logo umr
Génétique Quantitative et Évolution - Le Moulon

DEAP - 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.

wheat fields of the DEAP team

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 : 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
  • 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 : 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.


DEAP is attached to the LabEx BASC, Biodiversité, Agroécosystèmes, Société, Climat.

Members

  • Emmanuelle Blanc PhD student (INRAE)
  • Florence Dubs Postdoctoral fellow (INRAE)
  • Jérôme Enjalbert Senior Investigator (INRAE)
  • Timothée Flutre Research scientist (INRAE)
  • Meije Gawinowski PhD student (INRAE)
  • Isabelle Goldringer Senior Investigator (INRAE)
  • Benedikt Haug PhD student (FiBL)
  • Baptiste Rouger PhD student (INRAE)
  • Adrien Speck PhD student (Terre de Lin)
  • Gaël Vieceli CDD Assistant engineer (INRAE)

Former members

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), Sophie Pin Technician (2009-2017), 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)

Publications

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) Restoring cultivated agrobiodiversity: The political ecology of knowledge networks between local peasant seed groups in France. Ecological Economics, (179) 106821
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
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
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, Goldringer I. (2017) Semences et transition agroécologique : initiatives paysannes et sélection participative comme innovations de rupture. Nat. Sci. Soc., (25) S55-S59
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
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.
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
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
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. , 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, 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
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
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