Overcoming the Phenotyping Bottleneck

Transcription

1 Mitglied der Helmholtz-Gemeinschaft Overcoming the Phenotyping Bottleneck Challenges Networks Technologies Implementation Trends Prof. Ulrich Schurr IBG-2: Plant Sciences Forschungszentrum Jülich Germany

2 Take-home messages There is no single phenotyping - but.. many New technologies (non-invasive) develop quickly, provide new options - but. are by far no guarantee for relevant results integrated R&D approaches are necessary (multi-disciplinary, beyond projects) - but. even then networks beyond a single workgroup are required Phenotyping chain concept need to integrate Plants from lab to field - Temporal and spatial scales Environments from lab to field - Temporal and spatial scales Phenotyping requires integration in the workflow of users to be applied, because Phenotyping is a TOOL practical (not very sophisticated), infrastructure, data management, usability ACCESS modes for use There is a lot to do together!

3 Phenotyping in breeding and plant management Breeding Objective: e.g. enhancing yield and biomass through optimizing plant phenomics CROP DESIGN GENETIC RESOURCES Pre-Breeding GENETIC ANALYSIS BREEDING Management Trait identification Understanding of G x E x M Detailed analysis Phenotypic Experimental High There Characterization many of phenotypic characterization of parent population throughput genetic resources Phenotyping processes/ Selection from methods Marker required Landraces populations platforms Field and controlled Synthetics environment Population analysis Translocation Wild relatives Physiological traits From lab to field Field/ plot phenotyping Strategic crossing Link to management and precision agriculture Precision agriculture Transgenic approaches MAS, GS, Wide Crossing DATA MANAGEMENT and MODELLING

4 Demands in Plant Phenotyping Climate change Molecular biology Genetics Breeding G x E x M Breeding and agronomy Sustainable agriculture Projects Infrastructure - Education

5 Plant phenotyping did develop dynamically 2008

6 Plant phenotyping did develop dynamically 2015

7 Phenotyping - Challenges Development is rapid Demand is Increasing and diverse Often linked to special expertise for development Often requires specialised infrastructures plant characteristics environmental simulation Europe is a global leader, but competition is growing globally Network Interact Use Develop, apply and disseminate infrastructure

8 Phenotyping Networks National platforms European projects/ networks Crop specific aspects General development International networks

9 State-of-the-Art Phenotyping Deep phenotyping - tomographic Plant MRI-PET Center, Jülich Live imaging of structure and function root shoot Hounsfield micro-ct, Nottingham 3D-structures

10 Non-invasive, live imaging of structure,growth and carbon transport on root systems in real soil Short-term and Day-to-day dynamics Quantitative, non-invasive morphology Structure-function analysis Root growth in soil Root diameter Nodules

11 State-of-the-Art Phenotyping High throughput phenotyping greenhouse/ growth chamber WHIWAM Gent Fluogrowscreen Jülich Root Carousel Jülich

12 State-of-the-Art Phenotyping High-throughput in controlled environment PhenoArch, Montpellier Extended Lemnatec, Gatersleben GrowScreenRhizo, Jülich PPHD, Dijon

13 DPPN SEED: Phenotyping of structure and function of seeds Arabidopsis PhenoSeeder A robot system for phenotyping single seeds Rapeseed wide range of species Quantitative traits of single seeds (size, shape, weight, ) Internal structures (in the future) Maize

14 PhenoSeeder in action

15 Phenotyping of individual seeds with phenoseeder (example) Application cases Analysis of seed populations Reducing statsistical noise in phenotyping Seed physiology Seed banks

16 Contrasting genotypes for strategies for water and nutrient acquisition Trait cluster analysis Morphological and functional limitations

17 State-of-the-Art Phenotyping Intensive field sites CO 2 (FACE) Rainout shelters Protected sites (GMO) Hyper-intensive field Phenomobiles BreedFace Jülich/ Bonn Mobile Shelters Clermont Stationary field sensor networks Flying platforms Avignon Jülich.

