MAGE : Modelling and Analysis of Genotype x Environment interactions

Themes  Staff  Selected publications  Key facts  Partnership  Funded projects  Former staff

Themes

We aim at identifying traits and alleles which can give comparative advantages (crop production, yield stability and resilience, environmental balance, ecosystem services, …) under climatic scenarios affected by climate changes including periods of drought and high temperature, different cropping systems and management practices.

The strategy of MAGE is based on the fact that each genotypic trait/allele associated with tolerance to any constraint can have positive or negative consequences on crop production, depending on the environmental scenario and management practices (G x E x M).

In this context, MAGE adopts an innovative approach at the confluence of quantitative genetics, ecophysiological dissection, high throughput phenotyping, and plant modelling.

1) Analyse the time courses of expansion rates (leaf, maize silks, whole plant shoot, …), tillering, reproductive abortion, transpiration, under contrasted environmental scenarios of water deficit, evaporative demand, CO2 and light, and develop models at the process scale.

2) We analyse the genetic variability and the set of constraints and genetic correlations between traits defining the set of possibilities of responses to abiotic constraints in cereal species. MAGE drives networks of field experiments and phenotyping in high throughput phenotyping platforms (M3P) in maize and wheat, for diversity panels and new genetic diversity currently locked into maladapted maize material. We analyse the genetic controls of these parameters/traits by quantitative genetics.

3) We develop crop models (SiriusQuality for wheat and Sirius maize) including in order to analyse the consequences of the genetic variability on crop production in diverse scenarios.

Staff

You can find the team's trombinoscope here.

Selected Publications (2020 - 2024)

Affortit P, Effa-Effa B, Ndoye MS, Moukouanga D, Luchaire N, Cabrera-Bosquet L, Perálvarez M, Pilloni R, Welcker C, Champion A, Gantet P, Diedhiou AG, Manneh B, Aroca R, Vadez V, Laplaze L, Cubry P, Grondin A (2022) Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud. J Exp Bot 73 (15):5279-5293. doi:10.1093/jxb/erac156

Albasha R, Manceau L, Webber H, Chelle M, Kimball B, Martre P (2024) MONTPEL: A multi-component Penman-Monteith energy balance model. Agric For Meteorol 358:110221. doi:https://doi.org/10.1016/j.agrformet.2024.110221
Bastias CC, Estarague A, Vile D, Gaignon E, Lee CR, Exposito-Alonso M, Violle C, Vasseur F (2024) Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe. Nat Comm 15 (1). doi:10.1038/s41467-024-49267-0

Bergès SE, Vasseur F, Bediée A, Rolland G, Masclef D, Dauzat M, van Munster M, Vile D (2020) Natural variation of Arabidopsis thaliana responses to Cauliflower mosaic virus infection upon water deficit. PLOS PATHOGENS 16 (5). doi:10.1371/journal.ppat.1008557

Bouidghaghen J, Moreau L, Beauchêne K, Chapuis R, Mangel N, Cabrera-Bosquet L, Welcker C, Bogard M, Tardieu F (2023) Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field. Nat Comm 14 (1). doi:10.1038/s41467-023-42298-z

Choquette NE, Holland JB, Weldekidan T, Drouault J, de Leon N, Flint-Garcia S, Lauter N, Murray SC, Xu WW, Wisser RJ (2023a) Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize. New Phytol 238 (2):737-749. doi:10.1111/nph.18769

Choquette NE, Weldekidan T, Brewer J, Davis SB, Wisser RJ, Holland JB (2023b) Enhancing adaptation of tropical maize to temperate environments using genomic selection. G3-Genes Genomes Genetics. doi:10.1093/g3journal/jkad141

Desbiez-Piat A, Ressayre A, Marchadier E, Noly A, Remoué C, Vitte C, Belcram H, Bourgais A, Galic N, Le Guilloux M, Tenaillon M, Dillmann C (2023) Pervasive G x E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics 225 (4). doi:10.1093/genetics/iyad186

