Domestication rewired gene expression and nucleotide diversity patterns in tomato
Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species.
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dig-cirad-fr-5843392024-01-29T00:17:34Z http://agritrop.cirad.fr/584339/ http://agritrop.cirad.fr/584339/ Domestication rewired gene expression and nucleotide diversity patterns in tomato. Sauvage Christopher, Rau Andrea, Aichholz Charlotte, Chadoeuf Joël, Sarah Gautier, Ruiz Manuel, Santoni Sylvain, Causse Mathilde, David Jacques, Glemin Sylvain. 2017. Plant Journal, 91 (4) : 631-645.https://doi.org/10.1111/tpj.13592 <https://doi.org/10.1111/tpj.13592> Domestication rewired gene expression and nucleotide diversity patterns in tomato Sauvage, Christopher Rau, Andrea Aichholz, Charlotte Chadoeuf, Joël Sarah, Gautier Ruiz, Manuel Santoni, Sylvain Causse, Mathilde David, Jacques Glemin, Sylvain eng 2017 Plant Journal F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/584339/1/The%20Plant%20Journal%202017%20Sauvage.pdf text Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1111/tpj.13592 10.1111/tpj.13592 info:eu-repo/semantics/altIdentifier/doi/10.1111/tpj.13592 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1111/tpj.13592 |
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Biblioteca del CIRAD Francia |
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F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 |
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F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 Sauvage, Christopher Rau, Andrea Aichholz, Charlotte Chadoeuf, Joël Sarah, Gautier Ruiz, Manuel Santoni, Sylvain Causse, Mathilde David, Jacques Glemin, Sylvain Domestication rewired gene expression and nucleotide diversity patterns in tomato |
description |
Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species. |
format |
article |
topic_facet |
F70 - Taxonomie végétale et phytogéographie F30 - Génétique et amélioration des plantes Solanum lycopersicum expression des gènes domestication des plantes Solanum génétique des populations plante sauvage plante de culture génie génétique variation génétique évolution bioinformatique http://aims.fao.org/aos/agrovoc/c_4475 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_7216 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_37958 |
author |
Sauvage, Christopher Rau, Andrea Aichholz, Charlotte Chadoeuf, Joël Sarah, Gautier Ruiz, Manuel Santoni, Sylvain Causse, Mathilde David, Jacques Glemin, Sylvain |
author_facet |
Sauvage, Christopher Rau, Andrea Aichholz, Charlotte Chadoeuf, Joël Sarah, Gautier Ruiz, Manuel Santoni, Sylvain Causse, Mathilde David, Jacques Glemin, Sylvain |
author_sort |
Sauvage, Christopher |
title |
Domestication rewired gene expression and nucleotide diversity patterns in tomato |
title_short |
Domestication rewired gene expression and nucleotide diversity patterns in tomato |
title_full |
Domestication rewired gene expression and nucleotide diversity patterns in tomato |
title_fullStr |
Domestication rewired gene expression and nucleotide diversity patterns in tomato |
title_full_unstemmed |
Domestication rewired gene expression and nucleotide diversity patterns in tomato |
title_sort |
domestication rewired gene expression and nucleotide diversity patterns in tomato |
url |
http://agritrop.cirad.fr/584339/ http://agritrop.cirad.fr/584339/1/The%20Plant%20Journal%202017%20Sauvage.pdf |
work_keys_str_mv |
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1792499278484078592 |