[Defended thesis] Hong Anh Nguyen : Connecting the dots between High-throughput Root Phenotyping Platforms, Crop Growth Models and Root Architecture Models

Connecting the dots between High-throughput Root Phenotyping Platforms, Crop Growth Models and Root Architecture Models

My name is Hong Anh Nguyen. I started my PhD in November 2019, at the Laboratoire d'Ecophysiologie Végétale sous Stress Environnemental (LEPSE), at INRAE in Montpellier. My specialty is plant improvement.

I completed the master's program Seeds and Plants in Mediterranean and Tropical Regions (SEPMET) at the Institut Agro de Montpellier, which aims to provide adaptive tools for global change in agriculture using innovation technology. Following my Master 2 internship, I developed an interest in studying the root system to improve plant performance under difficult conditions. This experience inspired me to pursue a thesis, to study the effect of root system architecture on the adaptation of wheat crops to uncertain and variable environmental conditions.
My project aims to: (i) improve the representation of root system architecture and function in crop models, to better understand their potential benefits under different environmental scenarios, including drought and low nitrogen; (ii) link data from high-throughput phenotyping platforms to RAM parameters; (iii) explore the value of root plasticity traits in enhancing plant responses to spatially and temporally variable water and nitrogen supply under defined environmental scenarios.

I believe that the model developed could be widely used, for different purposes:

- by the breeder, to identify the ideotype(s) in defined drought and nitrogen deficiency scenarios in order to improve wheat adaptation to new growth conditions, which should become the direct pre-selection process or target the necessary trait(s) ;

- by the biologist, to test functional hypotheses;

- by the agronomist, to choose a better die design, irrigation system or test scenarios.

• Starting date: 1st November 2019
• University: Institut Agro 
• PhD school: GAIA
• Scientific field: Ecophysiology and adaptation of plants - BIDAP - Biology, Interactions, Adaptive Diversity of Plants
• Thesis management: Bertrand Muller, Lepse, Inrae et Pierre Martre, Lepse, Inrae
• Thesis supervisors: Région Occitanie and Inrae
• #DigitAg : Labeled PhD – Axe 6: Modélisation et simulation  – Challenge 2 : Le phénotypage rapide

Keywords: root system, wheat, crop model, nitrogen, water deficit

Abstract: Crop growth models (CGMs) are powerful tools to predict and optimize crop performance under various environmental conditions. However, the representation of roots is often simplified, hampering our capacity to account for potential improvement by breeding roots in response to the environment. In parallel, more or less detailed root architecture models (RAMs) have been developed to account for a diversity of architectures and interactions with the surrounding rhizosphere. To better account for the role of root systems in crop performance, a strategy is thus to couple RAMs and CGMs. This work stepped into the coupled model SiriusQuality::ArchiSimple (that has been done in parallel with this thesis) to explore three domains. First, we evaluated the capacity of two different high throughput root phenotyping platforms to capture the genetic variability of key ArchiSimple parameters. A significant effect of the experimental setup was found for all measured parameters while no significant correlation across a panel could be detected. Differences in temperature and/or irradiance but also the developmental stage between experiments and setups may partly explain the differences observed, highlighting the need for considering both developmental and environmental drivers in root phenomics studies and RAM construction and parametrization. Second, using the coupled SiriusQuality::ArchiSimple model, five ideotypes with contrasted root architecture were simulated in a combination of seven European sites and four contrasted soil types during 30 consecutive growing seasons (1990-2020). Simulations confirmed that the benefits of specific root architectural features greatly vary depending on soil and climate. The carbon cost of these architectures as well as their environmental impact on water and minerals remain to be accounted for to fully consider their cost-benefit balance, in support of a more virtuous agriculture. Finally, we challenged the over-simplistic hypotheses of ArchiSimple about primary root emission as well as the dynamic of their elongation rate and diameter. We confirmed that in wheat, primary axis emission could be easily modeled from the knowledge of tillering dynamics while their elongation rate and diameter follow predictable patterns. These results provide the foundation to develop an improved version of ArchiSimple.

Jury compound:

Mme. Alexandra JULLIEN, AgroParisTech - Rapporteur
Mme. Marion PRUDENT, INRAE - Rapporteur
M. Jacques DAVID, Institut Agro - Examinateur
M. Guillaume LOBET, UCLouvain - Examinateur
M. Bertrand MULLER, INRAE - Direction de thèse
M. Pierre MARTRE, INRAE -  Co-direction de thèse 

Contact : hong-anh.nguyen [AT] inrae.fr​