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Génétique Quantitative et Évolution - Le Moulon

ATIP-Avenir Insern CNRS - Ecological genomics of biotic interactions

Welcome to Amandine Cornille team at the Génétique Quantitative and Evolution lab, Univ. Paris Saclay!

Amandine Cornille is currently group leader of a young ATIP / AVENIR team created in January 2019 at the Genetic Quantitative and Evolution (France) working on plant and insect population and evolutionary genomics, in particular on the ecological genomics of apple-aphid interaction.

Amandine Cornille has recently been awarded of the CNRS Paoletti prize 2020 for her outstanding research as a young scientist in the field of biology!!!

photo apple sylvestris
photo apple sylvestris

We work on the evolutionary forces underlying the adaptation of populations and the emergence of new species, using population genetics and genomics approaches combined with field experiments. We study both short and long evolutionary timescales (domestication and wild species divergence, respectively) to investigate the ecological factors and genomic processes underlying adaptation.

In particular, we focus on plant biotic interactions, which are fundamental to our understanding of biodiversity and adaptation. We focus on the adaptive genomics of apple-aphid interactions in the context of domestication to understand the impact of apple domestication on the adaptation of a major apple aphid pest Dysaphis plantaginea (the rosy apple aphid), to its apple hosts in Eurasia, the cultivated (Malus domestica) and wild apples (Malus sylvestris, Malus sieversii and Malus orientalis). Recently, we have also started to focus on the aphid-endosymbiotic bacteria interaction.

We have also built an orchard of wild apples at Univ. Paris Saclay for scientific, mediation and conservation purposes [link to the DEEV website SOON!]. See the progress of the projects on [@CornilleAmand] & [@PommierVerger] and here website of the wild apple orchad & here movie of the wild apple orchad.

Génétique Quantitative et Évolution - Le Moulon
Ferme du Moulon
F-91190 Gif-sur-Yvette
e-mail : amandine.cornille[at]gmail.com, amandine.cornille[at]inrae.fr
Phone: + 33 1 69 33 23 52
Google Scholar profile
Research Gate
Twitter : @CornilleAmand & @Pommier_verger

Keywords: adaptation, introgressions, gene flow, conservation, agroforestery, carbon footprint, breeding, ecology, domestication, coevolution, pest evolution, endosymbiotic bacteria, citizen science.


Anthony Venon
Sergio Vazquez is enrolled in a Ph.D. (Doctoral School “Science du Végétal”) on the ecological and genomic bases of local adaptation of a major apple pest, the rosy apple aphid, under the supervision of Dr. Amandine Cornille. He holds a Master in Science at the University of Tsukuba in Tsukuba, Ibaraki, Japan (2017-2019).

Anthony Venon
Xilong Chen is a ATIP-Avenir postdoc supervised by Amandine Cornille, and works on the adaptive genomics of apple domestication, and before, he got his Ph.D. at Northwest A&F University, China.

Yongshua Jiang is a one-year visiting scholar supervised by Amandine Cornille, and works on the genomics of adaptation in aphids. Before, she got her Ph.D. at Northwest A&F University, and currently employed by Guangdong Academy of Agricultural Sciences, China.

Anthony Venon
Anthony Venon is a plant biologist Master 2 student (Cellular and Molecular biology Master, Sorbonne University, Paris, France) co-advised by Amandine Cornille and Karine Alix, and works on the evolution of transposable elements in apples. Before, he was an INRA research technician at the Quantitative Genetics and Evolution - Le Moulon lab (Gif-Sur-Yvette, France) for 4 years.

Noémie Delprouve
Noémie Delprouve is a Master 2 student in Biodiversity, Ecology and Evolution (University of Lille) making a five months internship, supervised by Amandine Cornille and Stéphane Bazot, about climate effects on wild apple trees.

