High Throughput Phenotyping Tools at ARVALIS-Institut du végétal

ARVALIS-Institut du végétal is a French applied research institute focusing on agronomic studies concerning cereals, maize, sorghum, potato, flax, grasslands and tobacco. It is mainly funded by farmers and aims at developing and disseminating relevant information and tools to produce more and better, taking into account the economic and environmental contexts.
Climate changes are starting to make crop production conditions more and more uncertain. Adaptation of the cropping system to unpredictable combinations of stresses - abiotic (water, nitrogen, etc.) and biotic (foliar diseases, pests, etc.) - requires innovative solutions. To do so, research programs must leverage all the technical resources available: improved genetics (pre-breeding and breeding programs), new inputs (fertilizers, bio-stimulants, etc.) and decision support tools (fertilization, irrigation, pesticide applications…). In all cases, crop observation is a key element for identifying factors of success.

To face this ambitious challenge, ARVALIS decided in 2010 to invest in the development of new high throughput phenotyping tools to boost the efficiency of its research programs and those of its partners (public research and private companies).

The result of some fruitful partnerships

Such research tools cannot be developed without strong scientific and industrial partnerships. Based on a prototype from INRA-Toulouse, a first phenotyping device was developed by ARVALIS and INRA during the PhenoBlé project (ANR funding, 2011-2013). The current phenotyping arch released in 2017 (ALPHI®, see next section) originated from this first prototype and was supported by the Carnot-Plant2Pro fund. From 2014, the UMT CAPTE consortium (founded by ARVALIS, INRA-Avignon, ITB and TERRES-INOVIA, and later joined by GEVES, CTIFL and the HiPhen company) has produced the PHENOMOBILE®, a programmable automaton (see next section). In addition, a fully integrated sensor data processing chain has been developed to analyze in a standardized way datasets from all phenotyping tools developed by ARVALIS and its partners. Last, the PHENOME project (ANR-PIA project started in 2012), also known as FPPN/Emphasis France, provided the scientific framework and the funding to develop some new and ambitious high throughput phenotyping field facilities in ARVALIS, INRA and TERRES-INOVIA research stations. For ARVALIS, this has resulted in building the PHENOFIELD® facility which combines a set of sensors mounted on mobile gantries and mobile shelters, irrigation system and soil sensors to control and monitor water stress experienced by crops. Some other projects are underway to broaden the capacity of ARVALIS to phenotype different crops in different agro-climatic contexts.
Besides the scientific partnership, all these innovative tools have been developed through tight industrial partnerships, particularly with the Meca3D and Robopec companies.

The facilities available in 2018

ARVALIS operates three high throughput phenotyping tools located in specific French agro-climatic areas (see figure "Location"). Their complete and specific descriptions are given in the following sections. All these facilities implement the same set of sensors (see next chapter) and are dedicated to : 
 1) trials carried out by ARVALIS for its internal research activities,
 2) experiments conducted as part of scientific projects with other research organizations,
 3) commercial services for private companies.

ALPHI® is a high throughput phenotyping arch carried by a tractor. It is located in Northern France. The main topics being studied are the response to nutrient stress (nitrogen, phosphorus...) and to foliar diseases. This tool is dedicated to crops with a maximum height of 1.3 m (cereals, potato and flax).

is a field facility which combines phenotyping sensors mounted on mobile gantries and a set of mobile shelters, irrigation system and soil sensors to control and monitor abiotic stress experienced by crops. It is located in the Beauce region
See the Video : Phenofield® : looking for drought-resistant varieties
The topics being studied are the response to abiotic stress (nitrogen and water) and to foliar diseases. Considering the height of the sensors, PhénoField®  can virtually phenotype many types of crops. Practically, the research station is focusing on maize and cereals.

is a programmable phenotyping robot located in the South East region. The main topics being studied are the response to nutrient stress (nitrogen, phosphorus...), water and heat stress. This tool is dedicated to crops with a maximum height of 1.3 m (cereals).

Figure : Location of the high throughput tools and facilities developed by ARVALIS-Institut du vegetal and its partners.

Sensors and related agronomic traits

Our three high throughput phenotyping tools display the same set of sensors which provides relevant traits to characterize the impact of various experimental treatments on the physiology of the crops studied (Table "traits" and examples given in the tool specific sections).
8 to 16 dates of measurements can be made on each experiment carried out with these facilities. All sensor data is computed with the same data processing platform developed in the UMT CAPTE with our partners INRA and the HiPhen Company. Furthermore, ARVALIS is involved in several research projects to expand the range of calculated agronomic traits. This can be done by integrating new sensors and developing new processing algorithms.

Table : Sensors, variables and related agronomic traits. Modified from Fred Baret courtesy UMT CAPTE

List of research projects involving ARVALIS High Throughput Phenotyping Tools

• PhénoBlé (2011-2014), ANR funding, led by ARVALIS-Institut du végétal, partners: BIOGEMMA, INRA.
• Breedwheat (2012-2019), ANR funding, led by INRA, partners: ARVALIS-Institut du végétal BIOGEMMA, INRA, GEVES, Céréales Vallée, RAGT 2n, BIOPLANTE, LIMAGRAIN EUROPE, SYNGENTA, AGRI OBTENTIONS S.A., MOMONT, CAUSSADE SEMENCES, BAYER SAS-Bayer CropScience, SECOBRA Recherches.
• Amaizing (2012-2019), ANR funding, led by INRA, partners: ARVALIS-Institut du végétal, BIOGEMMA, INRA, Maïsadour Semences, Euralis, Limagrain, Caussade Semences, Syngenta, KWS France, RAGT, Aelred.
• Solace (2017-2022), H2020 funding, led by INRA Montpellier UMR Eco&Sols (Ph. Hinsinger) and 24 partners (France, Austria, Italy, Switzerland, UK, Denmark, Turkey, Sweden, Belgium, Portugal, Germany, Spain, Hungary, Netherlands); Research Institute, Universities, Technical Centers and Firms)
• GPDur (2017-2020), FSOV funding, led by ARVALIS-Institut du végétal, partners : RAGT, SYNGENTA, INRA
• Idéotype sud, Regional PACA (04) funding, led by ARVALIS-Institut du végétal.
• INNO-VEG (2018-2022), Interreg 2 seas funding, led by ADAS, partners : DELPHY, INAGRO et ARVALIS


Global partnership and information 

Jean-Pierre COHAN, Head of Department Crop Physiology | Biotechnology | Crop Phenotyping
Benoît DE SOLAN, sensor phenotyping expert and co-leader of UMT CAPTE  
Katia BEAUCHENE, coordinator of the High Throughput Phenotyping Tools facilities    

Specific questions on a facility/tool (also refer to the dedicated pages)

Signal processing and data computing Platform : Benoît DE SOLAN and Samuel THOMAS 

Read more
PhénoField® : a special field structure for crop benchmarking under drought conditions
PhénoMobile® system
ALPHI®, a Light Arch of Innovative Phenotyping