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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. Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant Journal, 91 (4) : pp. 631-645.

Journal article ; Article de revue à facteur d'impact
[img] Published version - Anglais
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The Plant Journal 2017 Sauvage.pdf

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[img] Published version - Anglais
Access restricted to CIRAD agents
Use under authorization by the author or CIRAD.
Sauvage_et_al-2017-The_Plant_Journal.pdf

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Quartile : Outlier, Sujet : PLANT SCIENCES

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Solanum lycopersicum, Expression des gènes, Domestication des plantes, Solanum, Génétique des populations, Plante sauvage, Plante de culture, Génie génétique, Variation génétique, Évolution, Bioinformatique

Classification Agris : F70 - Plant taxonomy and geography
F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Sauvage Christopher, INRA (FRA)
  • Rau Andrea, INRA (FRA)
  • Aichholz Charlotte, INRA (FRA)
  • Chadoeuf Joël, INRA (FRA)
  • Sarah Gautier, INRA (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (COL) ORCID: 0000-0001-8153-276X
  • Santoni Sylvain, INRA (FRA)
  • Causse Mathilde, INRA (FRA)
  • David Jacques, Montpellier SupAgro (FRA)
  • Glemin Sylvain, ISEM (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/584339/)

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