Célia Lougmani
Célia Lougmani is a Master 1 student (Biodiversity, Ecology and Evolution Master at Sorbonne University, Paris, France) co-supervised by Amandine Cornille, Karine Alix and Xilong Chen for a four-month research internship, and works on the evolution of transposable elements in aphids and their role in the adaptation to their host, the apple tree.

Anne-Flore Didelot is a biotechnology engineer (ENSAIA, Lorraine University, Nancy, France) + Master 2 (Plant and environment interactions, Faculty of Sciences and Technologies, Nancy) student supervised by Amandine Cornille for a 6 month-internship. She works on the evolutionary history of the fungus Microbotryum sp. in Europe.


photo de l'équipe1
Aurélien Forler is a Bachelor student in forestery (Licence 3) at AgroParisTech Nancy, France, and was in the team for a two-month research experience study period to work on the genetic determinants of population structure in wild and cultivated apples.

Thomas Kaczmarek is preparing a Master of Science in Engineering at AgroParisTech and was in the team for a five-month research experience study period to work on the genomic bases of host-pathogen interaction using different models : Microbotryum-Dianthus and apple-aphid models. In 2020, he will start a Master 2 « Biodiversité, écologie, évolution » at Paris Saclay University.

Ana Agapito Ana is a plant biologist Master student and was in the team for reconstructing the domestication history of apples using demographic inferences. Ana did her M.Sc. in Biological Sciences, Universidad del Bío-Bío (Chili). She is doing her PhD at ETH Zürich (Switzerland).


Stéphane Bazot, Univ. Paris Saclay, France

Karine Alix, AgroParisTech, France

Fabrice Legeai, INRAE, Rennes, France

Dominique Lavenier, INRIA, Rennes, France

Tatiana Giraud, Univ. Paris Saclay, France

Maud Tenaillon, Univ. Paris Saclay

Ammar Alhmedi and Tim Bellien, PC-Fruit, Belgium

Enrique Dapena and Marcos Minarros, SERIDA, Asturias, Spain

Jia-Long Yao, The New Zealand Institute for Plant & Food Research Limited, Auckland

Clément Lafon-Placette, Univ. Charles, Pragues, Czech Republic

Hamed Yousefzadeh, Univ. Tarbiat Modares, Iran

Véronique Decroocq, INRAE, Bordeaux, France


photo de l'équipe1
ECOTRON project 2020-2021 : “Impact of climate changes on apples” [http://www.cereep.ens.fr/spip.php?article9&lang=fr]

photo de l'équipe1
ATIP-Avenir 2019-2021: “Genomic bases of local adaptation in plant-pest interactions: insights from the cultivated apple and its aphid pests”.

photo de l'équipe1
Projet européen INTERREG France-Wallonie-Vlaanderen « PROVERBIO 2019-2022: Protection des vergers par lutte biologique : une sélection adaptée des auxiliaires», avec le soutien du Fonds européen de développement régional, Met steun van het Europees Fonds voor Regionale Ontwikkeling

photo de l'équipe1
LabEX Biodiversity Agrosystem Climate and Society Emergence project 2016-2018 “Impact of domestication of pest adaptation to fruit trees”.

La Diagonale “Coup de pouce” 2019: Scientific divulgation Scientific mediation around the valorization of a living heritage collection of endangered wild apple trees and its associated biodiversity in an experimental and educational orchard on the Paris Saclay plateau.

photo de l'équipe1
IDEEV 2020: On the genomic bases of adaptation in the aphid-bacteria interaction.

European LEADER project “Building a conservation orchads of wild apples on the Saclay Plateau”

ATIP-Avenir Insern CNRS is attached to the LabEx SPS, Sciences des Plantes de Saclay.


