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Génétique Quantitative et Évolution - Le Moulon

DEAP - Diversity, Evolution and Adaptation of Populations

Diversity, Evolution and Adaptation of Populations

Our research aims to manage and enhance the cultivated diversity for the agro-ecological transition. They are based on three methodologies, (i) mechanistic modelling and simulation, (ii) statistical modelling for inference and prediction, and (iii) participatory design and experimentation. Our model species is bread wheat.

Axis 1. Optimization of intra-parcel genetic diversity

  • ecophysiology-genetic modeling of a heterogeneous stand:
    • model development of competition for light: WALTer (Lecarpentier et al., 2019)
    • impact of plant-plant interactions on the evolution of mixtures: PhD E. Blanc
  • methodology for the selection of variety and species associations:
    • model development for the genetics of mixing ability: GMA/SMA (Forst et al., 2019), lme4mix
    • design of new breeding programs for mixing ability
  • design of new breeding programs for mixing ability
    • assembly of varieties for the adaptation to the local context
    • better integrate GxExM interactions in organic agriculture
    • development of a multi-criteria assessment tool : Optimix

Projects: MoBiDiv, Wheatamix, PICRI, LIVESEED, CASABio, ReMIX

Major academic collaborators: T. Mary-Huard, P. Barbillon, A. Gauffreteau, V. Allard, B. Haug

Non-academic partners: ITAB, GAB Ile-de-France, Chambres d‘Agriculture, TERRENA, FiBL, ARVALIS

Axis 2. Network management – Decentralized participatory selection – Landscape diversity

  • modeling of management and on-farm selection networks:
    • development of a simulation software for cultivated metapopulations: CropMetapop
    • modelling the evolution of populations in a seed exchange network: video
  • selection and participatory on-farm evaluation methodology:
    • optimization of decentralized evaluation of on-farm populations (Van Frank et al., 2019), PPBstats
    • characterization of natural and human selection pressures
    • evaluation of selection schemes for population mixtures
  • Varietal deployment at the landscape scale:
    • evolution of genetic diversity at the departmental level
    • deployment of resistance at the European scale and sustainability

Projects: MoBiDiv, Diversifood, Solibam, UGeBio, RustWatch

Major academic collaborators: M. Thomas, P. Barbillon, E. Berthet, O. David, Y. De Oliveira, M. Hovmoller

Non-academic partners: RSP, RSR

See also: INRA has published a dossier on “Conventional or participatory selection, several strategies for organic wheat”, which can be consulted on the institute’s website, where the work of the DEAP team can be found.

In the press:


The members of the DEAP team contribute to many training courses within the University Paris-Saclay and its components such as AgroParisTech, as well as in other institutions (e.g. Institut Agro Montpellier).

The DEAP team is attached to the graduate school SEVE (Plant sciences: from genes to ecosystems).

DEAP is attached to the LabEx SPS, Sciences des Plantes de Saclay.


Former members

Adrien Amé Assistant engineer (2021-2023), Meije Gawinowski PhD student (2019-2023), Baptiste Rouger PhD student (2018-2022), Adrien Speck PhD student (2018-2022), Benedikt Haug PhD student (2018-2021), Emmanuelle Blanc PhD student and postdoctoral fellow (2017-2021), Gaël Vieceli Assistant engineer (2020-2021), Roma Hooge Engineer (2020-2021), Florence Dubs postdoctoral fellow (2019-2020), Gaëlle Van Frank PhD student and postdoctoral fellow (2015-2020), Emma Forst PhD student and postdoctoral fellow (2014-2020), Audrey Postec Assistant engineer (2019), Abdel Kader Naino Jika Postdoctoral fellow (2017-2019), Samuel Joseph Technician (2018), Christophe Lecarpentier PhD student and postdoctoral fellow (2012-2018), Julie Borg Engineer (2014-2018), Alexandre Duclouet Technician (2017), Nathalie Galic Technician (2009-2017), Rémi Perronne Postdoctoral fellow (2015-2017), Pauline Lhote Assistant engineer (2014-2016), Pierre Rivière PhD student (2010-2014), Stéphanie Thépot PhD student (2010-2014), Abdul Rehman Kahn PhD student (2009-2013), Mathieu Thomas PhD student (2008-2011), Yves Rousselle PhD student (2006-2010), Julie Dawson Postdoctoral fellow (2008-2010), Bénédicte Rhoné PhD student (2004-2008), Anne-Laure Raquin PhD student (2001-2005)