Ding L, Milhiet T, Parent B, Meziane A, Tardieu F, Chaumont F (2022) The plasma membrane aquaporin ZmPIP2;5 enhances the sensitivity of stomatal closure to water deficit. Plant Cell and Environment 45 (4):1146-1156. doi:10.1111/pce.14276

Drouault J, Palaffre C, Millet EJ, Rodriguez J, Martre P, Johnson K, Parent B, Welcker C, Wisser RJ (2024) A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation. bioRxiv:2024.2007.2010.602692. doi:10.1101/2024.07.10.602692

Dueri S, Brown H, Asseng S, Ewert F, Webber H, George M, Craigie R, Guarin JR, Pequeno D, Stella T, Ahmed M, Alderman PD, Basso B, Berger AG, Bracho Mujica G, Cammarano D, Chen Y, Dumont B, Eyshi Rezaei E, Fereres E, Ferrise R, Gaiser T, Gao Y, Garcia-Vila M, Gayler S, Hochman Z, Hoogenboom G, Kersebaum KC, Nendel C, Olesen JE, Padovan G, Palosuo T, Priesack E, Pullens JWM, Rodríguez A, Rötter RP, Ruiz Ramos M, Semenov MA, Senapati N, Siebert S, Srivastava AK, Stöckle C, Supit I, Tao F, Thorburn P, Wang E, Weber TKD, Xiao L, Zhao C, Zhao J, Zhao Z, Zhu Y, Martre P (2024) Winter wheat experiments to optimize sowing dates and densities in a high-yielding environment in New Zealand: Field experiments and AgMIP-Wheat multi-model simulations. Open Data journal for Agricultural Research 10:14-21. doi:https://doi.org/10.18174/odjar.v10i0.18442

Dueri S, Léonard J, Chlebowski F, Rosso P, Berg-Mohnicke M, Nendel C, Ehrhardt F, Martre P (2023) Sources of uncertainty in simulating crop N2O emissions under contrasting environmental conditions. Agric For Meteorol 340:109619. doi:https://doi.org/10.1016/j.agrformet.2023.109619

Estarague A, Vasseur F, Sartori K, Bastias CC, Cornet D, Rouan L, Beurier G, Exposito-Alonso M, Herbette S, Bresson J, Vile D, Violle C (2022) Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana? Ann Bot 129 (3):343-356. doi:10.1093/aob/mcab149

Estarague A, Violle C, Vile D, Hany A, Martino T, Moulin P, Vasseur F (2023) Plant-herbivore interactions: Experimental demonstration of genetic variability in plant-plant signalling. EVOLUTIONARY APPLICATIONS 16 (4):772-780. doi:10.1111/eva.13531

Eyland D, Luchaire N, Cabrera-Bosquet L, Parent B, Janssens SB, Swennen R, Welcker C, Tardieu F, Carpentier SC (2022) High-throughput phenotyping reveals differential transpiration behaviour within the banana wild relatives highlighting diversity in drought tolerance. Plant Cell and Environment 45 (6):1647-1663. doi:10.1111/pce.14310

Fang L, Martre P, Jin K, Du X, van der Putten PEL, Yin X, Struik PC (2023) Neglecting acclimation of photosynthesis under drought can cause significant errors in predicting leaf photosynthesis in wheat. Glob Chang Biol 29 (2):505-521. doi:10.1111/gcb.16488

Fang L, Struik PC, Girousse C, Yin X, Martre P (2024) Source–sink relationships during grain filling in wheat in response to various temperature, water deficit, and nitrogen deficit regimes. J Exp Bot 75 (20):6563-6578. doi:10.1093/jxb/erae310

Fang L, Yin X, van der Putten PEL, Martre P, Struik PC (2022) Drought exerts a greater influence than growth temperature on the temperature response of leaf day respiration in wheat (Triticum aestivum). Plant Cell Environ 45 (7):2062-2077. doi:https://doi.org/10.1111/pce.14324

