Combining mortality and STP-Chips, we identified thermal thresholds where stocking was ineffective given too much stress/mortality. PI: Dr. Steven Cooke, Carleton University.
Brook Trout + Thermal Stress + Anthropogenic Stress: Andrew Howarth (PhD student) used non-lethal gill biopsies to assess catch-and-release angling impacts on brook trout in the thermally stressed Credit River. Because the Credit River is under so much thermal stress, there is interest in also using transcriptomics for future work. Indeed, the local Trout Unlimited chapter is keen to support such work moving forward. PI: Dr. Steven Cooke, Carleton University.
Bull Trout
Bull Trout + Thermal Stress + Hypoxia Stress: Partnering with DFO, Bull Trout gametes were collected from Smith-Dorrien Creek in Alberta and brought to the Freshwater Institute in Winnipeg in multiple years to rear for acclimation studies. HQP Dr. Carol Best and Dr. Analisa Lazaro-Côté used transcriptional profiling using salmonid 56 gene thermal and hypoxia stress STP-Chips to characterize the effects of acclimation temperatures on bull trout at multiple life stages.
- Best, C., Durhack, T.C., Chapelsky, A.J., Aminot, M., Islam, S.S., Heath, D.D., Mochnacz, N.J. and Jeffries, K.M., 2024. Transcriptional profiling provides insights on sublethal thermal stress thresholds in juvenile bull trout. Canadian Journal of Fisheries and Aquatic Sciences, in press.
Chinook Salmon
Chinook Salmon + Immune Stress: In collaboration with Yellow Island Aquaculture Ltd. MSc student Xiaoqing Dang conducted an infection trial on Chinook salmon using V. anguillarum and compared the utility of STP-Chip (immune function) qPCR vs real time PCR analysis of immune gene expression. Her conclusion was that the chip based assays reflected what was seen in other methods. This work is being prepared for submission. PI: Dr. Brian Dixon, University of Waterloo.
Lake Sturgeon
Lake Sturgeon + Thermal Stress + Diet Stress: HQP Hossein Haghighi and Kye Madden used RNA-sequencing data from Atlantic Sturgeon, Shortnose Sturgeon, and Lake Sturgeon to generate sequence data for designing a 56 gene Acipenser sturgeons STP-Chip. The chip was tested on Lake Sturgeon that were acutely exposed to high temperatures or were fasted. PI: Dr. Ken Jeffries, University of Manitoba.
- Penny, FM, Bugg, WS, Kieffer, JD, Jeffries, KM, Pavey, SA. 2023. Atlantic Sturgeon and Shortnose Sturgeon exhibit highly divergent transcriptomic responses to acute heat stress. Comparative Biochemistry and Physiology – Part D: Genomics and Proteomics 45: 101058.
Lake Sturgeon + Thermal Stress: MSc student Kyle Madden studied the effects of depleted energy reserves on thermal tolerance in Lake Sturgeon. Liver and gill transcriptional profiling using the sturgeon general stress STP-chip provided mechanistic insights into the trade-offs associated with the metabolic responses of lake sturgeon to fasting and thermal challenges. This completed work was performed at the Ontario Aquaculture Research Centre (Agricultural Research and Innovation Ontario), and a manuscript is in preparation for peer review. PI: Dr. Nicholas Bernier, University of Guelph.
Lake Trout
Lake Trout + Thermal Stress + Hypoxia Stress: Juvenile Lake Trout were held at four acclimation temperatures in normoxia and in hypoxia to understand the cumulative effects of both relevant stressors on Lake Trout. HQP Dr. Alyssa Weinrauch and Dr. Analisa Lazaro-Côté used transcriptional profiling using salmonid 56 gene thermal and hypoxia stress STP-Chips to characterize the effects of temperature and hypoxia on three tissues in lake trout and included mucus as a potential tissue for non-lethal transcriptional profiling. PI: Dr. Ken Jeffries, University of Manitoba.
- Weinrauch, A.M., Lazaro‐Côté, A., Durhack, T.C., Enders, E.C. and Jeffries, K.M., 2025. Cellular responses to thermal stress and moderate oxygen limitation in juvenile lake trout. Journal of Fish Biology, in press.
