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The DADI team has as objectives:

   Using broad genetic diversity, whether natural or induced, to meet the challenges of agro-ecology.

Increasing the genetic diversity of cultivated species is a key factor in agroecology. The gene pools needed to select varieties adapted to agro-ecological management are available in cultivated and wild compartments and in related species. To this end, we are seeking to

• gain in-depth knowledge of the structure of genetic diversity, from domestication to current elite diversity,
• characterize the potential of genetic resources in wild and related compartments, 
• understand the reproductive barriers between cultivated and wild compartments and between cultivated and related species, and how to overcome them,
• master the methods for generating genetic diversity,
• develop the analytical tools needed to use this diversity (phenotyping and genotyping),
• create suitable pre-breeding material

Exploring the different plant defense mechanisms against pathogens to reduce the use of pesticides

Exploring the genetic determinants controlling quantitative resistance to multiple pathogens remains a priority. The core collections available in the unit and their genomic characterization are perennial resources of high value for investigating the question of plant resistance. How are resistance loci distributed across the genome and organized on a finer scale? Are there genetic determinants controlling several pathogens or acting as functional hubs? In this context we are conducting GWAS studies to identify the genetic determinants controlling quantitative resistance. The pests considered are oomycetes, necrotrophic and biotrophic fungi, insects, nematodes, viruses, bacteria and a phytoplasma.

Defining, characterizing and exploiting resilience

Resilience is one of the 10 fundamental elements of agroecology. To reduce the use of pesticides, we need to select varieties with multiple and sustainable resistances and tolerances. For fruit crops, our aim is to ensure that the trees maintain their production under low-input conditions over the years despite attacks and climatic hazards, i.e. their 'resilience'. This concept is used in many fields and is always closely linked to the ability to return to an initial state after a disturbance.

Varietal improvement involves translating this capacity into a selection target called an ideotype, i.e. the set of characteristics that enable adaptation to a given production method and environment. Resilient ideotypes are not defined for fruit trees and it is necessary to identify and prioritize a combination of adaptive traits that guarantee the profitability of an orchard under low-input conditions over the duration of the plantation.

Exploring the determinants of quality and benefiting from G×E×M interactions to increase the adaptation of varieties to multiple abiotic stresses and climatic hazards

The genotype-environment interaction (G×E, in the broad sense, i.e. including the practical aspect in E) is one of the main sources of variability in plants. This interaction is the result of complex biological mechanisms involving several levels of plant organization. We are dissecting the G×E interactions to understand the relationships between genotype and phenotype, and thus identify new avenues for creating varieties adapted to specific environmental conditions.

The aim is therefore to identify the determinants of production and quality under stress conditions and to analyze the impact of environmental changes on these determinants.

• Studying the impact of heat, water and salt stresses and low nitrogen nutrition in tomatoes;
• Taking environmental conditions into account when analyzing trials and understanding environmental impacts in order to define environmental co-variables and/or environmental scenarios to better capture the proportion of variability due to the environment and understand G×E interactions.
• Taking the advantage of ecophysiological modelling, coupled with phenomenological and genomic approaches, for the identification of new traits of interest and for predicting/simulating their response to new environmental conditions.
• Integrating multi-omics data (GWAS of metabolomic and transcriptomic traits) in the modelling of plant response.

Using genome editing to broaden the functional diversity of interest

In tomato, priority is being given to candidate genes identified using GWAS approaches for fruit quality (acid and sugar content) and important candidate genes for response to salt and nitrogen stresses. The emphasis is on technological developments (base- and especially prime-editing). However, we are initiating a new area of chromosome engineering research at the interface between the DADI and REDD teams on tomato. This involves attempting to modulate recombination in order to target the selection of traits more precisely and to limit the regions of introgression of wild species in order to avoid collateral negative traits.

The aim is to extend the application of genome editing to all species (and accessions) worked on at GAFL (melon, pepper, prunus). This will involve removing the barriers of transformation for recalcitrant accessions and species.

Developing innovative high-throughput phenotyping for new traits for agroecology

The aim is to develop high-throughput phenotyping in order to (i) increase the accuracy of trait measurement, (ii) gain access to dynamic behavior and new traits (e.g. vigor, growth, photosynthetic activity) and (iii) improve characterization of the environment in our trials.

Developing phenotype-genotype modelling to predict plant behaviour

• Physiological variables, accessible on the phenotyping platform, combined with plant and fruit development models, are used to predict how the plant functions.
• Subsequently, process-based models are used to predict major functions such as photosynthesis or the development of fruit quality.
• Combined with environmental conditions, these variables can be assembled to predict yield using crop models.
• These models can then be used for genomic prediction under a range of environmental conditions, to define ideotypes by environmental scenario.

Combining tools to increase the efficiency of prebreeding and transfer to private partners

The aim of prebreeding work is to make the results of upstream research operational, to supplement them with issues specific to the needs of the industry and then to integrate them into an impact pathway so that they can be made available to end users. They concern the characterization of genetic resources and the development of progenitors, the development of selection tests and/or markers linked to traits of interest, the deployment of multi-trait selection methods and making them available in a usable, reliable and robust format.

Six basic building blocks are an integral part of the prebreeding approach:

• Control of genetic diversity
• Genetic and molecular determination of traits of interest
• Selection methodology
• Prioritization of traits and combinations of expected traits using an ideotyping approach
• Prebreeding: optimized combination of traits and characterization methods to produce progenitors
• PreBreeding-Breeding continuum: impact and services to the industry

TEAM DADI