Know more

About cookies

What is a "cookie"?

A "cookie" is a piece of information, usually small and identified by a name, which may be sent to your browser by a website you are visiting. Your web browser will store it for a period of time, and send it back to the web server each time you log on again.

Different types of cookies are placed on the sites:

  • Cookies strictly necessary for the proper functioning of the site
  • Cookies deposited by third party sites to improve the interactivity of the site, to collect statistics

Learn more about cookies and how they work

The different types of cookies used on this site

Cookies strictly necessary for the site to function

These cookies allow the main services of the site to function optimally. You can technically block them using your browser settings but your experience on the site may be degraded.

Furthermore, you have the possibility of opposing the use of audience measurement tracers strictly necessary for the functioning and current administration of the website in the cookie management window accessible via the link located in the footer of the site.

Technical cookies

Name of the cookie


Shelf life

CAS and PHP session cookies

Login credentials, session security



Saving your cookie consent choices

12 months

Audience measurement cookies (AT Internet)

Name of the cookie


Shelf life


Trace the visitor's route in order to establish visit statistics.

13 months


Store the anonymous ID of the visitor who starts the first time he visits the site

13 months


Identify the numbers (unique identifiers of a site) seen by the visitor and store the visitor's identifiers.

13 months

About the AT Internet audience measurement tool :

AT Internet's audience measurement tool Analytics is deployed on this site in order to obtain information on visitors' navigation and to improve its use.

The French data protection authority (CNIL) has granted an exemption to AT Internet's Web Analytics cookie. This tool is thus exempt from the collection of the Internet user's consent with regard to the deposit of analytics cookies. However, you can refuse the deposit of these cookies via the cookie management panel.

Good to know:

  • The data collected are not cross-checked with other processing operations
  • The deposited cookie is only used to produce anonymous statistics
  • The cookie does not allow the user's navigation on other sites to be tracked.

Third party cookies to improve the interactivity of the site

This site relies on certain services provided by third parties which allow :

  • to offer interactive content;
  • improve usability and facilitate the sharing of content on social networks;
  • view videos and animated presentations directly on our website;
  • protect form entries from robots;
  • monitor the performance of the site.

These third parties will collect and use your browsing data for their own purposes.

How to accept or reject cookies

When you start browsing an eZpublish site, the appearance of the "cookies" banner allows you to accept or refuse all the cookies we use. This banner will be displayed as long as you have not made a choice, even if you are browsing on another page of the site.

You can change your choices at any time by clicking on the "Cookie Management" link.

You can manage these cookies in your browser. Here are the procedures to follow: Firefox; Chrome; Explorer; Safari; Opera

For more information about the cookies we use, you can contact INRAE's Data Protection Officer by email at or by post at :


24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal Logo GAFL Logo GAFL

Home page GAFL

Axis 1: Genomic diversity and domestication

Domestication in Solanaceae


The consequences of domestication on the nucleotide and expression patterns have been examined using RNAseq data in a set of crop and wild accessions (, Sarah et al., 2016). We extended this approach to the Solanaceae family to conduct a comparative genomic approach in pepper, eggplant and wild green-fruited tomatoes to test for convergent domestication. RNAseq data have been produced for 24 accessions (12 crops/12 wild) in the three species. Thus, from site frequency spectrum, we aim at modelling the most probable demographic scenario that occurred during the domestication phase in these three species and compare these scenarios together.

Relevant Publications

Zhao JT, C Sauvage, J Zhao, F Bitton, G Bauchet, D Liu, S Huang, D Tieman, HJ Klee, and M Causse (2019) Meta-analysis of genome-wide association studies provide new insights into genetic control of tomato flavour. Nat Comm vol.10;

Burgos E, De Luca B, Diouf I, de Haro LA, Albert E, Sauvage C, Zhao J, Bermudez L, Asís R, Nunes Nesi A, Guiraud T, Matringe M, Brehelin C, Ferrand C, Atienza I, Jorly J , Mauxion JP, Baldet P, Fernie AR, Quadrana L, Rothan C, Causse M, Carrari F (2021) Vitamin E contents in tomato fruits is associated to natural variation in chorismate metabolism. Plant J 105,907-923.

