Selecting for cooperative crops to develop sustainable agriculture – SCOOP

WP1 – Identification of cooperative alleles and phenotypes

Two field experiments involved 180 lines grown in binary mixtures. Above-ground traits and components of selective value were analysed to identify markers and traits involved in plant-plant interactions. In addition, two candidate traits that are difficult to measure in the field—phenotypic plasticity to shading and root exudation—were studied under controlled conditions. An original exudate sampling protocol was developed and ultimately applied to the domestication series (WP2) in order to limit experimental costs while maintaining consistency in objectives.

We conducted three experiments under controlled conditions to analyse the ecophysiological mechanisms involved in plant-plant interactions in binary mixtures of genotypes, varying growth conditions (neighbour identity, resource availability). One of these experiments was also replicated in the field to assess the transferability of results between field and controlled conditions. Aerial, root and phenological traits, as well as biomass and yield variables, were measured.

WP2 – Evolution of cooperation in durum wheat

The genetic approach focused on the Green Revolution period, during which reducing competition became a major challenge for varietal selection. Based on WP1, we tested the hypothesis of an increase in the frequency of cooperative alleles during durum wheat improvement. The results on shade plasticity complemented this approach.

At the phenotypic level, 39 genotypes representative of the domestication series were grown in pots, alone or in competition with the same neighbour. Biomass and functional traits above and below ground were measured to characterise the competitiveness and plasticity of the traits. The root exudation profile is currently being established.

WP3 – Evaluation of selection schemes

An evolutionary experiment that we have been conducting since four years explores the dynamics of selection on two traits (height, specific leaf area) involved in competition. Ninety trays were sown with four phenotypically contrasting lines and subjected to two selection regimes: intra-tray (favouring competitive genotypes) and inter-tray (favouring cooperative genotypes). Phenotypic trajectories are monitored annually, supplemented by an innovative genetic approach to estimate the relative contribution of each genotype to seed production.

On a theoretical level, we developed a model of competition for light, based on kinship selection theory (Montazeaud et al., 2020), which was extended to incorporate temporal growth dynamics and phenotypic plasticity, using tools from optimal control theory.

WP1 – Identification of cooperative alleles and phenotypes

We have identified a locus involved in interactions, for which allelic richness increases disease and reduces yield. This effect is consistent with a ‘green beard’ gene promoting cooperation (Montazeaud et al 2022, 2024). The number of genomic regions associated with interactions increases with crop density. Analyses are underway to test whether these regions have contributed to the evolution of cooperation. Under controlled conditions, we have shown that genotypes with strong root development benefit from the presence of weaker competitors, reflecting a relaxation of competition (Montazeaud et al 2025). Finally, traits measured on binary mixtures explain yield better than those from isolated plants, confirming the importance of plant-plant interactions and the environment.

WP2 – Evolution of cooperation in durum wheat

Genetic analyses we have conducted to date confirm that post-Green Revolution varietal selection has reduced competition between plants. The selection of shorter, cooperative plants through the introduction of dwarfism during the Green Revolution (Rht gene) may also have led to a counter-selection of height plasticity, further limiting competition for light (Colombo et al 2022). This gene also influences mycorrhizal interactions (Alaux et al 2024). The phenotypic approach shows that the trait space of durum wheat is structured by the same functional trade-offs as at the interspecific level (Lemoine et al. 2023). Domesticated forms perform better in competition than their ancestors, despite reduced plasticity (Lemoine et al. 2025, JExpBot). Allometric relationships between vegetative and reproductive biomass remain stable during domestication (Lemoine et al 2025, PRSPB). Finally, through a review of the literature, we show a decrease in cooperation during domestication, opening up avenues for restoring it in sustainable agricultural systems (Fréville et al 2022).

WP3 – Evaluation of selection schemes

The evolution experiment is still ongoing. Initial results indicate the effectiveness of the selection schemes tested. On a theoretical level, progress on this task has been slowed by three unsuccessful attempts to recruit a postdoctoral researcher. Collaboration with P. Avila has made it possible to extend the plant growth model to a closed-loop framework that incorporates the relative size of competitors. Using a mathematical framework she developed, she has reproduced known results for an open-loop model, corresponding to the case where plant size is solely a function of time.

Finally, three review articles were published on root traits (Fort 2023; Rongsawat et al 2021) and on ‘green beard’ genes (Montazeaud et al 2024).

