Postdoctoral Research Fellow based in Montpellier, France

Location	LEPSE – INRAE, Institut Agro, Montpellier, France
Lab Website	https://www6.montpellier.inrae.fr/lepse_eng/
Date of Hire	As soon as possible
Duration	18 Months
Gross annual salary	42,672 – 49,248 € (commensurate with experience and qualification)

Job Description

INRAE is seeking an outstanding, motivated candidate for a position of Post-Doctoral Research Fellow in plant ecophysiology to work as part of the H2020 SolACE and EPPN200 projects. Through these projects a genetic panel of both bread and durum wheat has been extensively phenotyped in high-throughput phenotyping platforms in controlled environment and semi-field conditions. By analyzing this large dataset you will study the phenotypic plasticity of wheat tillering under contrasted scenarios of water deficit.

In addition to giving new insight regarding the physiological responses of wheat to chronic drought and rewatering, your research will allow a generic approach of parameterization of crop growth models for bread and durum wheat and will identify potential sources of improvement of wheat adaptation and resilience to drought. You will conduct your research in close collaboration with another Post-Doctoral Research Fellow in applied mathematics and artificial intelligence who will develop methods for time-series analyses of in situ 3D images to characterize the evolution of the spatial structure of plants over time.

 As a postdoctoral researcher, you will be led to:

• Develop and evaluate phenomic methods to quantify traits related to cereal shoot expansion and architecture.
• Analyze the links and trade-offs between the components of shoot expansion (leaf appearance rate, individual leaf expansion, and tillering) and their sensitivities to water deficit.
• Carry out multivariate analyses on physiological traits to define the structure of the genetic diversity of wheat shoot expansion and its response to water deficit (phenotypic space) that maximizes the genetic variability to water and nitrogen deficit.
• Write and publish articles in peer-reviewed journals.

Location

The position is open at the Laboratory for Plant Ecophysiology under Environmental Stress (LEPSE) of the French National Research Institute for Agriculture, Food and Environment (INRAE). You will join a multi-disciplinary group of plant ecophysiologists, modelers, geneticists, and computer scientists. You will have access to state of the art laboratory, experimental, and computer facilities. Montpellier is a city of 270,000 ideally located in the south of France, on the Mediterranean sea. With over 3,000 researchers, Montpellier is the largest European center for plant sciences and agronomy.

Education and Experience Requirements

• PhD degree in plant ecophysiology, phenomics, modeling or a closely related field.
• Experience with handling large, multi-source and multi-scale datasets and analyses of experimental data.
• Proficiency in R or Python programming is highly desirable.
• Proven record of research publications in peer-reviewed international journals.
• Willingness to collaborate with others as part of a multi-disciplinary research team.
• Proficiency in spoken and written English.

Application conditions

Candidate of any nationality may apply. The candidates must have doctoral degree at recruitment date (French doctorate, PhD or foreign doctorate of equivalent level) for less than five years.

How to apply

To apply you should submit a letter of interest, complete curriculum vitae with a list of publications, the names and addresses (including telephone and email) of three referees who are knowledgeable about the applicant’s professional qualifications and work experience.

For further information and to apply, please contact Dr Pierre Martre (pierre.martre@inrae.fr) and Dr. Boris Parent (boris.parent@inrae.fr). Applications will be received until a suitable candidate is found.

https://www6.montpellier.inrae.fr/lepse/Travailler-et-etudier-avec-nous/Post-Doctorats/Phenotypic-plasticity-and-genetic-variability-of-shoot-expansion-in-response-to-drought-in-wheat

Postdoctoral Research Fellow based in Montpellier, France

Location	LEPSE – INRAE, Institut Agro, Montpellier, France
Lab Website	https://www6.montpellier.inrae.fr/lepse_eng/
Date of Hire	As soon as possible
Duration	24 Months
Gross annual salary	42,672 – 49,248 € (commensurate with experience and qualification)

Job Description

We are seeking an outstanding, motivated candidate for a two-years Post-Doctoral position in root system modeling as part of the H2020 project SolACE. SolACE is inspired by the aim of finding “Solutions for improving Agroecosystem and Crop Efficiency for water and nutrient use”. In that project, our task is finding the best combinations of belowground traits to optimize plant foraging efficiency in suboptimal water and N supply scenarios.

Our strategy is to use crop models that are popular tools in plant sciences to integrate our knowledge about complex plant processes and performance as influenced their environment and their genotype (Muller and Martre, 2019). However, whereas above-ground processes have been the main focus in crop models for decades, the root part has been largely ignored and/or simplified due to difficulty and complexity in root phenotyping and limited access to root data. To fill this gap, you will develop an ecophysiological model of root growth and plasticity in response to spatio-temporal variations of soil water and nitrogen resources. The starting point will be the 3D root architectural model ArchiSimple that we have recently integrated into the wheat crop model SiriusQuality. An important aspect of the model will be that several genotypic parameters will be estimated in root phenotyping platforms. This will allow you to use this model to explore the value of root traits that have already been phenotyped for a bread and durum genetic panel in root platforms (4PMI, INREA; RootPhAir, UCLouvain) and in semi-field conditions (RadiMax, Univ. Copenhagen) and propose root ideotypes to improve wheat performance in suboptimal water and N supply scenarios.

