Improving carbon fixation and drought stress tolerance in poplar trees for production purposes

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Forests are effective in mitigating some of the causes and consequences of climate change, particularly through CO₂ sequestration. In this context, maintaining healthy and functional forests is a key lever of the French National Low-Carbon Strategy (SNBC3) and the European Climate Law. Furthermore, forest trees produce wood, a renewable material that stores carbon and can replace products with a negative carbon footprint, such as concrete. Forests are themselves victims of climate change, and their capacity to act as carbon sinks is diminishing. Among the various solutions proposed for adapting forests to climate change, one strategy involves selecting the most resilient individuals of a given species while maintaining a certain level of wood production.

In this thesis, the species studied is poplar (Populusspp.), an economically important tree with rapid growth and therefore a high capacity for CO₂ sequestration. It is also a model organism in biology, for which we have genomic sequences² and expertise in various cell engineering techniques. BioForA developed the clone INRA 717-1B4 (P. tremula x P. alba), used as an international reference in functional genomics³,⁴. BioForA also leads the poplar breeding program within the framework of the Scientific Interest Group "Genetics, Improvement and Protection of Poplar" (GIS Poplar). This program aims to provide high-performing varieties, adapted to economic needs and resilient to climate change. It relies on the natural genetic diversity of black poplar (P. nigra) to develop high-performing interspecific hybrids, P. x canadensis (P. deltoides × P. nigra), the most widely planted hybrid varieties in France.

Resilience to environmental stresses and wood production are complex multigenic traits. However, genome-wide association studies (GWAS) and functional genomics studies using transgenesis have identified genes with a significant impact on these traits. For example, studies on natural populations of P. nigra identified a gene encoding a chalcone isomerase (CHI), strongly associated with radial trunk growth⁵. Another study, on natural populations of P. tremula, also highlighted the gene encoding an oxoglutarate dehydrogenase (OGDH), strongly associated with growth characteristics⁶. Functional validation studies using transgenesis have demonstrated a link between wood cell wall thickness and drought tolerance in trees. For example, in poplars overexpressing a laccase (PtrLAC17), the lignin content increases in guard cell walls and xylem, and their drought tolerance is enhanced⁷.

CRISPR-Cas technology enables targeted genome editing with unprecedented efficiency in many non-model species, including woody plants⁸. It is commonly used for knock-out mutations (loss-of-function) and is being improved for precise genome rewriting via Prime Editing⁹ and for the introduction of small enhancer sequences to create gain-of-function mutants¹⁰.

Based on current knowledge of the genetic control of wood formation and resilience to water stress, we hypothesize that it is possible to produce poplars with improved carbon sequestration and increased drought tolerance. We will use a genome editing approach to rapidly combine different alleles of genes of interest.

Thesis Objectives

This thesis aims to: (1) implement genome editing strategies to combine favourable alleles for traits of interest on the INRA 717-1B4 poplar reference genotype, which can be rapidly modified, and then on genotypes of interest for the poplar breeding program (P. nigra, P. x canadensis); and (2) evaluate these plants under water deficit conditions in order to validate or refute the working hypothesis.

Methods and Collaborations

Part 1 = Selection of the editing strategy for candidate genes and rapid validation of editing vectors in a poplar protoplast system. An initial list of 12 candidate genes was established during the CARBOOST project design phase. To become familiar with the subject, the PhD student will conduct a comprehensive literature review to continuously enrich this list by identifying genes/alleles of interest for the combinations. Depending on the context, they will develop the editing strategy based on loss or gain of function. They will develop a rapid method for evaluating editing vectors based on a transient expression system on protoplasts, particularly for vectors intended for gain-of-function editing.

Part 2 = Production and molecular characterization of the edited lines in different genetic contexts. The most efficient editing vectors will be used to generate easily modifiable poplar lines in the INRA 717-1B4 genetic database for different genotypes of P. nigra and P. x canadensis. The genetic modifications will be characterized at the molecular level to select lines for greenhouse experiments under water stress.

Part 3 = Phenotyping of plants under water deficit. The modified lines will be grown under water stress conditions on the Toulouse High-Throughput Automated Phenotyping Platform (TPMP). Their phenotype will be characterized by biochemical and microphenotyping strategies, particularly growth and wood quality.

This thesis will be conducted in close collaboration with the Regulation and Dynamics of Wood Formation team at the LRSV (CNRS, University of Toulouse), a partner in the CARBOOST project. It also relies on the existing collaboration with VIB (University of Ghent, Belgium) for access to genotyping data of 735 black poplar genomes from the ERC POPMET project.

References

 

1.        Migliavacca, M. et al. Securing the forest carbon sink for the European Union’s climate ambition. Nature 643, 1203–1213 (2025).

2.        Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (80-. ). 313, 1596–1604 (2006).

3.        Mader, M. et al. Whole-genome draft assembly of Populus tremula x P. Alba clone INRA 717-1B4. Silvae Genet. 65, 74–79 (2016).

4.        Zhou, R. et al. Populus VariantDB v3.2 facilitates CRISPR and functional genomics research. Tree Physiol. 45, 143–148 (2025).

5.        Duruflé, H. et al. Natural variation in chalcone isomerase defines a major locus controlling radial stem growth variation among Populus nigra populations. Peer Community J. 5, e50 (2025).

6.        Escamez, S. et al. Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock. Biotechnol. Biofuels Bioprod. 16, 1–16 (2023).

7.        Shen, M. et al. PtrLAC17 act as a key laccase in catalyzing lignin polymerization in both the stem xylem cell walls and the guard cell walls, coordinately regulating drought tolerance in Populus. Int. J. Biol. Macromol. 321, 146547 (2025).

8.        Anders, C., Hoengenaert, L. & Boerjan, W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. Curr. Opin. Plant Biol. 71, 102329 (2023).

9.        Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2021).

10.      Claeys, H. et al. Coordinated gene upregulation in maize through CRISPR/Cas‐mediated enhancer insertion. Plant Biotechnol. J. 22, 16 (2023).

Training and skills

Recommended training: Master degree or engineering degree in plant biology

Required Knowledge: Plant physiology and biotechnology

Desired Experience: Research internship in a laboratory

Desired Qualities: Curiosity, motivation, and ability to work in a team

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

The selection process consists of two stages: the host team will first shortlist three candidates based on their written application and an interview; these candidates will then attend an audition in early June in front of the Doctoral School of “Health, Biological Sciences and Chemistry of Living Organisms” (Santé, Sciences Biologiques et Chimie du Vivant) at the University of Orléans.

For the first stage of selection, please submit your application by May 3^rd 2026 (CV, cover letter and contact details of at least two referees). Interviews will take place on Monday May 11^th 2026.