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Transposons are important contributors to gene expression variability under selection in rice populations

Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism expression quantitative trait locus mapping using expression data from 208 varieties from the Oryza sativa s...

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Autores principales: Castanera, Raúl, Morales-Díaz, Noemia, Gupta, Sonal, Purugganan, Michael, Casacuberta, Josep M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10393045/
https://www.ncbi.nlm.nih.gov/pubmed/37467142
http://dx.doi.org/10.7554/eLife.86324
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author Castanera, Raúl
Morales-Díaz, Noemia
Gupta, Sonal
Purugganan, Michael
Casacuberta, Josep M
author_facet Castanera, Raúl
Morales-Díaz, Noemia
Gupta, Sonal
Purugganan, Michael
Casacuberta, Josep M
author_sort Castanera, Raúl
collection PubMed
description Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism expression quantitative trait locus mapping using expression data from 208 varieties from the Oryza sativa ssp. indica and O. sativa ssp. japonica subspecies. Our data show that TE insertions are associated with changes of expression of many genes known to be targets of rice domestication and breeding. An important fraction of these insertions were already present in the rice wild ancestors, and have been differentially selected in indica and japonica rice populations. Taken together, our results show that small changes of expression in signal transduction genes induced by TE insertions accompany the domestication and adaptation of rice populations.
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spelling pubmed-103930452023-08-02 Transposons are important contributors to gene expression variability under selection in rice populations Castanera, Raúl Morales-Díaz, Noemia Gupta, Sonal Purugganan, Michael Casacuberta, Josep M eLife Evolutionary Biology Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism expression quantitative trait locus mapping using expression data from 208 varieties from the Oryza sativa ssp. indica and O. sativa ssp. japonica subspecies. Our data show that TE insertions are associated with changes of expression of many genes known to be targets of rice domestication and breeding. An important fraction of these insertions were already present in the rice wild ancestors, and have been differentially selected in indica and japonica rice populations. Taken together, our results show that small changes of expression in signal transduction genes induced by TE insertions accompany the domestication and adaptation of rice populations. eLife Sciences Publications, Ltd 2023-07-19 /pmc/articles/PMC10393045/ /pubmed/37467142 http://dx.doi.org/10.7554/eLife.86324 Text en © 2023, Castanera et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Castanera, Raúl
Morales-Díaz, Noemia
Gupta, Sonal
Purugganan, Michael
Casacuberta, Josep M
Transposons are important contributors to gene expression variability under selection in rice populations
title Transposons are important contributors to gene expression variability under selection in rice populations
title_full Transposons are important contributors to gene expression variability under selection in rice populations
title_fullStr Transposons are important contributors to gene expression variability under selection in rice populations
title_full_unstemmed Transposons are important contributors to gene expression variability under selection in rice populations
title_short Transposons are important contributors to gene expression variability under selection in rice populations
title_sort transposons are important contributors to gene expression variability under selection in rice populations
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10393045/
https://www.ncbi.nlm.nih.gov/pubmed/37467142
http://dx.doi.org/10.7554/eLife.86324
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