AGAP Institute

To contribute to meeting the challenges of Mediterranean and tropical agriculture (food security, sustainability of agrosystems, climate change, energy and ecological transition), Agap Institute develops crops that are better suited to various agrosystems. It combines a wide range of skills, approaches and resources, including:

• the organization and diversity of genomes;

• the management and optimum utilization of agricultural biodiversity;

• the genetic and functional bases of development and adaptation to the environment, along with product quality;

• data integration and modelling (of plant stands) to help define varietal ideotypes;

• the latest phenotyping and genotyping methods;

• the integration of knowledge for varietal innovation and novel selection methods.

Some twenty Mediterranean and tropical crop species are studied, divided into  self‑fertilizing annual species (rice, wheat, sorghum, cotton, groundnut), vegetatively propagated species (citrus, roots and tubers, banana, sugarcane), and perennial species (eucalyptus, oil palm, apple, vine, olive, rubber, cocoa). Varietal creation is undertaken in partnership for most of these species.

Four AGAP teams are working on rice:

GIV: The Genetics and Variety Innovation (GIV) team develops, tests and optimizes breeding strategies taking into account the specificities of the genetic resources (indica, temperate japonica and tropical japonica groups), the schemes (pedigree breeding, rapid generation advance, recurrent selection on synthetic populations, decentralized participatory breeding) and the target traits of three selection programs: production stability and nutritional quality (upland rice and irrigated rice in Latin America), productivity (irrigated rice in Asia), nitrogen use efficiency (upland rice in Madagascar highlands). The GIV team studies the genetic control of traits of relevance to the breeding programs, and develops molecular markers for fastening the introgression of such valuable traits. GIV implements genomic prediction and selection and also investigates the potential of modulating somatic and meiotic recombination for enhanced diversity shuffling and favorable variation capture.

DARS : The Adaptive Development of Rice and Sorghum (DARS) combines molecular genetics, cell biology, dynamic imaging and bioinformatics approaches to identify the networks of genes involved in root formation and growth. In this respect, DARS is developing novel tools for phenotyping, 4D cell imaging and targeted genome modification by the CRISPR/CAS9 technology in rice.

DDSE: The Dynamics of Diversity, Societies and Environments (DDSE) team seeks to understand the evolutionary dynamics of crop diversity. More specifically, this team studies the temporal and spatial processes in which the environment and societies, past or present, play a major role. These forces shape the evolution and diversification of species, with a major role in domestication, diffusion, selection, creation and maintenance of diversity. Thus, DDSE focuses on analyzing and understanding of rice diversity using the 3 000 rice genome resource and machine learning methods to trace back the founding events of rice varieties and to delineate introgressions between groups.

PHENOMEN: The PHEnotyping and Modelling of plants in their agro-climatic ENvironment (PhenoMEN) team aims at guiding varietal selection and crop management, to co-design agro-ecological options to increase cropping systems performances while reducing use of inputs and mitigating climate change impact. The team develops knowledge and tools (models, methods) for analyzing the genetic and environmental determinants of phenotype variability. PhenoMEN rice research focuses on understanding plant plasticity, creating phenotypic tools and designing new cropping systems. High throughput phenotyping platforms and crop models are improved and used as tools for trait dissection and G x E x M understanding. This research provides (i) climate change adaptation and mitigation strategies, (ii) plant source-sink carbon related traits contributing to grain yield formation and quality, (iii) strategies to improve rice adaptation to agro-ecological systems (crop rotations and agroforestry). These studies are validated in field in low-input rainfed rice (Madagascar, Latin America and South East Asia) and irrigated (agroecosystems (Colombia, Brazil, South East Asia, Senegal, France).

Besides these four research teams, the AGAP institute platforms for bioinformatics, (https://www.southgreen.fr) ecophysiology, cell imaging, cell engineering and gene editing propose tools, methods and resources that have been largely applied to rice.

The Biological Resource Centre GAMéT is proposing a large collection of rice accessions.