Sauvage C, Rau A, Aichholtz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. The Plant J 91, 631-645 ; doi: 10.1111/tpj.13592

Bauchet  G, S Grenier, N Samson, V Segura, A Kende, J Beekwilder, K Cankar, JL Gallois, J Gricourt, J Bonnet, C Baxter, L Grivet, M Causse (2017) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit and implications for flavor improvement. New Phytologist (doi: 10.1111/nph.14615)

Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M (2017) Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor Appl Genet 130(5), 875-889 ; DOI 10.1007/s00122-017-2857-9

Pascual L, E Albert, C Sauvage, J Duangjit, JP Bouchet, F Bitton, N Desplat, D Brunel, MC Le Paslier, N Ranc, L Bruguier, B Chauchard, P Verschave, M Causse (2016) Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Science 242: 120-130

Blanca J, J Montero-Pau, C Sauvage, G Bauchet, E Illa, MJ Diez, D Francis, M Causse, E van der Knaap and J Cañizares (2015) Genomic variation in the tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16 : 257, doi:10.1186/s12864-015-1444-1

Lin T, G Zhu, J Zhang, X Xu, Q Yu, Z Zheng, Z Zhang, Y Lun, S Li, X Wang, Z Huang, J Li, Ci Zhang, T Wang, Y Zhang, A Wang, Y Zhang, K Lin, C Li, G Xiong, Y Xue, A Mazzucato, M Causse, Z Fei, JJ Giovannoni, R T Chetelat, D Zamir, T Städler, J Li, Z Ye, Y Du & S Huang 2014. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics 46: 1220-1226; doi:10.1038/ng.3117

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

Prunus diversity


The collections conserved in the GRC and in the team is a valuable resource which can be exploited in order to:

  • screen our genetic resources for different traits in order to broaden the genetic basis used in crosses, including wild-relative species;
  • search for resilient genotypes to be used as genetic backgrounds in which to introgress targeted traits;
  • study the structure and diversity of our collections, analyze the polymorphism of loci of interest;
  • develop GWAS analyses.

Relevant Publications

Pérez de los Cobos, F., P. J. Martínez-García, et al. (2021). Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars. Horticulture Research 8(1): 11. 10.1038/s41438-020-00444-4

Groppi, A., S. Liu, et al. (2021). Population genomics of apricots unravels domestication history and adaptive events. Nature Communications 12(1): 3956.

Cirilli, M., S. Gattolin, et al. (2021). The Di2/pet Variant in the PETALOSA Gene Underlies a Major Heat Requirement-Related QTL for Blooming Date in Peach [Prunus persica (L.) Batsch]. Plant and Cell Physiology 62(2): 356-365.

Cirilli, M., S. Micali, et al. (2020). The multi-site PeachRefPop collection: a true cultural heritage and international scientific tool for fruit trees. Plant Physiology: pp.01412.02019.

Jung, M., Roth, M., Aranzana, M.J. et al. The apple REFPOP—a reference population for genomics-assisted breeding in apple. Hortic Res 7, 189 (2020).

Alioto, T., K. G. Alexiou, et al. (2020). Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. The Plant Journal 101(2): 455-472.

Conrad, A. O., J. Yu, et al. (2019). Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca). Tree Physiology 39(7): 1136-1148.

Gattolin, S., M. Cirilli, et al. (2018). Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae. The Plant Journal.

Hollender, C. A., T. Pascal, et al. (2018). Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. Proceedings of the National Academy of Sciences 115(20): 4690-4699.

Le Bourvellec, C., Gouble, B., Bureau, S., Reling, P., Bott, R., Ribas-Agusti, A., Audergon, J. M., Renard, C. (2018). Impact of canning and storage on apricot carotenoids and polyphenols. Food Chemistry, 1-50. , DOI : 10.1016/j.foodchem.2017.07.147

 Hernández Mora, J. R., Micheletti, D., Bink, M., Van de Weg, E., Cantín, C., Nazzicari, N., Caprera, A., Dettori, M. T., Micali, Banchi, Campoy, J. A., Dirlewanger, E., Lambert, P., Pascal, T., Troggio, Bassi, D., Rossini, L., Verde, Quilot-Turion, B., Laurens, F., Arus, P., Aranzana (2017). Integrated QTL detection for key breeding traits in multiple peach progenies. BMC Genomics, 18 (1). , DOI : 10.1186/s12864-017-3783-6

Bourguiba, H., Batnini, M.-A., Krichen, L., Trifi-Farah, N., Audergon, J. M. (2017). Population structure and core collection construction of apricot (Prunus armeniaca L.) in north Africa based on microsatellite markers. Plant Genetic Resources Characterization and Utilization, 15 (1), 21-28.

Ayour, J., Gouble, B., Reling, P., Ribas-Agustí, A., Audergon, J. M., Maingonnat , J. F., Benichou, M., Renard, C. (2017). Impact of cooking on apricot texture as a function of cultivar and maturity. LWT - Food Science and Technology, 85 (Part B), 385-389. , DOI : 10.1016/j.lwt.2016.10.040