Towards innovative cropping systems : High Throughput Phenotyping of plant biotic interactions.

Transcription

1 Towards innovative cropping systems : High Throughput Phenotyping of plant biotic interactions. Christophe SALON 1,2 Christian JEUDY 1 Céline BERNARD 2 1 UMR Legumes Genetics and Ecophysiology (LEG), INRA 17 rue Sully, BP86510 Dijon Cedex, France 2 Experimental Unit Greenhouse and Phenotyping platform, INRA, 17 rue Sully, BP86510 Dijon Cedex, France

2 Large Research Unit «Agroecology» Goals Research units gathered around knowledge for conception & evaluation of the performance of innovative cropping systems EcolDur GEAPSI IPM MERS Ecology of communities and durability of agricultural systems Genetic environmental determinisms of plant adaptation to innovative cropping systems Mechanisms management of plant-micro organisms interactions, Microbiological and environmental sanitary risks Various thematics PPHD Dijon, Phenodays, Slide 2/18

3 Large Research Unit «Agroecology» Goals A variety of research objects EcolDur GEAPSI IPM MERS Legumes, Weeds, Cereals, Brassica Legumes, Legumes/Ce reals Associations Legumes, Arabidopsis, Wine, Tobacco, Tomato Listeria and root tissues PPHD Dijon, Phenodays, Slide 3/18

4 Filling the gap Goals Pheno and Geno mix Available: - large genetic var. - «omic s» Automated plateforms! Combine similar phenotyping and genotypage rates PPHD Dijon, Phenodays, Slide 4/18

5 Example : case studies of legume plants Phenotyping plant architecture, flowering, senescence, [NO3 - ] Phenotyping pods and seeds Seeds : Number, size and shape P. sativum M. truncatula Phenotyping roots and interactions with micro organisms (nodules, µr), Mutants (Tilling..) RILs Ecotypes collections CONTROLED ENVIRONMENTAL CONDITIONS Kroj et al. Development (2003) 130, Fluorescence: GFP In vitro kinetic development PPHD Dijon, Phenodays, Slide 5/18

6 Measuring «manually» phenotypes (1/3) Proportion of germinated seeds Cumulated proportion of germinated seeds Dynamic analysis of weed germination under various environmental conditions C 6 C 20 C Days since water addition Cumulated degree-days ( C) since water addition Soil water Germination date % viable seeds, dormancy Model parameters Establishing traits/functional relations Gardarin et al. (2011),Ecol. Modelling 222: Gardarin et al. (2010), Weed Res. 50: Gardarin et al. (2010),Seed Sci. Res.20: Sester et al. (2007) Ecol. Modelling 204: Sester et al. (2006) Eur. J. Agron. 24: PPHD Dijon, Phenodays, Slide 6/18

7 Measuring «manually» phenotypes (2/3) ( Analytical approaches + model: leaf area is a relevant phenotypic target for detecting any contrasted N nutrition among various genotypes. SURFACE FOLIAIRE PROJETEE Efficience de conversion de N en surface projetée PAR (mol m -2 jour -1 ) QUANTITE TOTALE D AZOTE Efficience biologique 3,5 3,0 2,5 2,0 1,5 1, PAR (mol m -2 jour -1 ) [NO 3- ] Date de début de fixation de N ,3 [NO - 3 ] (mm) 0,4 Prélèvement de N 0,2 0,3 spécifique AVANT 0,2 0,1 la date de début de 0,1 fixation de N 2 0,0 0, Thèse Delphine Moreau 13 avril 2007 [NO - 3 ] (mm) PAR (mol m -2 jour -1 ) [NO - 3 ] (mm) BIOMASSE TOTALE Coefficients d ajustement 1,5 1,0 0,5 0,0 BIOMASSE SOUTERRAINE PAR (mol m -2 jour -1 ) Prélèvement de N spécifique APRES la date de début de fixation de N 2 Genotypes of Medicago RIL ranked for ability to uptake N! Model Dynamic Leaf area measurement Moreau et al. (2006), Plant, Cell and Envir., 29: Moreau et al. (2007), Plant, Cell and Envir., 30: Moreau et al. (2008), J. Exp. Bot., 59: PPHD Dijon, Phenodays, Slide 7/18

