Ontology highlight
ABSTRACT:
PROVIDER: PRJNA809196 | ENA |
REPOSITORIES: ENA
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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: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: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: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:Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNA interference phenotypes in C. elegans provides an excellent model to study this phenomenon, and whilst studies have implicated both chromatin modifications and small RNA pathways in heritable silencing their relative contributions remain unclear. Here we demonstrate that the histone methyltransferases SET-25 and SET-32 are required for the establishment of a transgenerational silencing signal, but not for long-term maintenance of this signal between subsequent generations suggesting that transgenerational epigenetic inheritance is a multi-step process, with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNA (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
2018-10-30 | PXD008754 | Pride
Project description:HP1 proteins bind dynamically to H3K9 methylation and are essential for establishing and maintaining transcriptionally silent epigenetic states, known as heterochromatin. HP1 proteins can dimerize, forming a binding interface that interacts with and recruits diverse chromatin-associated factors. HP1 proteins rapidly evolve through sequence changes and gene duplications, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impact epigenetic inheritance, we performed a targeted mutagenesis screen of the dimerization and protein interaction domain of the S.pombe HP1 homolog Swi6. We discovered that substitutions mapping to an auxiliary motif in Swi6 outside the dimerization interface can lead to complete functional divergence. Specifically, we identified point mutations at a single amino acid residue that resulted in either persistent gain or loss of function in epigenetic inheritance without affecting heterochromatin establishment. These substitutions increase Swi6 chromatin occupancy in vivo and alter Swi6-protein interactions that selectively affect H3K9me inheritance. Based on our findings, we propose that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance, underscoring the remarkable plasticity associated with HP1 proteins and their ability to evolve new functions.
2024-08-10 | PXD047651 | Pride