Lake Trout + Anthropogenic Stress: Declan Burton (PhD student) partnered with OMNR, USGS, and USFWS to assess the extent to which Lake Trout and Bloater could be nonlethally sampled. He also used the STP-Chip to assess whether there were differences in the physiological status of fish that died vs fish that survived post stocking. PI: Dr. Steven Cooke, Carleton University.
Rainbow Trout
Rainbow Trout + Anthropogenic Stress: Jakub Sokolowski (BSc), Brett Culbert (PhD), and Shayla Larson (PhD) studied the effects of repeated gill or muscle non-lethal biopsies on the process of compensatory growth in rainbow trout. Liver, gill, and muscle transcriptional profiling using the salmonid general stress STP-chip provided insights into the physiological and metabolic effects of repeated tissue biopsies on the regulation of growth. This completed work was performed at the Ontario Aquaculture Research Centre (Agricultural Research and Innovation Ontario), and a manuscript is in preparation for peer review. PI: Dr. Nicholas Bernier, University of Guelph.
Redside Dace
Redside Dace + Thermal Stress + Transport Stress + Water Quality Stress:
Round Goby
Round Goby + Anthropogenic Stress: HQP Riley Beach, Grace Dycha, and Elise Bull examined noise and handling stress in free-swimming representatives of Yellow Perch, Round Goby and Spottail Shiner in local waters using an integrated multi-species approach. We showed both noise stressors and handling stress can interact in novel ways to alter transcriptional levels and that these stressors manifest differently in species with different auditory sensitivities. PI: Dennis Higgs, University of Windsor.
- Riley K. Beach, Jonathon Leblanc & Dennis M. Higgs. An Integrated Approach to Understanding Noise Stress in Two Auditorily Diverse Species of Freshwater Fish Accepted. Can J Fish Aq Sci 2025.
Sea Lamprey
Sea Lamprey + Thermal Stress + Water Quality Stress: HQP: Dr. Alyssa Weinrauch and Elli Hung used RNA-sequencing data and publicly available genomes to produce a sea lamprey 56 gene STP chip. This was tested on sea lamprey that were exposed to high water temperature or were exposed to chemical pesticides as well as was tested on the northern brook lamprey.
Shortnose Sturgeon
Shortnose Sturgeon + Thermal Stress: PhD student Faith Penny performed pioneering work on the transcriptomics of heat stress. She was the first to compare Atlantic Sturgeon (dipliod) and Shortnose Sturgeon (polyploid) and found they had completely different transcriptomic responses to heat stress. PI: Dr. Scott Pavey, University of New Brunswick
Shortnose Sturgeon + Thermal Stress + Diet Stress: HQP Hossein Haghighi and Kye Madden used RNA-sequencing data from Atlantic Sturgeon, Shortnose Sturgeon, and Lake Sturgeon to generate sequence data for designing a 56 gene Acipenser sturgeons STP-Chip. The chip was tested on Lake Sturgeon that were acutely exposed to high temperatures or were fasted. PI: Dr. Ken Jeffries, University of Manitoba.
- Penny, FM, Bugg, WS, Kieffer, JD, Jeffries, KM, Pavey, SA. 2023. Atlantic Sturgeon and Shortnose Sturgeon exhibit highly divergent transcriptomic responses to acute heat stress. Comparative Biochemistry and Physiology – Part D: Genomics and Proteomics 45: 101058.
Sockeye Salmon
Sockeye Salmon + Thermal Stress + Hypoxia Stress: In partnership with the Gitanyow Fisheries Authority, Carolyn Knapper (MSc student) used the 112-gene Salmoniformes General Stress STP-Chip to assess transcriptional changes that occur in juvenile Sockeye Salmon over the summer months in Gitanyow Lake when temperatures rise and dissolved oxygen becomes low and creates a “habitat squeeze”. We found an increase in gene transcription for most functional groups, except some of the enzyme association with glycolysis and lipid metabolism. By the fall, the transcriptional pattern returned to that observed in the late spring. We also used the 28-gene Salmoniformes Osmoregulatory STP-Chip to examine smolts leaving the lake and compared their transcriptional pattern to smolts leaving Babine Lake, the largest population of Sockeye Salmon in the Skeena River watershed. There was little difference in gene transcription between smolts captured from the two lakes, although the intrapopulation variation was greater for Babine Lake than Gitanyow Lake. PI: Dr. Mark Shrimpton, University of Northern British Columbia.