18 Phenotyping chains - beyond lab experiments Practical experiments From single plant to field Systematic Meta-analysis Identification of major differences and how to overcome them (Poorter et al 2016) Phenotyping chains (scales)

19 Simulation of future environments Breed-FACE: Free Air CO 2 Enrichment (FACE) Setup at Campus Kleinaltendorf

20 State-of-the-Art Phenotyping Breeders practical field sites Portable sensors ( cheap ) Easy carriers Flying platforms

21 Common experiment with breeders and in breeders plots Wheat Barley Corn Rape

22 Remote sensing of photosynthesis Airborne mapping of sun-induced fluorescence From plot scale to global Airborne system

23 Remote sensing of photosynthesis From plot scale to global FLEX - the next Earth Explorer satellite

24 State-of-the-Art Phenotyping Modelling Disentangling complex traits Genetic analysis of complex traits Crop climate optimisation What is the relationship between root structure and nutrient use efficiency? What is the sensitivity of leaf growth to drought? Which genotype would work best in which environment scenario?

25 Mitglied der Helmholtz-Gemeinschaft SimRoot a functional structural plant model List of studied traits / factors Growth Angles Lateral Branching density Root cortical aerenchyma Root cortical senescence Planting density Interspecies root competition Root hairs Trait synergisms Develop ideotypes Integration with phenotyping experiments (virtual testing, proxy identification) Linking lab to field

26 Mitglied der Helmholtz-Gemeinschaft Integration of omics with Phenotyping data

27 Next step of integration European Infrastructure National platforms European projects/ networks European Infrastructure European Infrastructure for Multi-Site Plant Phenotyping And Simulation for Food Security in a Chancing Climate

28 EMPHASIS why going European? Generating synergies Special equipment Data management: Standards/ protocols/ interoperability Education/ training and outreach Boost different roles of academia and industry Access Development access Use access Dissemination access Generating novel opportunities Unique installations Link field phenotyping in diverse climate/ environment zones Phenotyping as a tool link to user demands Handle diversity of solutions Link to models (bilateral) Link to omics

29 EMPHASIS partnership EMPHASIS project partners (from 4 governments) EMPHASIS associated partners (from 15 countries) Academia Industry Technology Providers Other partners : Field networks of seed companies EMPHASIS - open for additional partners

30 EMPHASIS infrastructures Phenotyping platforms for high resolution, high throughput phenomics Semi-controlled field systems for high throughput phenomics Network of practical field experiments for lean-phenotyping Modelling for improving phenotypic processes and for testing existing or virtual combinations of alleles in a variety of climatic scenarios and management practices Joint data management and e-infrastructure

31 EMPHASIS - Mission developing infrastructures and providing access for multi-scale phenotyping to analyse genotype performance in diverse environments and quantify the diversity of traits. And Objectives develop an integrated pan-european network of instrumented phenotyping platforms able to test genotypes using current and future agro-climatic scenarios, thereby providing community access to platforms featuring controlled and field conditions. link data acquisition to a European-level data management system and to state-of-the art crop models to simulate plants and crops in current and future climates. develop, evaluate and disseminate novel technologies, thereby providing new opportunities to European SMEs involved in phenotyping and precision agriculture

32 EMPHASIS and EMPHASIS-PREP: timelines > 2021 EMPHASIS propsal Preparatory phase Implementation / Routine operation ESFRI ROADMAP - EMPHASIS on ESFRI Roadmap EMPHASIS-PREP - legel framework business plan - community building EMPHASIS - legal entity - sustainable operation - RI life cycle: new infrastructure 2026 EMPHASIS LANDMARK EMPHASIS community

33 EMPHASIS Stakeholders EMPHASIS-PREP will establish a transparent, open and inclusive process for the foundation of future operation of EMPHASIS EMPHASIS-PREP CORE GROUP EMPHASIS-SUPPORT GROUP EMPHASIS PREP Core Group Members of the EMPHASIS-PREP EU funded project EMPHASIS PREP Support Group Representatives of national phenotyping communities Ministry mirror group (Min-MG) Funders board (F-AB) Industry advisory board (Ind AB)

34 EMPHASIS preparatory phase Deliverable of the preparatory phase: BUSINESS PLAN for EMPHASIS Develop national phenotyping hubs as the basis for interaction; Relationship hub and national centres Develop stakeholder relations (users, partners, associates; academia, industry, politics) Quality criteria and sustainability E-infrastructure (data management, standards, hard- and software roadmap, ) Business plan (legal entity; governance; financial and cost models) Looking forward to intensive cooperation

35 Mitglied der Helmholtz-Gemeinschaft Overcoming the Phenotyping Bottleneck Challenges Networks Technologies Implementation Trends Prof. Ulrich Schurr IBG-2: Plant Sciences Forschungszentrum Jülich Germany