Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations
Evolutionary genomics has benefited from methods that allow identifying evolutionarily important genomic regions on a genomewide scale, including genome scans and QTL mapping. Recently, genomewide scanning by means of microarrays has permitted assessing gene transcription differences among species o...
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ftpubmed:oai:pubmedcentral.nih.gov:2034609 2023-05-15T15:31:35+02:00 Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations Roberge, C. Guderley, H. Bernatchez, L. 2007-10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034609 http://www.ncbi.nlm.nih.gov/pubmed/17720934 https://doi.org/10.1534/genetics.107.073759 en eng Copyright © 2007 by the Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034609 http://www.ncbi.nlm.nih.gov/pubmed/17720934 http://dx.doi.org/10.1534/genetics.107.073759 Copyright © 2007 by the Genetics Society of America Investigations Text 2007 ftpubmed https://doi.org/10.1534/genetics.107.073759 2013-09-01T05:03:23Z Evolutionary genomics has benefited from methods that allow identifying evolutionarily important genomic regions on a genomewide scale, including genome scans and QTL mapping. Recently, genomewide scanning by means of microarrays has permitted assessing gene transcription differences among species or populations. However, the identification of differentially transcribed genes does not in itself suffice to measure the role of selection in driving evolutionary changes in gene transcription. Here, we propose and apply a “transcriptome scan” approach to investigating the role of selection in shaping differential profiles of gene transcription among populations. We compared the genomewide transcription levels between two Atlantic salmon subpopulations that have been diverging for only six generations. Following assessment of normality and unimodality on a gene-per-gene basis, the additive genetic basis of gene transcription was estimated using the animal model. Gene transcription h2 estimates were significant for 1044 (16%) of all detected cDNA clones. In an approach analogous to that of genome scans, we used the distribution of the QST values estimated from intra- and intersubpopulation additive genetic components of the transcription profiles to identify 16 outlier genes (average QST estimate = 0.11) whose transcription levels are likely to have evolved under the influence of directional selection within six generations only. Overall, this study contributes both empirically and methodologically to the quantitative genetic exploration of gene transcription data. Text Atlantic salmon PubMed Central (PMC) Genetics 177 2 1011 1022 |
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Investigations Roberge, C. Guderley, H. Bernatchez, L. Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
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Investigations |
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Evolutionary genomics has benefited from methods that allow identifying evolutionarily important genomic regions on a genomewide scale, including genome scans and QTL mapping. Recently, genomewide scanning by means of microarrays has permitted assessing gene transcription differences among species or populations. However, the identification of differentially transcribed genes does not in itself suffice to measure the role of selection in driving evolutionary changes in gene transcription. Here, we propose and apply a “transcriptome scan” approach to investigating the role of selection in shaping differential profiles of gene transcription among populations. We compared the genomewide transcription levels between two Atlantic salmon subpopulations that have been diverging for only six generations. Following assessment of normality and unimodality on a gene-per-gene basis, the additive genetic basis of gene transcription was estimated using the animal model. Gene transcription h2 estimates were significant for 1044 (16%) of all detected cDNA clones. In an approach analogous to that of genome scans, we used the distribution of the QST values estimated from intra- and intersubpopulation additive genetic components of the transcription profiles to identify 16 outlier genes (average QST estimate = 0.11) whose transcription levels are likely to have evolved under the influence of directional selection within six generations only. Overall, this study contributes both empirically and methodologically to the quantitative genetic exploration of gene transcription data. |
format |
Text |
author |
Roberge, C. Guderley, H. Bernatchez, L. |
author_facet |
Roberge, C. Guderley, H. Bernatchez, L. |
author_sort |
Roberge, C. |
title |
Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
title_short |
Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
title_full |
Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
title_fullStr |
Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
title_full_unstemmed |
Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations |
title_sort |
genomewide identification of genes under directional selection: gene transcription qst scan in diverging atlantic salmon subpopulations |
publisher |
Copyright © 2007 by the Genetics Society of America |
publishDate |
2007 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034609 http://www.ncbi.nlm.nih.gov/pubmed/17720934 https://doi.org/10.1534/genetics.107.073759 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034609 http://www.ncbi.nlm.nih.gov/pubmed/17720934 http://dx.doi.org/10.1534/genetics.107.073759 |
op_rights |
Copyright © 2007 by the Genetics Society of America |
op_doi |
https://doi.org/10.1534/genetics.107.073759 |
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Genetics |
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