Guarin JR, Martre P, Ewert F, Webber H, Dueri S, Calderini D, Reynolds M, Molero G, Miralles D, Garcia G, Slafer GA, Giunta F, Pequeno DNL, Stella T, Ahmed M, Alderman PD, Basso B, Berger AG, Bindi M, Mujica GB, Cammarano D, Chen Y, Dumont B, Rezaei EE, Fereres E, Ferrise R, Gaiser T, Gao Y, Garcia-Vila M, Gayler S, Hochman Z, Hoogenboom G, Hunt LA, Kersebaum KC, Koch M, Nendel C, Olesen JE, Palosuo T, Priesack E, Pullens JWM, Rodríguez A, Rötter RP, Ruiz Ramos M, Semenov MA, Senapati N, Siebert S, Srivastava AK, Stöckle C, Supit I, Tao F, Thorburn P, Wang E, Weber TKD, Xiao L, Zhang Z, Zhao C, J. Z, Zhao Z, Zhu Y, Asseng S (2023) A high-yielding traits experiment for modeling potential production of wheat: field experiments and AgMIP-Wheat multi-model simulations. Open Data Journal for Agricultural Research 9:26-33. doi:https://doi.org/10.18174/odjar.v9i0.18573 

Guédon Y, Caraglio Y, Granier C, Lauri P-É, Muller B (2022) Identifying Developmental Patterns in Structured Plant PhenotypingPlant phenotyping Data. In: Lucas M (ed) Plant Systems Biology: Methods and Protocols. Springer New York, New York, NY, pp 199-225. doi:10.1007/978-1-0716-1816-5_10

Guiguitant J, Marrou H, Vile D, Sinclair TR, Pradhan D, Ramirez M, Ghanem ME (2021a) An exploration of the variability of physiological responses to soil drying in relation with C/N balance across three species of the under-utilized genus Vigna. Physiol Plant 172 (2):477-486. doi:10.1111/ppl.13224

Guiguitant J, Vile D, Ghanem ME, Wery J, Marrou H (2020) Evaluation of pulse crops' functional diversity supporting food production. Sci Rep 10 (1). doi:10.1038/s41598-020-60166-4

Guiguitant J, Vile D, Marrou H (2021b) Trait Diversity of Pulse Species Predicts Agroecosystem Properties Trade-Offs. FRONTIERS IN PLANT SCIENCE 12. doi:10.3389/fpls.2021.636915
Heidsieck G, de Oliveira D, Pacitti E, Pradal C, Tardieu F, Valduriez P (2021) Cache-aware scheduling of scientific workflows in a multisite cloud. Future Generation Computer Systems-the International Journal of Escience 122:172-186. doi:10.1016/j.future.2021.03.012

Hilty J, Muller B, Pantin F, Leuzinger S (2021) Plant growth: the What, the How, and the Why. New Phytol 232 (1):25-41. doi:10.1111/nph.17610

Lacube S, Manceau L, Welcker C, Millet EJ, Gouesnard B, Palaffre C, Ribaut J-M, Hammer G, Parent B, Tardieu F (2020) Simulating the effect of flowering time on maize individual leaf area in contrasting environmental scenarios. J Exp Bot 71 (18):5577–5588. doi:10.1093/jxb/eraa278

Leveau S, Parent B, Giunta F, Luchaire N, Cabrera-Bosquet L, Beauchêne K, Jezequel S, Motzo R, Martre P (2023) Tillering structures the genetic variability of wheat vegetative growth and its plasticity under water deficit. bioRxiv:2023.2007.2026.550706. doi:10.1101/2023.07.26.550706

Leveau S, Parent B, Zaka S, Martre P (2021) Differential sensitivity to temperature and evaporative demand in wheat relatives. J Exp Bot 72 (21):7580-7593. doi:10.1093/jxb/erab431

