Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Salvelinus Microarray experiment: cross-specific transcriptome in hybrids

ABSTRACT: The genetic mechanisms underlying hybridization are poorly understood despite their potentially important roles in speciation processes, adaptative evolution, and agronomical innovation. In this study, transcription profiles were compared among three populations of brook charr and their hybrids using microarrays to assess the influence of hybrid origin on modes of transcription regulation inheritance and on the mechanisms underlying growth. We found that twice as many transcripts were differently expressed between the domestic strain and the two wild populations (Rupert and Laval) than between wild ones, despite their deeper genetic distance. This could reflect the consequence of artificial selection during domestication. We detected that hybrids exhibited strikingly different patterns of mode of transcription regulation, being mostly additive (94%) for domestic × Rupert, and non-additive for Laval × domestic (45.7%) and Rupert × Laval hybrids (37.5%). Both heterosis and outbreeding depression for growth were observed among the crosses. Our results indicated that prevalence of dominance in transcription regulation seems related to growth heterosis, while prevalence of transgressive transcription regulation may be more related to outbreeding depression. Our study clearly shows, for the first time in vertebrates, that the consequences of hybridization on both the transcriptome level and the phenotype are highly dependent on the specific genetic architectures of crossed populations and therefore hardly predictable. Comparison between six crosses using a loop design: direct comparison of hybrids vs parental populations fishes for 8 families. Each individual was technically replicated on two bi-coloured distinct microarrays and dye-swapped.

ORGANISM(S): Salvelinus fontinalis

SUBMITTER: Berenice BOUGAS

PROVIDER: E-GEOD-22008 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr (Salvelinus fontinalis Mitchill).

Bougas Bérénice B Granier Sarah S Audet Céline C Bernatchez Louis L

Genetics 20100615 1

The genetic mechanisms underlying hybridization are poorly understood despite their potentially important roles in speciation processes, adaptative evolution, and agronomical innovation. In this study, transcription profiles were compared among three populations of brook charr and their hybrids using microarrays to assess the influence of hybrid origin on modes of transcription regulation inheritance and on the mechanisms underlying growth. We found that twice as many transcripts were differentl ...[more]

PMID: 20551437

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Project description:Parental effects represent an important source of variation in offspring phenotypes. Depending on the specific mechanisms involved, parental effects may be caused to different degrees by either the maternal or paternal parent, and these effects may in turn act at different stages of development. In order to detect parental effects acting on gene transcription regulation and length phenotype during ontogeny, the transcriptomic profiles of two reciprocal hybrids from LavalM-BM- M-CM-^WM-BM- Rupert and LavalM-BM- M-CM-^WM-BM- domestic populations of brook charr were compared at hatching, yolk sac resorption, and 15 weeks after exogenous feeding. Using a salmonid cDNA microarray, our results show that parental effects modulated gene expression among reciprocal hybrids only at the yolk sac resorption stage. In addition, LavalM-BM- M-CM-^WM-BM- domestic and LavalM-BM- M-CM-^WM-BM- Rupert reciprocal hybrids differed in the magnitude of theses parental effects, with 199 and 630 differentially expressed transcripts, respectively. This corresponds to a maximum of 18.5% of the analyzed transcripts. These transcripts are functionally related to cell cycle, nucleic acid metabolism and intracellular protein traffic, which is consistent with observed differences associated with embryonic development and growth differences in other fish species. Our results thus illustrate how parental effects on patterns of gene transcription seem dependent on the genetic architecture of the parents. In addition, in absence of transcriptomic differences, the non-transcriptomic deposits could also act to highlight the offspring differences in length before the yolk sac resorption. Pair-wise direct comparisons between 8 reciprocal hybrids (LavalRupert vs RupertLaval and LavalDomestic vs DomesticLaval) were performed at each developmental stage. For each developmental stage, cDNA of 8 samples from each cross were hybridized for a total of 48 microarrays analyzed. The distribution of dyes is equilibrated among each cross (4 samples with cy3 and 4 samples with Al647).

Project description:Genetic analyses of speciation have focused nearly exclusively on retrospective analyses of reproductive isolation between highly divergent species. Yet, a full understanding of the speciation process must encompass analysis of the consequences of genomic divergence in young lineages still capable of exchanging genes under natural conditions. The accumulation of conditionally neutral genetic variation may lead to the evolution of divergent gene networks. In a hybrid background, such mutations may no longer compensate one another, resulting in the appearance of selectively disadvantageous traits, including disruption of gene expression regulation. Here, we documented genome-wide patterns of gene expression divergence between young lineages of normal and dwarf lake whitefish and their backcross hybrids for which strong, yet incomplete post-zygotic isolation barriers exist. A significant proportion (33%) of backcross hybrids showed developmental abnormalities not seen in parental forms and eventually leading to death. While the transcriptome of parental forms was nearly identical during embryonic development, suggesting a role for stabilizing selection, all hybrids displayed strongly divergent patterns of gene expression. By comparing healthy, surviving hybrids against moribund ones, we observed that over 2000 genes were misregulated in these abnormal embryos. In particular, misregulation was significantly biased towards essential developmental genes which were strongly underexpressed. Furthermore, genes previously documented to be highly transgressive (exaggerated inter-individual variance) were almost invariably underexpressed in hybrids. Our results thus clearly showed a transcriptome-wide signature of hybrid breakdown in young, incipient species and demonstrated a persuasive link between misexpression of essential developmental genes and post zygotic isolation. Samples of dwarf, normal, backcross-healthy and backcross-moribund were hybridized in a loop design, involving eight biological replicates for the backcross-healthy and backcross-moribund comparison and six for the others. Dye swap was performed between each replicate. As a result, we obtained a final set of 32 microarray slides.

Project description:Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates. Microarray analyses were performed on five individual rainbow trout per group of pure wild, pure domesticated, GH transgenic strain 1 in wild, GH transgenic strain 2 in wild, GH transgenic strain 1 in wild-domestic hybrid, and GH transgenic strain 2 in wild-domestic hybrid hybridized (one slide per individual) against a common wild-type RNA pool.

Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. DomesticM-bM-^@M-^Swild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection. Salmon of three genotypes (strains: 1. wild (Stewiacke River salmon), 2. domesticated (Saint John River salmon), and 3. first generation hybrids between the two strains, were exposed to two environments (treatment: 1. suspended sediments, 2. control: clear water), using eight biological replicates (individuals) of each of the six experimental groups, summing up to 48 individuals, each individual has two technical replicates , each technical replicate has been labelled with a different dye, each technical replicate appears on a different array, dye swaps are equilibrated for arrays that combine individuals from different genotypes and for arrays that combine individuals from the same genotype but different environments. Technical replicates of individuals always appear once on arrays that compare between environments and once on arrays that compare among genotypes. In total there are 48 arrays.

Dataset Information

Salvelinus Microarray experiment: cross-specific transcriptome in hybrids

Publications

The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr (Salvelinus fontinalis Mitchill).

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