Location

The position is open at the Laboratory for Plant Ecophysiology under Environmental Stress (LEPSE) of the French National Research Institute for Agriculture, Food and Environment (INRAE) and you will collaborate with SolACE partners at INRAE, UCLouvain and Univ Copenhagen. You will join a multi-disciplinary group of plant ecophysiologists, modelers, geneticists, and computer scientists. You will have access to state of the art laboratory, experimental, and computer facilities. Montpellier is a city of 270,000 ideally located in the south of France, on the Mediterranean sea. With over 3,000 researchers, Montpellier is the largest European center for plant sciences and agronomy.

Education and Experience Requirements

• A PhD degree in plant modeling, ecophysiology or a closely related field
• Good skills in object oriented programming (C#, C++, or Java)
• Strong scientific knowledge in applied mathematics and numerical modelling
• Ability to creatively identify and solve problems, use observational data to improve models and implement alternative solutions
• Proven record of research publications in peer-reviewed international journals
• Willingness to collaborate with others as part of a multi-disciplinary research team
• Proficiency in spoken and written English

Application conditions

Candidate of any nationality may apply. You must have a doctoral degree at recruitment date (French doctorate, PhD or foreign doctorate of equivalent level) for less than five years.

How to apply

To apply you should submit a letter of interest, complete curriculum vitae with a list of publications, the names and addresses (including telephone and email) of three referees who are knowledgeable about your professional qualifications and work experience.

For further information and to apply, please contact Dr Pierre Martre (pierre.martre@inrae.fr) and Dr. Bertrand Muller (bertrand.muller@inrae.fr).
This position will remain open until filled.

https://www6.montpellier.inrae.fr/lepse/Travailler-et-etudier-avec-nous/Post-Doctorats/Modeling-root-system-plasticity-in-response-to-drought-and-low-nitrogen-in-wheat

Postdoctoral Research Fellow based in Montpellier, France

Location	LEPSE  – INRAE, Institut Agro, Montpellier, France                                      Zenith – LIRMM, Inria, CNRS, Univ. Montpellier, France
Lab Website	https://www6.montpellier.inrae.fr/lepse_eng/ https://team.inria.fr/zenith/
Date of Hire	As soon as possible
Duration	18 Months
Gross annual salary	42,672 – 49,248 € (commensurate with experience and qualification)

JOB DESCRIPTION:

We are seeking an outstanding, motivated candidate with established prior experience in deep learning, computer vision, and ideally image tracking for an 18-months Post-Doctoral position in computer science.

You will work within an INRAE-INRIA-CIRAD collective of ecophysiologists, plant modelers and computer scientists in the frame of the PHENOME-EMPHASIS and EPPN2020 projects to produce a complete solution for the analysis of plant development and architecture. The research effort will focus on the development of time-series analyses of in situ 3D images to characterize the evolution of the spatial structure of plants over time (growth curve, shape evolution) and its modulation according to environmental conditions, in order to allow a genetic analysis of these differences and to retrieve the values of parameters of plant growth simulation models.

You will benefit from large datasets consisting in time series of annotated 3D wheat, maize, sorghum, and rice plant images acquired in the PhenoArch platform and processed with the Phenomenal processing chain. You will first develop algorithms from a set of wheat plant images obtained in two experiments where several water and nitrogen deficit treatments resulted in contrasted plant size and development and for which a number of properties were measured (leaf size, number of leaves, number of tillers….). In a second step, these data will be used to extend different plant growth and development models (e.g. ADEL, SiriusQuality).

As a postdoctoral researcher, you will be led to:

• Analyze a variety of 3D volumetric temporal data to generate estimates of plant development dynamics properties.
• Contribute to the development of new automatic data processing algorithms to match the different 3D plant acquisitions.
• Work as a member of a multidisciplinary research team.
• Write technical reports and write and publish articles in peer-reviewed journals.

Skills needed:

• Strong skills in image analysis and deep learning.
• Demonstrated experience in 2-D and 3-D image processing techniques or in a related field.
• Excellent programming skills: must be expert in Python, C and C++.
• Strong scientific knowledge in mathematics, imaging techniques or numerical modelling.
• Ability to creatively identify and solve problems, use observational data to improve models and implement alternative solutions.
• Ability to collaborate with a multidisciplinary team of scientists, and to write publications in English.

APPLICATION CONDITIONS:

Candidate of any nationality may apply. You must have a doctoral degree at recruitment date (French doctorate, PhD or foreign doctorate of equivalent level) for less than five years.

HOW TO APPLY:

To apply you should submit a letter of interest, complete CV, with a list of publications, the names and addresses (including telephone and email) of three referees who are knowledgeable about your professional qualifications and work experience, and relevant certificates.

For further information and to apply, please contact Antoine Liuktus (antoine.liutkus@inria.fr), Christophe Pradal: (christophe.pradal@inria.fr), and Christian Fournier (christian.fournier@inrae.fr).

This position will remain open until filled.

https://www6.montpellier.inrae.fr/lepse/Travailler-et-etudier-avec-nous/Post-Doctorats/3D-4D-image-analysis-for-plant-architecture-phenotyping