Liu B, Martre P, Ewert F, Webber H, Waha K, Thorburn PJ, Ruane AC, Aggarwal PK, Ahmed M, Balkovič J, Basso B, Biernath C, Bindi M, Cammarano D, Cao W, Challinor AJ, De Sanctis G, Dumont B, Espadafor M, Eyshi Rezaei E, Fereres E, Ferrise R, Garcia-Vila M, Gayler S, Gao Y, Horan H, Hoogenboom G, Izaurralde RC, Jabloun M, Jones CD, Kassie BT, Kersebaum KC, Klein C, Koehler AK, Maiorano A, Minoli S, Montesino San Martin M, Müller C, Naresh Kumar S, Nendel C, O’Leary GJ, Olesen JE, Palosuo T, Porter JR, Priesack E, Ripoche D, Rötter RP, Semenov MA, Stöckle C, Stratonovitch P, Streck T, Supit I, Tao F, Van der Velde M, Wang E, Wolf J, Xiao L, Zhang Z, Zhao Z, Zhu Y, Asseng S (2023) AgMIP-Wheat multi-model simulations on climate change impact and adaptation for global wheat Open Data Journal for Agricultural Research 9:10-25. doi:https://doi.org/10.18174/odjar.v9i0.18092 

Liu S, Baret F, Abichou M, Manceau L, Andrieu B, Weiss M, Martre P (2021) Importance of the description of light interception in crop growth models. Plant Physiol 186 (2):977-997. doi:10.1093/plphys/kiab113

Martre P, Dueri S, Guarin JR, Ewert F, Webber H, Calderini D, Molero G, Reynolds M, Miralles D, Garcia G, Brown H, George M, Craigie R, Cohan J-P, Deswarte J-C, Slafer G, Giunta F, Cammarano D, Ferrise R, Gaiser T, Gao Y, Hochman Z, Hoogenboom G, Hunt LA, Kersebaum KC, Nendel C, Padovan G, Ruane AC, Srivastava AK, Stella T, Supit I, Thorburn P, Wang E, Wolf J, Zhao C, Zhao Z, Asseng S (2024a) Global needs for nitrogen fertilizer to improve wheat yield under climate change. Nat Plant 10 (7):pages 1081–1090. doi:10.1038/s41477-024-01739-3

Martre P, Motzo R, Mastrangelo AM, Marone D, De Vita P, Giunta F (2024b) Dissecting durum wheat time to anthesis into physiological traits using a QTL-based model. Eur J Agron 161:127379. doi:https://doi.org/10.1016/j.eja.2024.127379
Midingoyi CA, Pradal C, Athanasiadis IN, Donatelli M, Enders A, Fumagalli D, Garcia F, Holzworth D, Hoogenboom G, Porter C, Raynal H, Thorburn P, Martre P (2020) Reuse of process-based models: automatic transformation into many programming languages and simulation platforms. in silico Plants:diaa007. doi:10.1093/insilicoplants/diaa007

Midingoyi CA, Pradal C, Enders A, Fumagalli D, Lecharpentier P, Raynal H, Donatelli M, Fanchini D, Athanasiadis IN, Porter C, Hoogenboom G, Oliveira FAA, Holzworth D, Martre P (2023) Crop modeling frameworks interoperability through bidirectional source code transformation. Environ Model Softw 168:105790. doi:https://doi.org/10.1016/j.envsoft.2023.105790

Midingoyi CA, Pradal C, Enders A, Fumagalli D, Raynal H, Donatelli M, Athanasiadis IN, Porter C, Hoogenboom G, Holzworth D, Garcia F, Thorburn P, Martre P (2021) Crop2ML: An open-source multi-language modeling framework for the exchange and reuse of crop model components. Environ Model Softw 142:105055. doi:https://doi.org/10.1016/j.envsoft.2021.105055

Nguyen HA, Martre P, Collet C, Draye X, Salon C, Jeudy C, Rincent R, Muller B (2024) Are high-throughput root phenotyping platforms suitable for informing root system architecture models with genotype-specific parameters? An evaluation based on the root model ArchiSimple and a small panel of wheat cultivars. J Exp Bot 75 (8):2510-2526. doi:10.1093/jxb/erae009

