Root2Resilience: Root phenotyping and genetic improvement for rotational crops resilient to environmental change

Project Information

Root2Res

Grant agreement ID: 101060124

DOI

10.3030/101060124

EC signature date 7 June 2022

Start date 1 September 2022

End date 31 August 2027

Funded under

• Food, Bioeconomy Natural Resources, Agriculture and Environment

Total cost

€ 6 367 651,25

EU contribution

€ 6 367 651,25

Coordinated by

ARVALIS INSTITUT DU VEGETAL
France

Periodic Reporting for period 2 - Root2Res (Root2Resilience: Root phenotyping and genetic improvement for rotational crops resilient to environmental change)

Reporting period: 2024-03-01 to 2025-08-31

Summary of the context and overall objectives of the project

As agricultural systems face more and more constraints due to climate change, identifying and developing new crop cultivars able to make production more resilient is a priority. Root systems play a major role as an essential component of the tolerance against abiotic stress (water deficit or excess, nutrition deficiency) and in carbon storage in soils. Addressing root traits for breeders, geneticists and agronomists is a real challenge that needs efficient tools: root phenotyping tools both in field and controlled conditions, genetic tools with a set of relevant markers and genetic resources and modelling tools to extrapolate the results in other environments and agricultural contexts.

In this context, Root2Res will deliver novel tools to help design climate resilient crop systems adapted to a range of environments across Europe. Beyond the project, these future-proofed systems will provide plentiful, healthy, and nutritious food from crops that are resilient to stress, resource efficient and go some way to mitigating the impact of climate change by sequestering carbon in soils. Root2Res will then contribute to more sustainable and environmentally friendly cropping systems for Europe.

Key to the Root2Res approach is the design of new tools to evaluate root traits and understand the genetic control of root and rhizosphere function associated with adaptation to climate change and elucidate how these traits interact with the rhizosphere microbiome to help develop and evaluate more sustainable cultivars. Root2Res will focus on three main annual crop families: cereals, potatoes, and grain legumes based on their major role in food security and human diets. Root2Res will also investigate the potential role of emerging crops (i.e. sweet potato, and lentil) to enhance resilience to environmental change. Root2Res will develop a unique research framework where we will assess an extended root phenotype. Critically, we will measure trait heritability and plasticity to environmental stress in our set of reference crops, for which multiple genotypes are accessible for experimentation, and in a range of agroecosystems. Focussing on multiple stress (water deficit or excess), and interactions with other stresses (temperature, reduced nutrient availability), Root2Res will deliver fundamentally innovative genetic and modelling toolboxes that can be deployed for the development of climate smart crops. This will be achieved by uniting an interdisciplinary team of crop geneticists, physiologists, microbiologists, agronomists and breeders from across Europe to develop these tools that would allow selection and breeding of improved genotypes and their field evaluation in various environments.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The root ideotypes description of the three core crops across agroclimatic zones and stress conditions was completed. First validation field trials were launched across zones and with a range of additional stresses to assess their performance under real cropping conditions.
The phenotyping toolbox was refined and improved, with results shared across field networks, shovelomic measurements in potato and barley, and evaluations of the other different root phenotyping methods. For root and rhizosphere traits, exudate and microbiome analyses were conducted along with initial data evaluation, using samples from controlled environment experiments. A minimum protocol for field assessment of root traits was developed and communicated to apply to large populations. The envirotyping process was set up, including the development of models, methodologies, and the calculation of key variables.
Genetic populations were assembled and multiplied. Genetic marker data was collated for these populations and, where absent, produced. This information was shared to identify regions of the genome that contribute to variation in traits of interest. Genotyping data for all species was compiled to enable the identification of genetic regions and genes underpinning resilient root systems. First analyses from the genetic diversity trials were conducted.
Multilocation field trials for all core species were performed across agroclimatic zones to validate phenotyping tools and proxies for physiological root and rhizosphere traits under field conditions and to provide phenotyping data for genetics and modelling analysis.
Controlled environment trials focussed on phenotypic plasticity aligned with analysis of transcriptomic and metabolomic responses of plants were conducted using the mesocosm system. First analyses of datasets were carried out, applying the plasticity index and joint data analysis pipeline.
Root exudate modelling advanced and led to a publication, while a new version of OpenSimRoot was released. The modelling toolbox was expanded with novel rhizosphere models, functional-structural plant models, and crop modelling approaches to address on how exudates, microbial activity, and root architecture contribute to plant resilience under drought and low-nutrient conditions.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The phenotyping toolbox was improved, enhancing its usefulness and applicability for breeders, scientists and agricultural professionals across environments and crop species. A protocol for root phenotyping for different species at the scale required by breeders was developed. Ideotypes for core crops were defined, providing specific targets for breeding strategies and future testing under contrasting agroclimatic conditions.
Insights into the plasticity of root traits aligned to transcriptional and metabolomic responses of plants were gained, offering new understanding of how plants adapt their root systems to stress and resource availability.
A new version of plant model OpenSimRoot was released, extending its capacity to simulate plant structure (root architecture) in given environments. These improvements support model development for new crop species, root plasticity responses to soil conditions such as local soil drying, proliferation in nutrient patches, and soil compaction.
The project generated large scale, original datasets from field experiments, integrating below and aboveground traits across crop species, sites and conditions. These datasets offer open-access resources for scientific and practitioner communities and will feed into further modelling, breeding, and design of resilient cropping systems.
Further efforts are needed in the last stages of the project, including validation and demonstration of ideotypes and root plasticity traits under large-scale field conditions, and integration of datasets and modelling outputs into breeding programmes. Interactions with policy makers and practitioners will support translation of advances into operational breeding and farming practices.

Root2Res Logo

Ideoptype Diagram

Root field phenotyping protocol for potato