Transcriptomics

Dataset Information

3

Gene expression in natural subyearling fall Chinook salmon in the Snake and Clearwater Rivers


ABSTRACT: We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings. We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration. Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill Na+/K+-ATPase activity development, which then declined into autumn. In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr. Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts. Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status. By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics. We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways. Non-migrating and migrating natural subyearling fall Chinook salmon were collected from the Snake River. Non-migrating natural subyearling fall Chinook salmon were collected from the Clearwater River. Twelve fish were collected at each of four different time points for a total of 48 fish. Total RNA was extracted from the liver of each fish. Equal amounts of RNA from three fish were pooled to create four pools of RNA per time point. Each RNA pool was hybridized to an array for a total of 16 arrays with four arrays per time point.

ORGANISM(S): Oncorhynchus tshawytscha  

SUBMITTER: Helena E Christiansen   Kenneth F Tiffan  Helena Christiansen 

PROVIDER: E-GEOD-58670 | ArrayExpress | 2014-06-20

SECONDARY ACCESSION(S): GSE58670PRJNA253132

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

2010-06-01 | E-MEXP-2210 | ArrayExpress
1000-01-01 | S-EPMC4231598 | BioStudies
2019-01-01 | S-EPMC6788492 | BioStudies
2011-06-12 | GSE22346 | GEO
2012-01-01 | S-EPMC3434914 | BioStudies
2011-06-12 | E-GEOD-22346 | ArrayExpress
2017-01-01 | S-EPMC5731093 | BioStudies
2007-01-01 | S-EPMC1905918 | BioStudies
2012-06-03 | E-GEOD-33715 | ArrayExpress
1000-01-01 | S-EPMC4983599 | BioStudies