Plessis A, Ravel C, Risacher T, Duchateau N, Dardevet M, Merlino M, Torney F, Martre P (2023) Storage protein activator controls grain protein accumulation in bread wheat in a nitrogen dependent manner. Sci Rep 13 (1):22736. doi:10.1038/s41598-023-49139-5

Przybylska MS, Violle C, Vile D, Scheepens JF, Lacombe B, Le Roux X, Perrier L, Sales-Mabily L, Laumond M, Vinyeta M, Moulin P, Beurier G, Rouan L, Cornet D, Vasseur F (2023) AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana. SCIENTIFIC DATA 10 (1). doi:10.1038/s41597-023-02189-w

Przybylska MS, Violle C, Vile D, Scheepens JF, Munoz F, Tenllado A, Vinyeta M, Le Roux X, Vasseur F (2024) Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana. New Phytol 243 (2):620-635. doi:10.1111/nph.19870

Rolhauser AG, Isaac ME, Violle C, Martin AR, Vasseur F, Lemoine T, Mahaut L, Fort F, Rotundo JL, Vile D (2024) Phenotypic limits of crop diversity: a data exploration of functional trait space. New Phytol 244 (2):708-718. doi:10.1111/nph.20050

Saint Cast C, Lobet G, Cabrera-Bosquet L, Couvreur V, Pradal C, Tardieu F, Draye X (2022) Connecting plant phenotyping and modelling communities: lessons from science mapping and operational perspectives. in silico Plants 4 (1). doi:10.1093/insilicoplants/diac005

Vasseur F, Westgeest AJ, Vile D, Violle C (2022) Solving the grand challenge of phenotypic integration: allometry across scales.  150 (3-4):161-169. doi:10.1007/s10709-022-00158-6

Welcker C, Spencer NA, Turc O, Granato I, Chapuis R, Madur D, Beauchene K, Gouesnard B, Draye X, Palaffre C, Lorgeou J, Melkior S, Guillaume C, Presterl T, Murigneux A, Wisser RJ, Millet EJ, van Eeuwijk F, Charcosset A, Tardieu F (2022a) Physiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions. Nat Comm 13 (1 doi:10.1038/s41467-022-30872-w

Welcker C, Spencer NA, Turc O, Granato I, Chapuis R, Madur D, Beauchene K, Gouesnard B, Draye X, Palaffre C, Lorgeou J, Melkior S, Guillaume C, Presterl T, Murigneux A, Wisser RJ, Millet EJ, van Eeuwijk F, Charcosset A, Tardieu F (2022b) Physiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions. Nat Comm 13 (1 doi:10.1038/s41467-022-30872-w

Westgeest AJ, Vasseur F, Enquist BJ, Milla R, Gómez-Fernández A, Pot D, Vile D, Violle C (2024) An allometry perspective on crops. New Phytol 244 (4):1223-1237. doi:10.1111/nph.20129

Selected publications (2016 - 2019)

Baumont M, Parent B, Manceau L, Brown H, Driever SM, Muller B, Martre P (2019) Experimental and modeling evidence of carbon limitation of leaf appearance rate for spring and winter wheat. Journal of Experimental Botany 70: 2449-2462. doi:10.1093/jxb/erz012.

Millet E, Kruijer W, Coupel-Ledru A, Alvarez Prado S, Cabrera Bosquet L, Lacube S, Charcosset A, Welcker C, van Eeuwijk F, Tardieu F (2019) Genomic prediction of maize yield across European environmental conditions. Nature Genetics 51: 952-956. doi:10.1038/s41588-019-0414-y.

Muller B, Guédon Y, Passot S, Lobet G, Nacry P, Pagès L, Wissuwa M, Draye X (2019) Lateral roots: random diversity in adversity. Trends in Plant Science 24: 810-825. doi:10.1016/j.tplants.2019.05.011.

