Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptomics of environmental adaptation and survival in wild adult Pacific Sockeye Salmon (Oncorhynchus nerka) during spawning migration

ABSTRACT: a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities. Fish were captured fish at two marine sampling sites, one within Johnstone Strait (JS), BC. Canada and one within Juan De Fuca Strait (JDFS), BC Canada. Ocean sites were contrasted to fish sampled within the Fraser River at Whonnock (W), BC, Canada. Gill and liver tissues were dissected at each of these sites. Non-lethal biopsy sampling was performed on migrating sockeye salmon intercepted within the Fraser River at Mission, BC, Canada and genetically-based stock ID was used to determine the stock-specific spawning grounds for each fish, giving an intended end-point of migration for each of the stocks investigated in this study.Gene expression levels were determined by comparing the amount of mRNA transcript in the experimental samples relative to a reference sample. A total of 123 microarrays were used to generate the dataset, corresponding to individual hybridizations of both gill and liver samples collected from JS (gill n=14; liver n=15), JDFS (gill n=15; liver n=13), W (gill n=11; liver n=10), and biopsy sampled gill tissue collected at Mission (n=45).Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The reference contained the combined aRNA of all individuals used in the experiment, excluding bioposy sampled fish. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, and no dye swaps were perfromed.

ORGANISM(S): Oncorhynchus nerka

SUBMITTER: Tyler Evans

PROVIDER: E-GEOD-22346 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration.

Evans Tyler G TG Hammill Edd E Kaukinen Karia K Schulze Angela D AD Patterson David A DA English Karl K KK Curtis Janelle M R JM Miller Kristina M KM

Molecular ecology 20110927 21

Environmental shifts accompanying salmon spawning migrations from ocean feeding grounds to natal freshwater streams can be severe, with the underlying stress often cited as a cause of increased mortality. Here, a salmonid microarray was used to characterize changes in gene expression occurring between ocean and river habitats in gill and liver tissues of wild migrating sockeye salmon (Oncorhynchus nerka Walbaum) returning to spawn in the Fraser River, British Columbia, Canada. Expression profile ...[more]

PMID: 21951593

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Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series is of gill expression profiles from the study of fish sampled and tagged in the ocean and tracked as they entered the river system and swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish at the Weaver creek spawning grounds, and were observed for pre-spawning mortality or successful spawning. Weaver creek sockeye salmon (a late-run stock) spawn in an artificial spawning channel which has a controlled entrance and no exit, situated 100 km from the ocan. Females were dip-netted out of the entrance of the spawning channel, and placed into a sampling trough with flowing ambient water for the gill biopsy procedure and tagged with Petersen discs and returned to the spawning channel. Moribund fish were recovered daily and their gonads examined to assess whether they had spawned or not. Gene expression was assayed on the GRASP salmonid 32K cDNA microarray.

Dataset Information

Transcriptomics of environmental adaptation and survival in wild adult Pacific Sockeye Salmon (Oncorhynchus nerka) during spawning migration

Publications

Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration.

Similar Datasets

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