Domestication rewired gene expression and nucleotide diversity patterns in tomato |
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Authors: | Christopher Sauvage Andrea Rau Charlotte Aichholz Joël Chadoeuf Gautier Sarah Manuel Ruiz Sylvain Santoni Mathilde Causse Jacques David Sylvain Glémin |
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Institution: | 1. INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Montfavet Cedex, France;2. GABI, INRA, AgroParisTech, Université Paris‐Saclay, Jouy‐en‐Josas, France;3. Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Montpellier, France;4. CIRAD, UMR AGAP, Baillarguet, Montferrier‐sur‐Lez, France;5. Institut des Sciences de l'Evolution de Montpellier (ISEM‐UMR 5554 Université de Montpellier – CNRS‐IRD‐EPHE), Montpellier, France;6. Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden |
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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. |
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Keywords: | domestication gene co‐expression comparative genomics selective sweep tomato |
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