Gen2Bio 2026 will feature five plenary sessions under the theme "Agriculture: Innovations for Sustainable Agriculture." These sessions will present innovative perspectives and key advances in this field, offering an in-depth overview of the sector's current challenges and opportunities.

Plants are capable of producing an immense diversity of active substances, called specialized metabolites, whose taxonomic distribution is often restricted and which play a major role in the interactions between plants and their environment. Contemporary tools in genomics and metabolomics now allow numerous research teams to explore not only the diversity and evolutionary origin of the enzymes involved in the biosynthesis of these metabolites, but also to understand how allelic variations in certain genes modulate the phytochemical profiles that underlie plant-microbe, plant-insect, and plant-plant interactions. Ultimately, this type of knowledge could guide breeding strategies that incorporate the ecological functions conferred by these metabolic traits. In this presentation, I will present the work we are carrying out within our team at IGEPP on the characterization of the genetic determinants at the origin of the variation of specialized metabolite profiles in several cultivated or wild species related to the genus Brassica (cabbage, rapeseed, mustard…), and on the search for genetic and metabolomic factors involved in resistance to different bioaggressors (phytopathogenic microorganisms, parasitic plant and phytophagous insect).

Plants are heterogeneous materials composed of organs (stem, grains, leaves, etc.), themselves made up of various tissues comprising different types of cells. Their composition, relative proportions, and arrangement are under biological control and determine their final uses by humans. In the processes of transforming these agricultural raw materials, a grinding stage is often a prerequisite for any plant processing. This leads to the dissociation of these structures and the production of powders whose properties are explained by both the material itself and the powder.^st and the processes used. Processability, whether in animal feed (e.g., forage palatability) or in human food value chains (e.g., milling, biomass biorefining), is a quality of the material to be considered and requires characterizing both the organelles and the particles derived from them. Imaging biomass and particles allows for a better understanding of dissociation processes, thanks to various complementary techniques, from the macroscopic to the microscopic scale. Particular emphasis will be placed on autofluorescence multispectral imaging, which combines structural observation with chemical information.

In physiology, the term "stress" refers to an organism's response to a threatening situation, or one perceived as such. Indeed, when faced with a threat (whether a predator or a heatwave), individuals will mount a non-specific and stereotyped response, based on the release of catecholamines (adrenaline and noradrenaline) and cortisol, allowing them to return to equilibrium. While stress generally enables survival, when the magnitude of the threat exceeds the organism's response capacity at a given moment, this adaptive system becomes exhausted, and the detrimental consequences of stress appear.

In all types of livestock farming, as in nature, animals, like humans, are subject to various threats (climatic, infectious, psychological, nutritional, etc.) which they can face by mobilizing specific skills at the individual or social group level, and/or through farming conditions that allow them to be less sensitive to them.

In this presentation, I will discuss the results of our research aimed at understanding how stress mediators modulate the immune responses of animals, particularly pigs, depending on the context (nature of the stressor, duration of exposure, age, initial state, co-exposure, etc.), before presenting field data relating to the characterization of stress levels in pigs according to rearing conditions, for, ultimately, to propose changes in farming practices aimed at promoting the health and well-being of individuals.

Plant responses to biotic stresses involve a wide variety of molecules, including regulatory proteins and hormones. Among these, small peptides are part of the defense arsenal deployed by plants when they encounter pathogens. Capable of interacting directly with microorganisms or participating in intercellular signaling via recognition by membrane receptors, these peptides are produced from protein precursors through a post-translational maturation process, which complicates their characterization based solely on genomic sequence. Only a fraction of the genes capable of encoding secreted peptides have been described, and their structural and functional diversity has been greatly underestimated. We will illustrate how approaches combining bioinformatics, transcriptomics, and peptidomics can identify novel peptides potentially useful for modulating plant responses to biotic stresses, thus opening new opportunities for more sustainable crop management.

Knowledge of the variations in the DNA sequence that constitutes an individual's genome is central to genetic research. Next-generation sequencing has transformed the fields of quantitative and evolutionary genetics by enabling the discovery and genotyping of millions of variants across the genomes of animal and plant species. This makes genome-wide association studies (GWAS) of complex traits possible, as well as studies of genetic diversity and population structure. However, resequencing or genotyping large numbers of individuals at numerous single nucleotide polymorphisms (SNPs) remains a major economic challenge for accurately identifying the genes and variants involved in determining the traits under study. Genotype imputation refers to the process of predicting genotypes that are not directly analyzed in a sample of individuals. This has become a common practice in research to increase genome coverage and thus improve the accuracy of genomic selection and the resolution of GWAS. Imputation allows for the genotyping of a large number of low-density samples at a lower cost, followed by the imputing of genotypes at higher marker densities or even at the sequence level. Two methods are used for large-scale, genome-wide SNP genotyping. DNA microarray-based methods use flanking probe sequences to interrogate pre-identified SNPs. Alternative sequencing-based genotyping methods identify SNPs directly from the genome.

In aquaculture, access from the 2010s onwards to a small number of complete genomic sequences and the development of genotyping tools at low (a few hundred to a few thousand markers), medium (a few tens of thousands of genetic markers) or high density (several hundred thousand markers) has made it possible to implement genomic selection and to improve important traits in farming, such as the quality of fish fillets or their resistance to diseases.

In this presentation, I will discuss the research we are conducting at INRAE's GABI unit to develop genotyping tools and identify the regions of the genome involved in variations of traits of interest in trout farming. I will illustrate in particular how we have constructed a high-density DNA microarray and how we use it to detect, at a lower cost, genes associated with resistance to major biotic (bacteria, viruses) and abiotic (hypoxia, temperature) stresses in salmonids. I will also demonstrate the use of whole-genome resequencing to identify minor genetic determinants of sex in rainbow trout.