Sartori K, Vasseur F, Violle C, Baron E, Gerard M, Rowe N, Ayala-Garay OJ, Christophe A, Jalón LGd, Masclef D, Harscouet E, Granado MdR, Chassagneux A, Kazakou E, Vile D (2019) Leaf economics and slow-fast adaptation across the geographic range of Arabidopsis thaliana. Scientific reports 9: 10758. doi:10.1038/s41598-019-46878-2.

Alvarez Prado S, Cabrera-Bosquet L, Grau A, Coupel-Ledru A, Millet E, Welcker C, Tardieu F (2018) Phenomics allows identification of genomic regions affecting maize stomatal conductance with conditional effects of water deficit and evaporative demand. Plant, Cell and Environment 41: 314-326. doi:10.1111/pce.13083.

Martre P, Dambreville A (2018) A Model of Leaf Coordination to Scale-Up Leaf Expansion from the Organ to the Canopy. Plant Physiology 176: 704-716. doi:10.1104/pp.17.00986.

Parent B, Leclere M, Lacube S, Semenov MA, Welcker C, Martre P, Tardieu F (2018) Maize yields over Europe may increase in spite of climate change, with an appropriate use of the genetic variability of flowering time. Proceedings of the National Academy of Sciences of the United States of America 115: 10642-10647. doi:10.1073/pnas.1720716115.

Roucou A, Violle C, Fort F, Roumet P, Ecarnot M, Vile D (2018) Shifts in plant functional strategies over the course of wheat domestication. Journal of Applied Ecology 55: 25-37. doi:10.1111/1365-2664.13029.

Lacube S, Fournier C, Palaffre C, Millet EJ, Tardieu F, Parent B (2017) Distinct controls of leaf widening and elongation by light and evaporative demand in maize. Plant Cell and Environment 40: 2017-2028. doi:10.1111/pce.13005.

Gouesnard B, Zanetto A, Welcker C (2016) Identification of adaptation traits to drought in collections of maize landraces from southern Europe and temperate regions. Euphytica 209: 565-584. doi:10.1007/s10681-015-1624-8.

Millet EJ, Welcker C, Kruijer W, Negro S, Coupel-Ledru A, Nicolas SD, Laborde J, Bauland C, Praud S, Ranc N, Presterl T, Tuberosa R, Bedo Z, Draye X, Usadel B, Charcosset A, Van Eeuwijk F, Tardieu F (2016) Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios. Plant Physiology 172: 749-764. doi:10.1104/pp.16.00621.

Oury V, Tardieu F, Turc O (2016) Ovary apical abortion under water deficit is caused by changes in sequential development of ovaries and in silk growth rate in maize. Plant Physiology 171: 986-996. doi:10.1104/pp.15.00268.

Key facts 

Partnership 

Projects funded 

Former Staff 

J. Drouaul (PhD), Abu-Sambra Spencer Nadir (CDD IE), Ausset Aurélien (TR), Baumont Maëva (Doctorante), Bouidghaghen Jugurta (Doctorant), Chantereau Marion (CDD TR), Chapuis Romain (CDD IE), Correia Granato Italo (Post-doctorant), Cusin Alexandre (CDD TR), Dueri Sibylle (Post-doctorante), Galtier Raphaël (CDD TR), Grau Antonin (CDD IE), Holzinger Maria (CDD IE), Maiorano Andrea (Post-doctorant), Midingoyi Cyrille (Doctorant et post doctorant), Mielewczick Michaël (Post-doctorant), Millet Emilie (doctorante et Post-doctorante), Moreal de Brevans Théophile (CDD IE), Mujica Claudio (Post-doctorant), Nguyen Hong-Anh (Doctorante), Oury Vincent (Doctorant), Pennachi Joao Paulo (Post-doctorant), Perez Raphaël (Post-doctorant), Ptichers Julie (Doctorante), Rodriguez Jonas (Post-doctorant), Rouhai Aïda (CDD AI), Roux Lucille (CDD IE), Sidawy Pauline (CDD AI), Suard Erwann (CDD AT), Turc Olivier (CR, retraité)