  • Xilong Chen Postdoc (CNRS)
  • Amandine Cornille Junior Investigator (CNRS)
  • Thomas Kaczmarek (INRAE)
  • Sergio Vazquez PhD Student (INRAE)
  • Anthony Venon (INRAE)


  • Bina H., Yousefzadeh H., Venon A. , Remoué arine., Rousselet A., Falque M., Faramarzi S., Giraud T., Hossainpour B., Abdollahi H., Gabrielyan I., Nersesyan A., Cornille A. . (2021) An additional area of apple domestication with crop-wild gene flow, and also cultivation of the local wild apple, in the Caucasus. bioRxiv, 2021.03.28.437401
  • Denoirjean T., Doury G., Cornille A. , Chen X. , Hance T., Ameline A.. (2021) Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea. Scientific Reports, 1 (11) 5732
  • Koupilová K., Koubek T., Cornille A. , Janovský Z.. (2021) Local maladaptation of the anther-smut fungus parasitizing Dianthus carthusianorum. European Journal of Plant Pathology,
  • Cornille A. , Tiret M., Salcedo A., Huang H., Orsucci M., Milesi P., Kryvokhyzha D., Holm K., Ge XJ., Stinchcombe JR., Glemin S., Wright SI., Lascoux M.. (2020) Phenotypic plasticity, population structure and adaptation in a young weed species with a worldwide distribution. bioRxiv,
  • Hartmann FE., Snirc A., Cornille A. , Godé C., Touzet P., Van Rossum F., Fournier E., Le Prieur S., Shykoff J., Giraud T.. (2020) Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex. Molecular Ecology, n/a (n/a)
  • Cornille A. , Antolín F., Garcia E., Vernesi C., Fietta A., Brinkkemper O., Kirleis W., Schlumbaum A., Roldán-Ruiz I.. (2019) A Multifaceted Overview of Apple Tree Domestication. Trends in Plant Science, 8 (24) 770 - 782
  • Hartmann FE., Rodríguez de la Vega RC., Carpentier F., Gladieux P., Cornille A. , Hood ME., Giraud T.. (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annu. Rev. Phytopathol., 1 (57) annurev-phyto-082718-095947
  • Liu S., Cornille A. , Decroocq S., Tricon D., Chague A., Eyquard JP., Liu WS., Giraud T., Decroocq V.. (2019) The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events. Mol Ecol, mec.15296
  • Peace CP., Bianco L., Troggio M., van de Weg E., Howard NP., Cornille A. , Durel CE., Myles S., Migicovsky Z., Schaffer RJ., Costes E., Fazio G., Yamane H., van Nocker S., Gottschalk C., Costa F., Chagné D., Zhang X., Patocchi A., Gardiner SE., Hardner C., Kumar S., Laurens F., Bucher E., Main D., Jung S., Vanderzande S.. (2019) Apple whole genome sequences: recent advances and new prospects. Hortic Res, 1 (6) 59
  • Ruhsam M., Jessop W., Cornille A. , Renny J., Worrell R.. (2019) Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain. Forestry (Lond), 1 (92) 85-96
  • Volk GM., Cornille A. , Korban SS.. (2019) Genetic Diversity and Domestication History in Pyrus. , 51-62
  • Amirchakhmaghi N., Yousefzadeh H., Hosseinpour B., Espahbodi K., Aldaghi M., Cornille A. . (2018) First insight into genetic diversity and population structure of the Caucasian wild apple (Malus orientalis Uglitzk.) in the Hyrcanian forest (Iran) and its resistance to apple scab and powdery mildew. Genet Resour Crop Evol, 4 (65) 1255-1268
  • Besnard G., Terral JF., Cornille A. . (2018) On the origins and domestication of the olive: a review and perspectives. Annals of botany, 3 (121) 385-403
  • Feurtey A., Cornille A. , Shykoff JA., Snirc A., Giraud T.. (2017) Crop‐to‐wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe. Evolutionary Applications, 2 (10) 180-188
  • Petit E., Silver C., Cornille A. , Gladieux P., Rosenthal L., Bruns E., Yee S., Antonovics J., Giraud T., Hood ME.. (2017) Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Molecular Ecology, 7 (26) 1877-1890
