DEAP - Diversity, Evolution and Adaptation of Populations

 19/07/2024 -  GQE
Study of the genetic basis of local adaptation; dynamic management of cultivated biodiversity and its relevance for innovative sustainable agro-ecosystems; participatory selection.

Head :
Timothée Flutre (INRAE)

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).



  • 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
  • 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.. (2023) Efficient Bayesian automatic calibration of a functional-structural wheat model using an adaptive design and a metamodeling approach. Journal of Experimental Botany, erad339
  • 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
  • Becker C., Berthomé R., Delavault P., Flutre T. , Fréville H., Gibot-Leclerc S., Le Corre V., Morel JB., Moutier N., Muños S., Richard-Molard C., Westwood J., Courty PE., de Saint Germain A., Louarn G., Roux F.. (2022) The ecologically relevant genetics of plant–plant interactions. Trends in Plant Science, S1360138522002205
  • 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
  • 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
  • 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
  • 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., 12 mars 2021, Modélisation des conséquences évolutives de la compétition pour la lumière dans des populations composites de blé, PhD Thesis, 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
  • 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
  • Flutre T. , Diot J., David J.. (2019) PlantBreedGame: A Serious Game that Puts Students in the Breeder’s Seat. Crop Science, 0 (52) 1-2
  • 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
  • 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., 2018-03-29 29/03/18, 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, PhD thesis, Université Paris-Saclay
  • 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., 2018-06-12 06/12/18, Gestion participative de la diversité cultivée et création de mélanges diversifiés de blé tendre à la ferme, PhD Thesis, Université Paris-Saclay
  • 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