Spottail Shiner
Spottail Shiner + Anthropogenic Stress: HQP Riley Beach, Grace Dycha, and Elise Bull examined noise and handling stress in free-swimming representatives of Yellow Perch, Round Goby and Spottail Shiner in local waters using an integrated multi-species approach. We showed both noise stressors and handling stress can interact in novel ways to alter transcriptional levels and that these stressors manifest differently in species with different auditory sensitivities. PI: Dr. Dennis Higgs, University of Windsor.
- Riley K. Beach, Jonathon Leblanc & Dennis M. Higgs. An Integrated Approach to Understanding Noise Stress in Two Auditorily Diverse Species of Freshwater Fish Accepted. Can J Fish Aq Sci 2025.
Striped Bass
Striped Bass + Thermal Stress: PhD student Faith Penny’s work with Striped Bass tested the effect of thermal acclimation on heat tolerance and how it affected the transcriptomic response. She found increased acute thermal tolerance and little change to hematology following the acclimation to warm water in juvenile Striped Bass, Morone saxatilis.PI: Dr. Scott Pavey, University of New Brunswick.
Striped Bass + Anthropogenic Stress: MSc student Baptiste Brunet studied the effect of catch and release on survival and stress response of Striped Bass using the Perciformes General Stress STP-Chip. PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
- Brunet, Baptiste. 2024. Détermination des niveaux de stress et de la mortalité générés par la pratique de la pêche récréative avec remise à l’eau chez le bar rayé (Morone saxatilis). Mémoire de maîtrise, Université du Québec à Rimouski. Direction de thèse : C. Audet; co-direction : David Deslauriers, Université du Québec à Rimouski.
Striped Bass + Thermal Stress + Diet Stress: PhD student Nina Bellenger is studying the transcriptomic response of Striped Bass in relation to temperature conditions and to diet (rich in essential fatty acids; rich in precursors of fatty acids). The transcriptomes were financed from the RNA-Seq GEN-FISH budget and genes annotated based on the genome published by Scott Pavey. PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
Tessellated Darter
Tessellated Darter + Thermal Stress + Water Quality Stress + Hypoxia Stress:
Walleye
Walleye + Water Quality Stress + Anthropogenic Stress: Partnering with DFO, Walleye were non-lethally sampled for gills along a latitudinal gradient from south (closer to a Winnipeg wastewater effluent point source of pollution) to north in Lake Winnipeg. HQP Dr. Jennifer Jeffrey and Matt Thorstensen used RNA-sequencing to identify potential biomarkers of environmental stress in wild-caught Walleye and developed a suite of qPCR assays for transcriptional profiling. PI: Dr. Ken Jeffries, University of Manitoba.
- Jeffrey, JD, Thorstensen, MJ, Enders, EC, Treberg, JR, Jeffries, KM. 2023. Using transcriptomics to examine the physiological status of wild-caught walleye (Sander vitreus). FACETS 8: 1-15.
White Sucker
White Sucker + Thermal Stress + Water Quality Stress:
Yellow Perch
Yellow Perch + Thermal Stress: Myra Thapar (MSc and now PhD student) partnered with Kinectrics and the CANDU Operators Association to develop a mechanism to identify whether Yellow Perch died from cold shock or other sources. Such information is needed to accurately estimate the amount of fish killed by CANDU operators that can be attributed to their operations versus natural cold shock events. PI: Dr. Steven Cooke, Carleton University.
Yellow Perch + Anthropogenic Stress: HQP Riley Beach, Grace Dycha, and Elise Bull examined noise and handling stress in free-swimming representatives of Yellow Perch, Round Goby and Spottail Shiner in local waters using an integrated multi-species approach. We showed both noise stressors and handling stress can interact in novel ways to alter transcriptional levels and that these stressors manifest differently in species with different auditory sensitivities. PI: Dennis Higgs, University of Windsor.
- Riley K. Beach, Jonathon Leblanc & Dennis M. Higgs. An Integrated Approach to Understanding Noise Stress in Two Auditorily Diverse Species of Freshwater Fish Accepted. Can J Fish Aq Sci 2025.
