Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

Rise, Matthew L.; Schalburg, Kristian R. von; Brown, Gordon D.; Mawer, Melanie A.; Devlin, Robert H.; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A. R.; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A.; Nelson, Colleen C.; Jones, Simon R. M.; Smailus, Duane E.; Jones, Steven J.M.; Schein, Jacqueline E.; Marra, Marco A.; Butterfield, Yaron S.N.; Stott, Jeff; Ng, Serena; Davidson, William S.; Koop, Ben F.

doi:10.1101/gr.1687304

Cited by 279 publications

(230 citation statements)

References 49 publications

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“…Transcriptome profiles were obtained with a 16,006 cDNA microarray (version 2.0) developed for the Atlantic salmon (Salmo salar) by the consortium for Genomic Research on All Salmonids Project (cGRASP; Rise et al 2004) and successfully tested and applied to other salmonid species, including Coregonus clupeaformis Rise et al 2007;St-Cyr et al 2008). Gene identification with the corresponding EST sequence can be found at http:/ /web.uvic.ca/cbr/grasp/.…”

Section: Methodsmentioning

confidence: 99%

“…Transcript annotations correspond to EST library annotations of Rise et al (2004), with updates available on the cGRASP web page: http:/ /web.uvic.ca/cbr/grasp/. Significant eQTL were assigned to biological process categories with the AMIGO browser of Geneontology (http:/ /www.geneontology.…”

Section: Methodsmentioning

confidence: 99%

“…jp/kegg/pathway.html), and the UniProt database (http:/ / www.expasy.uniprot.org/), along with additional literature searches. For the same subset of transcripts showing significant linkages, transcripts classified by Rise et al (2004) as unknown were submitted to BLAST nucleotide and translated protein searches to determine if new gene identifications were possible. Some annotations by Rise et al (2004) appeared to be in error due to repetitive regions within clones.…”

Section: Methodsmentioning

confidence: 99%

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The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

Whiteley

Derôme

Rogers³

et al. 2008

Genetics

107

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We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between the sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development on the basis of colocalization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. Eighty-eight percent of eQTL-phenotypic QTL colocalization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots colocalized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc-finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of colocalization of brain eQTL with behavioral QTL, which provides insight into the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological, differences appear to play a key role in this divergence.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

Whiteley

Derôme

Rogers³

et al. 2008

Genetics

107

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“…Three replicates of RNA from three different individual fish were labeled (3 × 3 design). High density microarrays (16,000 cDNA spots per array) were obtained from GRASP project at the University of Victoria and were prepared as described in Rise et al (2004a). Fluorescently labeled cDNA was hybridized to the arrays overnight at 45° in a humidified chamber, then washed following Genisphere's protocols.…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

Dose–response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol

Hook

Skillman

Small

et al. 2006

Marine Environmental Research

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Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss, were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that diffierent doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose. KeywordsRainbow trout; cDNA microarray; EstrogensThe field of toxicogenomics holds great promise for environmental and aquatic toxicology. Specific applications of microarrays in ecotoxicological studies include the identification of contaminants through analysis of expression patterns measured via microarrays in test organism exposed to previously uncharacterized contaminant mixtures, the identification of chemical mode of action based on the mRNA expression patterns, and the development of tools to assess endpoints for chronic exposure to mixtures that are tied to population-level consequences (Miracle and Ankley, 2005). However, the baseline transcriptomic response in organisms exposed to model toxicants must be characterized before this technology can be meaningfully applied to contaminated field sites. The objective of this study is to determine the relationship between gene expression profile and toxicant dose for the synthetic estrogen, ethynylestradiol (EE2).Methods for exposure and EE2 kinetics are described in more detail in Skillman et al. (in press), while RNA preparation and labeling, microarray hybridization and data analysis are described in more detail in Hook et al. (2006). We used isogenic fish in this study to minimize the confounding effects of individual variability. Male isogenic Rainbow Trout (Oncorhynchus mykiss) were exposed to EE2 at nominal concentrations of 10, 50 and 100 ng/L EE2 (actual *Corresponding author., E-mail address: Sharon.Hook@pnl.gov (S.E. Hook). NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript concentrations were 8, 33, and 115 ng/L EE2) via methanol drip (methanol concentration was less than 0.02%) for seven days and compared to methanol only controls. Fish were euthanized, then RNA...

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“…Analysing brain gene expression profiles allows us to identify (i) how many genes vary in expression between sneaker and immature male brains; (ii) what biological processes are implicated and how they relate to known physiological, behavioural and morphological differences between tactics as well as to life-history theory predictions; (iii) genes previously not implicated in the sneaker tactic; and (iv) determine if expression patterns can classify individuals according to their tactic in wild animals. We measured brain gene expression profiles in four sneaker males and eight immature juveniles (four males and four females), collected at spawning time in October 2002 in a tributary of the Connecticut River, Massachusetts, USA, using a microarray constructed from salmonid cDNA libraries (Rise et al 2004), which allows the monitoring of the transcriptional level of thousands of genes simultaneously. We focused on differences between individuals of the same age (freshwater life before migration), but with different phenotypes, and therefore did not include large anadromous males and females, who are several years older and are protected.…”

Section: Introductionmentioning

confidence: 99%

Alternative life histories shape brain gene expression profiles in males of the same population

et al. 2005

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Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker.

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Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

Cited by 279 publications

References 49 publications

The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

Dose–response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol

Alternative life histories shape brain gene expression profiles in males of the same population

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