8 Measuring «manually» phenotypes (3/3) Nodule number and size, isotopic flux measurements to understand adaptative strategy of plants to N deficiency. NH4NO3 10 mm -N 14 days after inoculation KNO3 0.5 mm Root Dry Weight Nodules Dry Weight (g) Real number of nodules (g root/plant) 0,18 y = 0,000041x 2-0,001530x + 0,087432, R² = 0,839 0,16 0,14 0,12 0,10 0,08 0,06 0, Surface area 0,020 y = ln(x) , R² = ,018 0,016 0,014 0,012 0,010 0,008 0,006 0,004 0,04 0,06 0,08 0,10 0,12 0,14 0,16 0,18 Roots Dry Weight (g) 1000 y = x , R² = Morphometry versus functional strategy identifcation Number of nodules counted on the scan Split roots Nodules number and size, appearance Ruffel et al. (2008), Plant Physiol. 146: Salon et al. (2009), CRAS, 332 : Jeudy et al. (2010), New Phytol, New Phytol., 185: Bertin et al. (2010) J. Exp. Bot., 61: PPHD Dijon, Phenodays, Slide 8/18

9 PPHD s Objectives High throughput innovative technics of morphometry for: characterizing a large number of biological units, their interactions under different environmental conditions [Co 2 ] at various organizational levels (plant/plant, plant /organ) PPHD Dijon, Phenodays, Slide 9/18

10 Organisation Infrastructures and equipments: S1 Greenhouses and climatic chambers Nb Units Total surface (m2) Unit Surface (m2) Greenhouses m Climatic chambers m greenhouse units (total surface = 1000 m 2 ) 12 climatic chambers (total surface = 75m 2 ) PPHD Dijon, Phenodays, Slide 10/18

11 PPHD : S2 building, greenhouses, climatic chambers (1/3) Organisation A building, greenhouses ( m 2 ), And climatic chambers (80m 2 ) Lemnatec Phenotyping equipments PPHD Dijon, Phenodays, Slide 11/18

12 Organisation PPHD : S2 building, greenhouses, climatic chambers (2/3) «Scan 3D» system «Large» biological units Cameras: RVB Fluo NIR and rhizotrons (1000) InoviaFlow. PPHD Dijon, Phenodays, Slide 12/18

13 Organisation PPHD : S2 building, greenhouses, climatic chambers (3/3) «HTS» system «Small» biological units : petri dishes, seeds, plantlets Cameras: RVB Fluo NIR PPHD Dijon, Phenodays, Slide 13/18

14 European Funds (30%) INRA (31%) Burgundy Region(31%) French Minister (8%) Budget «Investments of future» Phénome (2800 K ) 2011/2012 PPHD Dijon, Phenodays, Slide 15/18

15 Positioning Local : Agrosup (partership for image analysis, data mining) Vitagora National: Réseau EFOR (partage pour plantes modèle) «Investissement d avenir» : Phenome LETI network International EU FP7 European Plant Phenomic Network (EPPN) EU FP7 ABSTRESS project (WP leader, 450K ) PPHD Dijon, Phenodays, Slide 16/18

16 Food for thoughts ( Do not forget: - to validate in the field to tackle G *E *M interactions - to combine approaches Phenotyping Approach + Analytical + approach Modelisation CO 2 SURFACE FOLIAIRE PROJETEE Efficience biologique 3,5 3,0 2,5 2,0 BIOMASSE TOTALE 1,5 1,0 CO 2 Efficience de conversion de N en surface projetée PAR (mol m -2 jour -1 ) PAR (mol m -2 jour -1 ) [NO 3- ] PAR (mol m -2 jour -1 ) Coefficients d ajustement 1,5 1,0 0,5 0, PAR (mol m -2 jour -1 ) N 2 Date de début de fixation de N 2 N NO - 3 QUANTITE TOTALE D AZOTE ,3 [NO - 3 ] (mm) 0,4 Prélèvement de N 0,2 0,3 spécifique AVANT 0,2 0,1 la date de début de 0,1 fixation de N 2 0,0 0, Thèse Delphine Moreau 13 avril 2007 [NO - 3 ] (mm) [NO - 3 ] (mm) BIOMASSE SOUTERRAINE Prélèvement de N spécifique APRES la date de début de fixation de N 2 Identifying differences among genotypes Interpreting the detected difference PPHD Dijon, Phenodays, Slide 17/18

17 Food for thoughts Thanks for your attention. PPHD Dijon, Phendays, The end