Atlantic Salmon
Atlantic Salmon + Stream Warming: As part of a collaboration with the Nova Scotia Salmon Association, the Margaree Salmon Association, and the Unamag’i Institute of Natural Resources, we are studying the behavioural transcriptomics of juvenile Atlantic Salmon to temperature stress and predation stress by Smallmouth Bass in the Southwest Margaree River, NS. MSc student Holly Mosco’s study will be validating in-field use of the Salmoniformes Mucus (Nonlethal) General Stress chip (in comparison to the Salmoniformes Osmoregulatory chip), determining whether pulses in Smallmouth Bass movements cause detectable changes in both salmon behavioural and molecular (i.e., transcriptomic) stress responses. We will also be using eDNA to determine relative Smallmouth Bass abundances throughout the season as the fish collectively move upstream and downstream, varying their exposure to juvenile salmon. PI: Dr. Christina Semeniuk, University of Windsor.
Atlantis Salmon + Transport Stress: In collaboration with OMNRF, graduate student Dane Roberts quantified the effects of transport stress in supplemental released Atlantic salmon reared and released in the Lake Ontario basin. The fish were sampled before transfer (resting), after transfer to the transport tank (handling stress) and at the time of release (handling and transport stress). The salmonid general stress chip was used to characterize the stress response. PI: Dr. Trevor Pitcher, University of Windsor.
Black Bass
Black Bass + Angling Stress: Declan Burton (PhD student), Myra Thapar (PhD student) and Luc LaRochelle (PhD student) have conducted a number of studies in partnership with Parks Canada, OMNR, various lake associations, and tournament organizers to assess different recreational fisheries issues related to Black Bass management. This has included a comparison of transcriptomic profiles of bass inside versus outside fishing sanctuaries, evaluating the state of bass following different types of fishing tournaments, and evaluating livewell care (especially the use of ice to chill fish) practices. PI: Dr. Steven Cooke, Carleton University.
Brook Trout
Brook Trout + Anthropogenic Stress: PhD student Julie Viana together with partnering Institut France-Québec pour la coopération scientifique en appui au secteur maritime (IFQM) and Fondation de France studied the genetics of small Brook Trout populations inhabiting the St-Pierre-and-Miquelon archipelago. Population genetics showed differences among the three main islands (St-Pierre, Langlande, Miquelon) and among hydrosystems present on the three islands. STP-Chips were used to see whether or not the genetic landscape was associated to a phenotypic landscape.
- Viana, J., G. Evanno, C. Audet et F. Teletchea. 2025. Fine-scale genetic structure of small fish populations in islands: the case of brook charr Salvelinus fontinalis (Mitchill, 1814) in Saint-Pierre and Miquelon (France). Evolutionary Applications 2025: 18:e70041. https://doi.org/10.1111/eva.70041.
Brook Trout + Transport Stress: In partnership with the Freshwater Fisheries Society of BC, Post-doc Dr. S. Islam performed controlled transport challenges on juvenile hatchery-reared brook trout. Gill and liver were collected before, during and after transport, as was eRNA and a mucus swab. The salmonid general stress STP-Chip was used and the data are being analyzed for publication. This work was also supported by a MITACS PDF scholarship to Dr. Islam. PI: Dr. Daniel Heath, University of Windsor; Dr. Ken Jeffries, University of Manitoba.
Chinook Salmon
Chinook Salmon + Salinity Stress: In collaboration with a commecial salmon farm in BC (Yellow Island Aquaculture Ltd) we explored the osmoregulatory response of Chinook Salmon exposed to various salinity challenges. This was done to assess the effect of full freshwater rearing required by a netpen ban in BC. All data have been collected and is being prepared for submission by graduated MSc student N. Tugui and PDF Dr. S. Islam. PI: Dr. Daniel Heath, University of Windsor.
Lake Trout
Lake Trout + Stocking Evaluation: Declan Burton (PhD student) partnered with OMNR, USGS, and USFWS to assess the extent to which Lake Trout and Bloater could be nonlethally sampled. He also used the STP-Chip to assess whether there were differences in the physiological status of fish that died vs fish that survived post stocking. PI: Dr. Steven Cooke, Carleton University.
