Machine learning and epigenotyping: a new lever for improving the prediction of phenotypes in plants in an agroecological context

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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

The proposed thesis (funding already secured) will be carried out as part of the PEPR national research programme ‘Agroecology and digital technology: data, agricultural equipment and genetic resources for the agro-ecological transition and adaptation to climate hazards’, which is one of the measures in the SADEA (Sustainable Agricultural Systems and Agricultural Equipment Contributing to the Ecological Transition) acceleration strategy for France 2030. It has a budget of €65 million for a period of eight years and is co-directed by INRAE and Inria https://www.pepr-agroeconum.fr/le-programme.

More specifically, the thesis will be carried out as part of the winning project of the 2023 call entitled ADAAPT for Agroecology and Digital Agriculture via Animal and Plant Epigenetics (https://www.pepr-agroeconum.fr/les-projets-finances/ressources-genetiques/laureat-aap/adaapt). 4 theses on 4 different species (including the thesis proposed here) will be funded as part of this project (2025-2030) with various interactions. 

 

 

Context and issues:

Agroecological transitions in today's agri-food systems are taking place against a backdrop of increasing pressure from climate change. To improve the sustainability of our agricultural systems in this context, it is essential to understand how individuals can adapt to environmental changes.

Genetic selection only accounts for a fraction of phenotypic variation, and current models assume that the ranking of individuals is not affected by environmental conditions. However, it has been shown, in various species, that environmental disturbances can influence the epigenome and phenotypic characteristics of organisms.

Faced with these challenges, which concern both cultivated plant species and farm animals, new phenotyping tools need to be developed to monitor the suitability of the individual (plant or animal) and its environment (exposome). Epigenetic modifications, such as DNA methylation, are molecular markers that have an impact on the phenotypic diversity of organisms.

Objectives:

The scientific challenge of the project is to use digital technologies such as machine learning to exploit epigenetic data in order to optimise the use of plant genetic resources (in this case poplar), including their microbiota (holobiont), from an agroecological perspective. This will also make it possible to model the phenotypic trajectories of cultivated plants in agroecological itineraries.

Its specific objectives include:

● Characterising the epigenetic profiles of genetic resources conserved in France in various exposomes linked to the agroecological transition, such as water resources on a model species of cultivated woody plant, poplar.

● Integrating genomic, transcriptomic, epigenetic, spectral and microbiota data for agricultural modelling using numerical methods.

The ADAAPT project proposes to meet these challenges by merging skills relating to crops, their microbiota, physiology, genetics, epigenetics, epigenomics and digital technologies for agriculture, from 13 different INRAE laboratories, two teams from the Institut Agro, a team from the University of Orléans and a team from INRIA. Such a consortium brings together biologists with solid expertise in various fields (geneticists, physiologists, microbiologists) and computer scientists (statisticians and bioinformaticians). It is important to note that the ADAAPT project will include 4 theses (including the present subject) which will form a network of exchanges between doctoral students and supervisors and the entire ADAAPT project community and, more broadly, the Agroecology and Digital PEPR. This provides a particularly favourable framework for innovation.

Work plan:

Methylome, genome, transcriptome and phenotype data, as well as spectral data (NIRS) on more than 200 individuals from natural poplar populations, already available and from previous projects (ANR Sybiopop and ANR EPITREE) will be analysed during this thesis. In addition, new data acquired as part of the ADAAPT project will supplement these datasets. Indeed, >200 genotyped individuals (SNP chip) from a cross between two poplar species (GIS poplar), installed in a nursery for 2 years and monitored in terms of phenotyping will be epigenotyped during the project. Four major areas have been selected for this analysis:

1.         Descriptive methods for the epigenetic diversity of poplar genetic resources

2.         Study and development of methods for imputing epigenetic data

3.         Association tests using epigenomics to identify major improvement loci (biomass production, wood quality, interaction with the microbiota, drought tolerance, rust tolerance).

4.         Testing and development of phenotypic prediction models 

Location: Institut Agro (Rennes)

Training and skills

A background in statistics and/or bioinformatics, with advanced notions of R and Python code would be desirable. Knowledge of biology and/or genomics and bioinformatics would be a plus. An appreciation of teamwork (3 units on 2 sites) and the ability to work independently will be essential. 

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

Please provide the following information

- A letter outlining your motivation for this project;

- A Curriculum Vitae with grades in L3, M1, M2 (semester 1);

- Contact details for 1 or 2 referees.