  • Bécu T., Barot S., Lata JC., Roux XL., Enjalbert J. , Niboyet A.. (2024) Increasing intraspecific diversity of wheat affects plant nutrient contents but not N recovery in the plant-soil system. Basic and Applied Ecology, (74) 24-34
  • Gawinowski M., Enjalbert J. , Cournède PH., Flutre T. . (2024) Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance. Field Crops Research, (310) 109368
  • Abu-Awad D., Waller D.. (2023) Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression. Peer Community Journal, (3) e8
  • Blanc E., Enjalbert J. , Flutre T. , Barbillon P., Lunn J.. (2023) Efficient Bayesian automatic calibration of a functional–structural wheat model using an adaptive design and a metamodelling approach. Journal of Experimental Botany, erad339
  • Dubs F., Enjalbert J. , Barot S., Porcher E., Allard V., Pope C., Gauffreteau A., Niboyet A., Pommier T., Saint-Jean S., Vidal T., Le Roux X.. (2023) Unfolding the link between multiple ecosystem services and bundles of functional traits to design multifunctional crop variety mixtures. Agron. Sustain. Dev., 6 (43) 71
  • Gawinowski M., 11/01/2023, Importance des interactions plante-plante dans les mélanges de variétés de blé tendre : étude de la compétition pour la lumière avec une approche interdisciplinaire entre expérimentation au champ et modélisation mécaniste, PhD, Université Paris-Saclay
  • Haug B., Messmer MM., Enjalbert J. , Goldringer I. , Flutre T. , Mary-Huard T., Hohmann P.. (2023) New insights towards breeding for mixed cropping of spring pea and barley to increase yield and yield stability. Field Crops Research, (297) 108923
  • Rouger B., Goldringer I. , Barbillon P., Miramon A., Naino Jika AK., Thomas M.. (2023) Sensitivity analysis of a crop metapopulation model. Ecological Modelling, (475) 110174
  • Taschen E., Dezette D., Guillot E., Abadie J., Arnal D., Plassard C., Taudière A., Wheatamix consortium, Violle C., Enjalbert J. , Le Roux X., Hinsinger P.. (2023) Wheat varietal diversity modulates nitrogen-related enzymatic activities but has limited impact on arbuscular mycorrhizal fungi. Plant Soil,
  • Von Gastrow L., Michel E., Legrand J., Amelot R., Segond D., Guezenec S., Rué O., Chable V., Goldringer I. , Dousset X., Serpolay‐Bessoni E., Taupier‐Letage B., Vindras‐Fouillet C., Onno B., Valence F., Sicard D.. (2023) Microbial community dispersal from wheat grains to sourdoughs: A contribution of participatory research. Molecular Ecology, 10 (32) 2413-2427
  • Demie DT., Döring TF., Finckh MR., van der Werf W., Enjalbert J. , Seidel SJ.. (2022) Mixture × Genotype Effects in Cereal/Legume Intercropping. Front. Plant Sci., (13) 846720
  • Gawinowski M., Enjalbert J. , Cournède PH., Flutre T. . (2022) Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance. Plant Biology,
  • Kiær LP., Weedon OD., Bedoussac L., Bickler C., Finckh MR., Haug B., Iannetta PPM., Raaphorst-Travaille G., Weih M., Karley AJ.. (2022) Supply Chain Perspectives on Breeding for Legume–Cereal Intercrops. Front. Plant Sci., (13) 844635
  • Montazeaud G., Flutre T. , Ballini E., Morel JB., David J., Girodolle J., Rocher A., Ducasse A., Violle C., Fort F., Fréville H.. (2022) From cultivar mixtures to allelic mixtures: opposite effects of allelic richness between genotypes and genotype richness in wheat. New Phytologist, 6 (233) 2573-2584
  • Speck A., Trouvé JP., Enjalbert J. , Geffroy V., Joets J., Moreau L.. (2022) Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.). Front. Plant Sci., (13) 871633
