E-GEOD-45151 - Influence of developmental stage and genotype on liver mRNA levels among wild, domesticated, and hybrid rainbow trout (Oncorhynchus mykiss)

Status
Released on 18 March 2013, last updated on 2 June 2014
Organism
Oncorhynchus mykiss
Samples (48)
Array (1)
Protocols (6)
Description
A 44K salmonid oligoarray was used to examine the influence of genotype and developmental stage on mRNA expression in wild-type (age matched and size matched to domesticated), domesticated and wild-domesticated hybrid populations. Significant differences were found in mRNA expression between genotypes. The largest proportion of differentially expressed mRNAs were found in comparisons of domesticated and wild-type groups. Significant differences were also noted in pairings of wild-domesticated hybrid progeny to both parental strains. Differences in gene expression were found in comparison of both wild-type age and size matched to each other and in combination with genotype analysis, showing a strong effect of fish developmental stage on differential gene expression. Domestication was found to modify biological pathways associated with transport, metabolism, cell tissue structure and development, stress and immune response and protein synthesis. Genotype analysis of hybrid progeny inheritance patterns showed similar levels of recessive, dominant and additive effects. Microarray analysis was performed on liver RNA from 6 individual fish per group of age-matched wild, size-matched wild, domesticated and wild-domesticated hybrids. Samples were hybridized against a common wild-type reference pool (n=6 wild size-matched fish). One individual from each of the groups was hybridized to one array on each of the individual slides (n=6) in the order of domestic, hybrid, age-matched wild and size-matched wild. In total, 6 4x44K oligoarray slides were used to complete the study.
Experiment type
transcription profiling by array 
Contacts
Samantha Louise White <samantha.white@dfo-mpo.gc.ca>, Dionne Sakhrani, Robert H Devlin, Roy G Danzman, Samantha L White
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-45151.idf.txt
Sample and data relationshipE-GEOD-45151.sdrf.txt
Raw data (2)E-GEOD-45151.raw.1.zip, E-GEOD-45151.raw.2.zip
Processed data (1)E-GEOD-45151.processed.1.zip
Array designA-GEOD-11299.adf.txt
Links