Research Topic

As a geneticist, I’m interest in the consequences of the domestication process at the genome-wide level in plant and animal species of economical interest. I trained in quantitative genetic and molecular biology during my PhD and turned to population and evolutionary genetic and bioinformatic as well.

Within the Qualitom team (Quality, Diversity and Environment in tomato), I use the tomato crop (Solanum lycopersicum) and its wild relatives to (1) characterize the genetic resources; (2) to detect the footprints of the domestication at the nucleotide and gene expressions levels; (3) identify the genetic bases of traits of economical interest using association genetic (GWAS) and (4) evaluate the genomic selection strategy in this crop.

Collaborators

Aurélien Tellier, Technical University Munich, Germany 

Thomas Stadler, ETH Zurich, Switzerland 

Sylvain Glémin, University of Montpellier 2, France 

Janejira Duangjit, Kasetsart University, Bangkok, Thaïland

Student supervising

PhD degree :

Stéphanie Arnoux (2015-2018): Comparative genomics study of the domestication in three Solanaceae

Elise Albert (2013-2017): Genetic and genomic bases of drought stress response in tomato and impact on fruit quality.

Master 2 :

Coralie Picard (SupAgro Montpellier) – 2015 : Evaluation of the genomic selection strategy in 3 experimental designs in tomato

Charlotte Aichholtz (SupAgro Rennes) – 2014 : Molecular evolution in a crop species
–
a genome-wide study in tomato using RNAseq data

Morgane Roth (SupAgro Rennes) - 2013 : Detection of loci associated to the bacterial canker Pseudomonas syringae in apricot (Prunus armeniaca Linneus)

Master 1 :

Francois-Xavier Babin (Rouen University) – 2015 : Building of a bioinformatic pipeline to analyse RNAseq data for the study of the genetic bases of adaptation of wild pepper populations during the domestication process

Henri Desaint (SupAgro Montpellier) – 2015 : In silico characterization of the chromosome 5 in potato and comparative study within the Solanaceae family

Education

2008 - 2011 Postdoc : Laval University, Québec, Canada. Institut de Biologie Intégrative et des Systèmes, Laboratory of L. Bernatchez 

-          Linkage mapping and QTL detection linked to growth, reproduction and stress response in the brook charr, Salvelinus fontinalis

-          Study of the transcriptional consequences of domestication in the brook charr (Salvelinus fontinalis)

-          Detection of selection footprints in 7 Solanaceae species

2004 – 2008 PhD : La Rochelle University, La Rochelle, France. Genetic and Pathology Laboratory, Ifremer 

-          Development of molecular markers linked summer mortality and resistance to herpes virus (OsHV1) in the pacific cupped oyster, Crassostrea gigas.

2003 – DEA (Diplôme d’Etudes Approfondies) option Biodiversity and Actual and Fossil Ecosystems, Lille 1 University, Lille, France 

Selected Publications

Sauvage, C., Rau, A., Aichholtz, C., Chadoeuf, J., Sarah, G., Ruiz, M., Santoni, S., Causse, M., David, J. and Glémin, S. Domestication rewired gene expression and nucleotide diversity patterns in tomato, Accepted in Plant Journal.

Clément, Y., Sarah, G., Holtz, Y., Homa, F., Pointet, S. Contreras, C., Nabholz, B., Sabot, F., Sauné, L., Ardisson, M., Bacilieri, R., Khadari, B., LAnaud, C., Pot, D., Sauvage, C., Scarcelli, N., Tregear, J., Vigouroux, Y., Yahiaoui, N., Ruiz, M., Santoni, S., Labouisse, J-P; Pham, J-L., David, J. and Glémin, S. Evolutionary forces affecting synonymous variations in plant genomes, Accepted in PLoS Genetics

2016

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros J-P, Labouisse J-P, Pham J-L, David J, Glémin S, Ruiz M. 2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources: DOI: 10.1111/1755-0998.12587. Link

Duangjit, J., Causse, M and Sauvage, C. (2016) Assessment of factor affecting genomic selection in a broad based population of tomato. Molecular Breeding 36:29. Link

2015

Blanca, J., Monterau-Pau, J., Sauvage, C., Bauchet, G., Illa, E., Diez, M.J., Francais, D. Causse, M., van der Knaap, E. and Canizares, J. (2015) Genomic variation in tomato throughout domestication, from wild ancestors to contemporary accessions. BMC Genomics 16:257. Link

2014

Sauvage, C., Segura, V., Bauchet, G., Stevens, R., Thi Do, P., Nikoloski, Z., Fernie, A.R., Causse, M. (2014) Genome Wide Association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiology 165: 1120-1132. Link

2013

Chakrabarti, M., Zhang, N., Sauvage, C., Muños, S., Blanca, J., Cañizares, J., Diez, M.J., Schneider, R., Mazourek, M., McClead, J., Causse, M., van der Knaap, E. (2013) A cytochrome P450 regulates a domestication trait in cultivated tomato. P.N.A.S: Proceedings of the National American Society 110(42): 17125-30. Link

2012

Sauvage, C.,Vagner, M.,Derôme, N., Audet, C., and Bernatchez, L. (2012a) Coding gene SNP mapping and QTL detection for physiological reproductive traits in brook charr, Salvelinus fontinalis. Genes | Genomes | Genetics (Bethesda) 2: 379-392. Link

Sauvage, C.,Vagner, M.,Derôme, N., Audet, C., and Bernatchez, L. (2012b) Coding gene SNP mapping reveals QTL linked to growth and stress response in brook charr (Salvelinus fontinalis)  Genes | Genomes | Genetics. Link

Lamaze, F., Sauvage, C., Marie, A., Garant, D., and Bernatchez, L. (2012) Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis) Molecular Ecology 21(12): 2877-2895. Link

2010

Sauvage, C., Derôme, N.,Normandeau, E., St-Cyr, J., Audet, C. (2010) Fast transcriptional responses to domestication in the brook charr Salvelinus fontinalis. Genetics 185:105-112. Link

Publications | Book Chapters | Posters

Link to all publications :

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