  • Blanc E., Barbillon P., Fournier C., Lecarpentier C., Pradal C., Enjalbert J. . (2021) Functional–Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures. Front. Plant Sci., (12) 734056
  • Blanc E., 2021-03, Modélisation des conséquences évolutives de la compétition pour la lumière dans des populations composites de blé, Theses, Université Paris-Saclay
  • Haug B., Messmer MM., Enjalbert J. , Goldringer I. , Forst E., Flutre T. , Mary-Huard T., Hohmann P.. (2021) Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept. Front. Plant Sci., (11) 620400
  • Haug B., 2021-12, Breeding for mixed cropping : lessons learned from a genetic analysis of pea (P. sativum L.) - barley (H. vulgare L.) mixtures, Theses, Université Paris-Saclay
  • Labarthe P., Coléno F., Enjalbert J. , Fugeray-Scarbel A., Hannachi M., Lemarié S.. (2021) Exploration, exploitation and environmental innovation in agriculture. The case of variety mixture in France and Denmark. Technological Forecasting and Social Change, (172) 121028
  • Mazé A., Calabuig Domenech A., Goldringer I. . (2021) Restoring cultivated agrobiodiversity: The political ecology of knowledge networks between local peasant seed groups in France. Ecological Economics, (179) 106821
  • Perronne R., Dubs F., de Vallavieille-Pope C., Leconte M., du Cheyron P., Cadot V., Vidal T., Enjalbert J. . (2021) Spatiotemporal Changes in Varietal Resistance to Wheat Yellow Rust in France Reveal an Increase in Field Resistance Level During the Period 1985–2018. Phytopathology®, 9 (111) 1602-1612
  • Vindras-Fouillet C., Goldringer I. , Frank G., Dewalque M., Colin A., Montaz H., Berthellot JF., Baltassat R., Dalmasso C.. (2021) Sensory Analyses and Nutritional Qualities of Wheat Population Varieties Developed by Participatory Breeding. Agronomy, 11 (11) 2117
  • David O., van Frank G., Goldringer I. , Rivière P., Turbet Delof M. . (2020) Bayesian inference of natural selection from spatiotemporal phenotypic data. Theoretical Population Biology, (131) 00-109
  • De Oliveira Y., Burlot L., Dawson JC., Goldringer I. , Madi D., Rivière P., Steinbach D., van Frank G., Thomas M.. (2020) SHiNeMaS: a web tool dedicated to seed lots history, phenotyping and cultural practices. Plant Methods, 1 (16) 98
  • Goldringer I. , van Frank G., Bouvier d’Yvoire C., Forst E., Galic N., Garnault M., Locqueville J., Pin S., Bailly J., Baltassat R., Berthellot JF., Caizergues F., Dalmasso C., de Kochko P., Gascuel JS., Hyacinthe A., Lacanette J., Mercier F., Montaz H., Ronot B., Rivière P.. (2020) Agronomic Evaluation of Bread Wheat Varieties from Participatory Breeding: A Combination of Performance and Robustness. Sustainability, 1 (12) 128
  • Mazé A., Calabuig Domenech A., Goldringer I. . (2020) Commoning the seeds: alternative models of collective action and open innovation within French peasant seed groups for recreating local knowledge commons. Agric Hum Values,
  • van Frank G., Rivière P., Pin S., Baltassat R., Berthellot JF., Caizergues F., Dalmasso C., Gascuel JS., Hyacinthe A., Mercier F., Montaz H., Ronot B., Goldringer I. . (2020) Genetic Diversity and Stability of Performance of Wheat Population Varieties Developed by Participatory Breeding. Sustainability, 1 (12) 384
  • Forst E., Enjalbert J. , Allard V., Ambroise C., Krissaane I., Mary-Huard T., Robin S., Goldringer I. . (2019) A generalized statistical framework to assess mixing ability from incomplete mixing designs using binary or higher order variety mixtures and application to wheat. Field Crops Research, (242) 107571
