Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression
Abstract Background Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional di...
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ftdatacite:10.6084/m9.figshare.c.3640229 2023-05-15T15:31:37+02:00 Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression Bicskei, Beatrix Taggart, John Glover, Kevin Bron, James 2016 https://dx.doi.org/10.6084/m9.figshare.c.3640229 https://figshare.com/collections/Comparing_the_transcriptomes_of_embryos_from_domesticated_and_wild_Atlantic_salmon_Salmo_salar_L_stocks_and_examining_factors_that_influence_heritability_of_gene_expression/3640229 unknown Figshare https://dx.doi.org/10.1186/s12711-016-0200-6 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Cell Biology Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences Collection article 2016 ftdatacite https://doi.org/10.6084/m9.figshare.c.3640229 https://doi.org/10.1186/s12711-016-0200-6 2021-11-05T12:55:41Z Abstract Background Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids. Results Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect. Conclusions Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males. Article in Journal/Newspaper Atlantic salmon Salmo salar DataCite Metadata Store (German National Library of Science and Technology) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Cell Biology Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences |
spellingShingle |
Cell Biology Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences Bicskei, Beatrix Taggart, John Glover, Kevin Bron, James Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
topic_facet |
Cell Biology Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences |
description |
Abstract Background Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids. Results Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect. Conclusions Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males. |
format |
Article in Journal/Newspaper |
author |
Bicskei, Beatrix Taggart, John Glover, Kevin Bron, James |
author_facet |
Bicskei, Beatrix Taggart, John Glover, Kevin Bron, James |
author_sort |
Bicskei, Beatrix |
title |
Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
title_short |
Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
title_full |
Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
title_fullStr |
Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
title_full_unstemmed |
Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression |
title_sort |
comparing the transcriptomes of embryos from domesticated and wild atlantic salmon (salmo salar l.) stocks and examining factors that influence heritability of gene expression |
publisher |
Figshare |
publishDate |
2016 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3640229 https://figshare.com/collections/Comparing_the_transcriptomes_of_embryos_from_domesticated_and_wild_Atlantic_salmon_Salmo_salar_L_stocks_and_examining_factors_that_influence_heritability_of_gene_expression/3640229 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
https://dx.doi.org/10.1186/s12711-016-0200-6 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3640229 https://doi.org/10.1186/s12711-016-0200-6 |
_version_ |
1766362139392475136 |