Rainbow Trout
Rainbow Trout + Contaminant Stress: Rainbow Trout were captured and sampled for liver tissue in streams adjacent to active mining sites in northern BC in collaboration with Hatfield Consulting. We used the salmonid general stress STP-Chip to test for stress associated with elevated selenium levels in the water. This project is on-going. PI: Dr. Daniel Heath, University of Windsor.
Redside Dace
Redside Dace + Road Salt Runoff: Britney Firth (Post-doctoral fellow), Dane Roberts (MSc student) and Olivia Galloway (MSc student)—in collaboration with Peel Region Municipality and Credit Valley Conservation Authority (that provided road salt levels and stream temperatures)—examined the effect of ecologically relevant road salt levels on swimming performance, schooling abilities, and thermal tolerance (using CTMax as a proxy). Non-lethal gill clips were collected before, during, and after the salt exposure (along with appropriate controls). The Cypriniformes General Stress STP-Chip was used and the data were analyzed and compiled into a manuscript that was submitted to the journal Endangered Species Research. The work was also supported by funding from Peel Region municipality, which is where much of the Redside Dace reside in Canada.
Sockeye Salmon
Sockeye Salmon + Thermal Stress + Hypoxia Stress: In partnership with the Gitanyow Fisheries Authority, Carolyn Knapper (MSc student) used the 112-gene Salmoniformes General Stress STP-Chip to assess transcriptional changes that occur in juvenile Sockeye Salmon over the summer months in Gitanyow Lake when temperatures rise and dissolved oxygen becomes low and creates a “habitat squeeze”. We found an increase in gene transcription for most functional groups, except some of the enzyme association with glycolysis and lipid metabolism. By the fall, the transcriptional pattern returned to that observed in the late spring. We also used the 28-gene Salmoniformes Osmoregulatory STP-Chip to examine smolts leaving the lake and compared their transcriptional pattern to smolts leaving Babine Lake, the largest population of Sockeye Salmon in the Skeena River watershed. There was little difference in gene transcription between smolts captured from the two lakes, although the intrapopulation variation was greater for Babine Lake than Gitanyow Lake. PI: Dr. Mark Shrimpton, University of Northern British Columbia.
Striped Bass
Striped Bass + Catch and Release Stress: MSc student Baptiste Brunet studied the effect of catch and release on survival and stress response of Striped Bass using the Perciformes General Stress STP-Chip. While few of the assays worked, the results were nevertheless presented at the AFS meeting (2023): Determination of stress levels and mortality rate generated by recreational catch and release of Striped Bass (Morone saxatilis). PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
Striped Bass + Thermal Stress + Diet Stress: PhD student Nina Bellenger is studying the transcriptomic response of Striped Bass in relation to temperature conditions and to diet (rich in essential fatty acids; rich in precursors of fatty acids). The transcriptomes were financed from the RNA-Seq GEN-FISH budget and genes annotated based on the genome published by Scott Pavey. PI: Dr. Céline Audet, Institut des sciences de la mer Université du Québec à Rimouski.
Walleye
Walleye + Pollution Stress: In collaboration with DFO, Post-doc Dr. Jennifer Jeffrey and PhD student Matt Thorstensen sampled Walleye non-lethally for gills and used RNA-sequencing to identify potential biomarkers of handling stress in wild-caught Walleye. PI: Dr. Ken Jeffries, University of Manitoba.
Walleye + Non-lethal Biopsy: Partnering with DFO, Walleye were non-lethally sampled for gills along a latitudinal gradient from south (closer to a Winnipeg wastewater effluent point source of pollution) to north in Lake Winnipeg. HQP Dr. Jennifer Jeffrey and Matt Thorstensen used RNA-sequencing to identify potential biomarkers of environmental stress in wild-caught Walleye and developed a suite of qPCR assays for transcriptional profiling. PI: Dr. Ken Jeffries, University of Manitoba.
Yellow Perch
Yellow Perch + Thermal Stress: Working with OMNRF, graduate student Patricia Voyer is analyzing the thermal stress response of natural populations of Yellow Perch in Ontario. All data is collected and Ms. Voyer is completing her MSc and submitting papers for peer review. PI: Dr. Daniel Heath, University of Windsor.