  • Lecarpentier C., Barillot R., Blanc E., Abichou M., Goldringer I. , Barbillon P., Enjalbert J. , Andrieu B.. (2019) WALTer: a three-dimensional wheat model to study competition for light through the prediction of tillering dynamics. Ann Bot, 6 (123) 961-975
  • van Frank G., Goldringer I. , Rivière P., David O.. (2019) Influence of experimental design on decentralized, on-farm evaluation of populations: a simulation study. Euphytica, 7 (215) 126
  • Ali S., Sharma S., Leconte M., Shah SJA., Duveiller E., Enjalbert J. , Vallavieille‐Pope C.. (2018) Low pathotype diversity in a recombinant Puccinia striiformis population through convergent selection at the eastern Himalayan centre of diversity (Nepal). Plant Pathology, 4 (67) 810-820
  • Borg J., Kiær LP., Lecarpentier C., Goldringer I. , Gauffreteau A., Saint-Jean S., Barot S., Enjalbert J. . (2018) Unfolding the potential of wheat cultivar mixtures: A meta-analysis perspective and identification of knowledge gaps. Field Crops Res, (221) 298-313
  • Forst E., 2018-03, Développement de méthodes d'estimation de l'aptitude au mélange pour la prédiction des performances et la sélection de mélanges variétaux chez le blé tendre, et co-conception d'idéotypes de mélanges adaptés à l'agriculture biologique, Theses, Université Paris Saclay (COmUE)
  • Lamichhane JR., Arseniuk E., Boonekamp P., Czembor J., Decroocq V., Enjalbert J. , Finckh MR., Korbin M., Koppel M., Kudsk P., Mesterhazy A., Sosnowska D., Zimnoch‐Guzowska E., Messéan A.. (2018) Advocating a need for suitable breeding approaches to boost integrated pest management: a European perspective. Pest Management Science, 6 (74) 1219-1227
  • Perronne R., Goldringer I. . (2018) Application of a partitioning procedure based on Rao quadratic entropy index to characterize the temporal evolution of in situ varietal and genetic diversity of bread wheat in France over the period 1981–2006. Theor Appl Genet, 4 (131) 775-786
  • van Frank G., 2018-12, Gestion participative de la diversité cultivée et création de mélanges diversifiés de blé tendre à la ferme, Theses, Université Paris Saclay (COmUE)
  • Barot S., Allard V., Cantarel A., Enjalbert J. , Gauffreteau A., Goldringer I. , Lata JC., Le Roux X., Niboyet A., Porcher E.. (2017) Designing mixtures of varieties for multifunctional agriculture with the help of ecology. A review. Agron. Sustain. Dev., 2 (37) 13
  • Demeulenaere Élise., Rivière P., Hyacinthe A., Baltassat R., Baltazar S., Gascuel JS., Lacanette J., Montaz H., Pin S., Ranke O., Serpolay-Besson E., Thomas M., Frank GV., Vanoverschelde M., Vindras-Fouillet C., Goldringer I. . (2017) La sélection participative à l’épreuve du changement d’échelle. À propos d’une collaboration entre paysans sélectionneurs et généticiens de terrain. Nat. Sci. Soc., 4 (25) 336-346
  • Demeulenaere Élise., Goldringer I. . (2017) Semences et transition agroécologique : initiatives paysannes et sélection participative comme innovations de rupture. Nat. Sci. Soc., (25) S55-S59
  • Lecarpentier C., 2017-01-25 25/01/17, Valorisation de la diversité intra-parcelle dans un contexte de changement climatique. Développement d'un modèle couplant écophysiologie 3D et génétique évolutive., PhD thesis, Université Paris-Saclay
  • Perronne R., Diguet S., Vallavieille-Pope C., Leconte M., Enjalbert J. . (2017) A framework to characterize the commercial life cycle of crop varieties: Application to the case study of the influence of yellow rust epidemics on French bread wheat varieties. Field Crops Research, (209) 159-167