  • Cornille A. , Salcedo A., Kryvokhyzha D., Glémin S., Holm K., Wright SI., Lascoux M.. (2016) Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Molecular Ecology, 2 (25) 616–629
  • Decroocq S., Cornille A. , Tricon D., Babayeva S., Chague A., Eyquard JP., Karychev R., Dolgikh S., Kostritsyna T., Liu S., Liu W., Geng W., Liao K., Asma BM., Akparov Z., Giraud T., Decroocq V.. (2016) New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Molecular Ecology, 19 (25) 4712–4729
  • Feurtey A., Gladieux P., Hood ME., Snirc A., Cornille A. , Rosenthal L., Giraud T.. (2016) Strong phylogeographic co-structure between the anther-smut fungus and its white campion host. New Phytologist, 3 (212) 668-679
  • Kryvokhyzha D., Holm K., Chen X. , Cornille A. , Glémin S., Wright S., Lagercrantz U., Lascoux M.. (2016) The influence of demographic history on gene expression variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). , 1106-21
  • Cornille A. , Feurtey A., Gélin U., Ropars J., Misvanderbrugge K., Gladieux P., Giraud T.. (2015) Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evolutionary Applications, n/a-n/a
  • Leforestier D., Ravon E., Muranty H., Cornille A. , Lemaire C., Giraud T., Durel CE., Branca A.. (2015) Genomic basis of the differences between cider and dessert apple varieties. Evolutionary Applications, 7 (8) 650-661
  • Yao JL., Xu J., Cornille A. , Tomes S., Karunairetnam S., Luo Z., Bassett H., Whitworth C., Rees-George J., Ranatunga C., Snirc A., Crowhurst R., de Silva N., Kumar S., Chagne D., Bus V., Volz R., Rikkerink E., Gardiner SE., Giraud T., Newcomb R., MacDiarmid R., Gleave AP.. (2015) A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal, 417-427
  • Cornille A. , Giraud T., Smulders MJM., Roldán-Ruiz I., Gladieux P.. (2014) The domestication and evolutionary ecology of apples. Trends in Genetics, 2 (30) 57-65
  • Schnitzler A., Arnold C., Cornille A. , Bachmann O., Schnitzler C.. (2014) Wild European Apple (Malus sylvestris (L.) Mill.) Population Dynamics: Insight from Genetics and Ecology in the Rhine Valley. Priorities for a Future Conservation Programme. PLoS ONE, 5 (9) e96596
  • Yuan JH., Cornille A. , Giraud T., Cheng FY., Hu YH.. (2014) Independent domestications of cultivated tree peonies from different wild peony species. Molecular Ecology, 1 (23) 82-95
  • Cornille A. , Gladieux P., Giraud T.. (2013) Crop-to-wild gene flow and spatial genetic structure in the wild closest relatives of the cultivated apple. Evolutionary Applications, 5 (6) 737-748
  • Cornille A. , Giraud T., Bellard C., Tellier A., Le Cam B., Smulders MJM., Kleinschmit J., Roldan-Ruiz I., Gladieux P.. (2013) Post-glacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple. Molecular Ecology, 8 (22) 2249-63
  • Cornille A. , Underhill JG., Cruaud A., Hossaert-McKey M., Johnson SD., Tolley KA., Kjellberg F., van Noort S., Proffit M.. (2012) Floral volatiles, pollinator sharing and diversification in the fig–wasp mutualism: insights from Ficus natalensis, and its two wasp pollinators (South Africa). Proceedings of the Royal Society of London B: Biological Sciences, 1734 (279) 1731-1739
  • Cornille A. , Gladieux P., Smulders MJ., Roldan-Ruiz I., Laurens F., Le Cam B., Nersesyan A., Clavel J., Olonova M., Feugey L., Gabrielyan I., Zhang XG., Tenaillon MI., Giraud T.. (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS genetics, 5 (8) e1002703
  • Lê Van A., Gladieux P., Lemaire C., Cornille A. , Giraud T., Durel CE., Caffier V., Le Cam B.. (2012) Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host. Evolutionary Applications, 7 (5) 694-704