Modelling the population history using population genomics : the tomato domestication as a case of study

Autor: Sauvage, Christopher, Aichholz, Charlotte, Sarah, Gautier, Ruiz, Manuel, Causse, Mathilde, David, Jacques, GLEMIN, Sylvain
Přispěvatelé: Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), Sativa Seeds, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Génétique et Amélioration des Fruits et Légumes (GAFL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bordeaux (UB). FRA., Unité de recherche Génétique et amélioration des fruits et légumes (GAFL)
Jazyk: angličtina
Rok vydání: 2015
Předmět:
Zdroj: 12. Solanaceae Conference
12. Solanaceae Conference, Oct 2015, Bordeaux, France
The 12th Solanacae Conference SOL2015 book of abstracts
12. Solanaceae Conference, Université de Bordeaux (UB). FRA., Oct 2015, Bordeaux, France
12. Solanaceae Conference, Bordeaux, FRA, 2015-10-25-2015-10-29
Popis: A bottleneck is commonly associated to the study of crop domestication, in which a population experiences a drastic reduction in size and nucleotide diversity. The population genomic era offers new opportunities to document this scenario through the study of the site frequency spectrum (SFS), a powerful method for summarizing genomic data at the genome-wide level. Using a diffusion approximation approach (Gutenkunst et al., 2009) to model SFS, we estimated the demographical history of a major crop, the cultivated tomato (Solanum lycopersicum) and its wild relative (S. pimpinellifolium). We compared the observed 2 dimensional SFS, obtained from 20 individuals and ~84,500 SNPs markers, to the modelled ones, obtained from four different scenarios. Variants were polarized to ancestral and derived alleles based on the eggplant outgroup sequences. Assuming a mutation rate of 3×10-9 and a generation time of 1 year, our results suggest that in the best fitting model, population split occurred ~3750 years ago (95%CI: 2985-4552 yrs), wild tomatoes experienced a dramatic bottleneck (effective population size: -87%; reduction of nucleotide diversity: -63%) that occurred ~420 years ago (95%CI: 337-541 yrs). After this bottleneck, migration rate, from cultivated to wild population, was estimated to less than ~1 migrant per generation. Although, 3.1% of the genes derived from neutral expectations suggesting evolutionary forces acting on. These results demonstrate the power of the approach and provide estimates of demographical parameters that fit previous studies of the tomato domestication (Blanca et al., 2015).
Databáze: OpenAIRE
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