Ontology highlight
ABSTRACT:
PROVIDER: PRJNA809196 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18095813_1.fastq.gz | Fastqsanger.gz | |||
| SRR18095813_2.fastq.gz | Fastqsanger.gz | |||
| SRR18095814_1.fastq.gz | Fastqsanger.gz | |||
| SRR18095814_2.fastq.gz | Fastqsanger.gz | |||
| SRR18095815_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Directional selection in the domestication of fish species has resulted in rapid gains of growth, body size, and other production-relevant traits in relatively few generations. While there is clear evidence of genetic divergence contributing to selection-related phenotypic changes, emerging research suggests that intergenerational epigenetic inheritance may also be a relevant mechanism explaining rapid evolutionary change in domestic fish lines. Epigenetic changes have also been implicated in fish species’ responses to warming associated with climate change. Domestic lines of Brook Charr (Salvelinus fontinalis) are the primary source of fish used for recreational fisheries stocking in many parts of Eastern North America and there are concerns about how these fish will fare when stocked into lakes in the coming decades. We jointly investigated the effects of directional selection for performance traits (i.e., absence of early sexual maturation and increased growth) and exposure to elevated temperatures on DNA methylation in sperm cells of two experimental lines (hereafter: Selected and Control lines) of Brook Charr . We used whole-genome bisulfite sequencing to characterize DNA methylation at over 17 million methylated sites and identified 393 selection-related differentially methylated regions (DMR). The putative functions of genes in proximity to these DMRs are consistent with well-characterized phenotypic differences between the lines, including lipid metabolism and precocial maturation, and support the hypothesis that rapid evolution of traits may be partially mediated by epigenetic inheritance. We subsequently detected 85 warming-related DMRs in the Control line and 302 DMRs in the Selected line. None of these regions were shared between the two lines, indicating that the directional selection regime significantly altered the environmentally sensitive epigenetic landscape.
2024-03-11 | GSE227271 | GEO
Project description:Domestication has been practiced for centuries yet directed towards relatively few terrestrial crops and animals. While phenotypic and quantitative genetic changes associated with domestication have been amply documented, little is known about the molecular changes underlying the phenotypic evolution during the process. Here, we have investigated the brook charr (Salvelinus fontinalis) responses to artificial selection by means of transcriptional analysis of ~ 32 000 cDNA features performed in both a selected and control populations reared under identical environmental conditions during four generations. Our results indicate that selective breeding led to significant changes in the transcription of genes at the juvenile stage, where we observed 4.16% (156/3750) of differentially expressed genes between the two lines. No significant genes were revealed at the earlier life stage. Moreover, when comparing our results to those of previous studies on Atlantic salmon that compared lines that were selected for 5-7 generations for similar traits (e.g. growth), genes with similar biological functions were found to be under selection in both studies. These observations indicate that (1) four generations of selection caused substantial changes in regulation of gene transcription between selected and control populations and (2) selective breeding for improving the same phenotypic traits (e.g. rapid growth) in brook charr and Atlantic salmon tended to select for the same changes in transcription profiles as the expression of a small and similar set of genes were affected by selection.
2010-02-24 | GSE20490 | GEO
Project description: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.
2010-07-01 | GSE22008 | GEO
Project description:Domestication has been practiced for centuries yet directed towards relatively few terrestrial crops and animals. While phenotypic and quantitative genetic changes associated with domestication have been amply documented, little is known about the molecular changes underlying the phenotypic evolution during the process. Here, we have investigated the brook charr (Salvelinus fontinalis) responses to artificial selection by means of transcriptional analysis of ~ 32 000 cDNA features performed in both a selected and control populations reared under identical environmental conditions during four generations. Our results indicate that selective breeding led to significant changes in the transcription of genes at the juvenile stage, where we observed 4.16% (156/3750) of differentially expressed genes between the two lines. No significant genes were revealed at the earlier life stage. Moreover, when comparing our results to those of previous studies on Atlantic salmon that compared lines that were selected for 5-7 generations for similar traits (e.g. growth), genes with similar biological functions were found to be under selection in both studies. These observations indicate that (1) four generations of selection caused substantial changes in regulation of gene transcription between selected and control populations and (2) selective breeding for improving the same phenotypic traits (e.g. rapid growth) in brook charr and Atlantic salmon tended to select for the same changes in transcription profiles as the expression of a small and similar set of genes were affected by selection. Two conditions environment: direct comparison of control vs domesticated fish for 20 families. No individual replicates but two individuals of the same family were hybridized on different slides
2010-06-24 | E-GEOD-20490 | biostudies-arrayexpress
Project description:Brook charr Salvelinus fontinalis high-density linkage map
| PRJNA308100 | ENA
Project description: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.
2010-07-01 | E-GEOD-22008 | biostudies-arrayexpress
Project description:Chromatin-based epigenetic memory relies on the equal distribution of parental histone tetramers, which serve as templates for duplicating parental chromatin, to newly synthesized daughter DNA strands. Histone chaperones within the replisome, such as the histone binding domains (HBDs) of Mcm2 and Pol alpha, are critical for transferring parental histones to the lagging strand. However, the mechanisms and impact of parental histone transfer on epigenetic inheritance remain debated. Using fission yeast heterochromatin assembly as a model, we discovered that replisome component Mrc1 is crucial for both epigenetic inheritance and transfer of parental histones to the lagging strand, akin to a Mcm2-HBD mutation. Isolation of separation-of-function mutations revealed that Mrc1s role in epigenetic inheritance is distinct form its DNA replication checkpoint and replisome speed control functions. Instead, Mrc1 prevents undesirable replisome interactions to facilitate interactions between Mcm2 and Pol alpha for the proper passage of parental histones. These findings unveil a novel function of Mrc1 and underscore the critical role of parental histone segregation in epigenetic inheritance.
2023-07-16 | MSV000092452 | MassIVE