  • Perronne R., Makowski D., Goffaux R., Montalent P., Goldringer I. . (2017) Temporal evolution of varietal, spatial and genetic diversity of bread wheat between 1980 and 2006 strongly depends upon agricultural regions in France. Agriculture, Ecosystems & Environment, (236) 12-20
  • Enjalbert J. , Allard V., Andrieu B., Barot S., Borg J., Cantarel A., Feret M., Cervek C., Coleno FC., Pope De Vallavieille C., Descoureaux D., Dubs F., Galic N., Gauffreteau A., Gilet JD., Goldringer I. , Hannachi M., Houivet G., Pin S., Jeuffroy MH., Kerbiriou C., Labarthe P., LATA JC., LeCarpentier C., Lejars L., Lemain B., Lemarié S., Leny F., Le Roux X., Le Viol I., Montagnier C., NIBOYET A., Omon B., Piaud S., Poly F., Pommier T., Porcher E., Saint-Jean S., Salmon S., Tropée D., Vidal T.. (2016) Increasing species richness and genetic diversity in agriculture: results of the Wheatamix project. HAL Archives Ouvertes, 40 p.
  • Labeyrie V., Thomas M., Muthamia ZK., Leclerc C.. (2016) Seed exchange networks, ethnicity, and sorghum diversity. Proceedings of the National Academy of Sciences of the United States of America, 1 (113) 98-103
  • Perronne R., Hannachi M., Lemarié S., Fugeray-Scarbel A., Goldringer I. . (2016) L’évolution de la filière blé tendre en France entre 1980 et 2006: quelle influence sur la diversité cultivée ?. Notes et Etudes Socio-Economiques (NESE), (41) 83-113
  • Thomas M., Caillon S.. (2016) Effects of farmer social status and plant biocultural value on seed circulation networks in Vanuatu. Ecol Soc, 2 (21) 13
  • Barbillon P., Thomas M., Goldringer I. , Hospital F., Robin S.. (2015) Network impact on persistence in a finite population dynamic diffusion model: application to an emergent seed exchange network. J. Theor. Biol., (365) 365-376
  • Rivière P., Dawson JC., Goldringer I. , David O.. (2015) Hierarchical Bayesian Modeling for Flexible Experiments in Decentralized Participatory Plant Breeding. Crop Science, 3 (55) 1053-1067
  • Rivière P., Goldringer I. , Berthellot JF., Galic N., Pin S., Kochko PD., Dawson JC.. (2015) Response to farmer mass selection in early generation progeny of bread wheat landrace crosses. Renewable Agriculture and Food Systems, 2 (30) 190-201
  • Thomas M., Verzelen N., Barbillon P., Coomes OT., Caillon S., McKey D., Elias M., Garine E., Raimond C., Dounias E., Jarvis D., Wencélius J., Leclerc C., Labeyrie V., Cuong PH., Hue Ngoc NT., Sthapit B., Rana RB., Barnaud A., Violon C., Arias RE., Latournerie Moreno L., De Santis P., Massol F., Woodward G., Bohan DA.. (2015) A Network-Based Method to Detect Patterns of Local Crop Biodiversity: Validation at the Species and Infra-Species Levels. , (53) 259–320
  • Thomas M., Thépot S., Galic N., Jouanne‐Pin S., Remoué C., Goldringer I. . (2015) Diversifying mechanisms in the on-farm evolution of crop mixtures. Molecular Ecology, 12 (24) 2937-2954
  • Thépot S., Restoux G., Goldringer I. , Hospital F., Gouache D., Mackay I., Enjalbert J. . (2015) Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat. Genetics, 2 (199) 609-623
  • Thépot S., Restoux G., Hospital F., Gouache D., Mackay I., Goldringer I. , Enjalbert J. , Ogihara Y., Takumi S., Handa H.. (2015) Interest of a Multiparental and Outcrossing Wheat Population for Fine Mapping. , 331-8
  • Mboup M., Bahri B., Leconte M., De Vallavieille-Pope C., Kaltz O., Enjalbert J. . (2012) Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation. Evol. Appl., 4 (5) 341-352
  • Rousset M., Bonnin I., Remoue C., Falque M., Rhone B., Veyrieras JB., Madur D., Murigneux A., Balfourier F., Le Gouis J., Santoni S., Goldringer I. . (2011) Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 6 (123) 907-26