The project results open up interesting prospects for research and innovation in the field of agroecology and plant breeding. The identification of genomic regions and traits that promote cooperation between plants provides an original conceptual and experimental framework for rethinking varietal selection at the population level, explicitly integrating interactions between individuals. These advances offer the possibility of directing varietal creation towards cooperative ideotypes adapted to dense cropping systems.

On a scientific level, the project has established new approaches combining experimentation and theory, which can be transferred to other cultivated species. Our results open up many interesting avenues to explore in the study of plant-plant interactions. Among these, (i) the project has highlighted the importance of focusing on phenotypic plasticity in interactions. The integration of models based on optimal control theory paves the way for both theoretical and experimental exploration of plasticity, a mechanism that has been little studied in the context of agriculture to date; (ii) The discovery of genes with effects compatible with those of ‘green beard’ genes involved in cooperation and documented in animals and microorganisms encourages us to explore the existence of such genes in plants.

At the economic and societal level, the project's results provide leverage for the transition to sustainable agriculture. By identifying the genetic and phenotypic determinants of cooperation, they offer avenues for sustaining productivity, while limiting the expansion of agricultural land. This knowledge can be transferred to public and private breeding programmes.

1. Montazeaud G, Rousset F, Fort F, Violle C, Fréville H*, Gandon S* (2020) Farming plant cooperation in crops. Proceedings of the Royal Society B 287, 20191290. dx.doi.org/10.1098/rspb.2019.1290. (* These authors contributed equally to this study).
2. Colombo M, Montazeaud G, Viader V, Ecarnot M, Prosperi J-M, David J, Fort F, Violle C, Fréville H. A genome-wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat. Soumis à Evolutionary Applications

In agriculture, intraspecific competition is undesirable, since it drives the evolution of traits toward phenotypic values lowering group performance. Plant height is a well-documented example: tall plants win access to light over shorter plants by diverting resources to vegetative structures, which leads to a negative correlation between height and seed production of the group. This motivated breeding for shorter plants during the Green Revolution. Agriculture is nowadays challenged by the need to ensure crop production while limiting environmental costs. Density is known to strongly affect competition for resources, and is a main limiting factor for crop yields. Breeding for cooperative phenotypes that do not invest resources in competitive interactions at high planting density could help sparing natural land from conversion to agriculture. Still, apart from height for plants competing for light, we know very little about the traits that affect the outcome of competition, the phenotypes that make a plant cooperative on such traits, and which breeding strategies can promote cooperative phenotypes.
The kin selection theory formalized by the evolutionary biologist W. Hamilton, has been very successful in explaining the evolution of cooperative phenotypes, which have a beneficial effect on group performance, including altruistic phenotypes whereby the individual pays a cost on its own performance. The weak competitor crop ideotype targeted by breeders during the Green Revolution can thus be viewed as a cooperative plant in the kin selection theory, shorts plants being altruistic. Interestingly, the kin selection theory has been poorly mobilized in agriculture.
In SCOOP, we ask whether breeding for cooperative crops can help designing more sustainable agrosystems with high productivity by taking an integrative approach linking evolutionary biology and functional ecology. The consortium comprises four partners (AGAP, CEFE, ISEM, BPMP) with scientists from CNRS, INRA and Montpellier SupAgro. Our model system includes the cultivated durum wheat Triticum turgidum L. subsp. durum, its wild form Triticum turgidum ssp. dicoccoides and its first domesticated form Triticum turgidum ssp. dicoccum. Durum wheat is a major source of staple food, mostly used for the production of pasta and semolina. In France, it is the fourth most important crop production.
In this project, we will address three main questions: (1) Which phenotypes and alleles are cooperative at high planting density? (2) Has cooperation evolved during domestication and breeding? (3) Which breeding schemes can select for cooperation?
SCOOP is organized into three work packages. In WP1, we will identify alleles and phenotypes on above- and belowground traits, which are cooperative in high-density plots, using a combination of experiments in the field and in controlled conditions. In WP2, we will test whether human selection has selected for more cooperative alleles and phenotypes during the evolutionary history of durum wheat. To do so, we will assess whether there has been a temporal shift in the frequency of cooperative alleles and in the mean phenotypic value of traits studied in WP1 among the three subspecies of Triticum turgidum. In WP3, we will assess the relevance of different selection schemes for promoting plant cooperation, by combining theoretical work and experimental evolution.
This project will help addressing fundamental questions in evolutionary biology and ecology, as well as pressing issues in agriculture. Indeed, SCOOP will contribute to improved comprehension of the evolution of traits driving plant-plant interactions in cultivated species. SCOOP will also have major implications for the design of novel and easy to implement breeding strategies needed for the development of sustainable agriculture.