Our divisions and teams
Bertrand Servin
TeamsBertrand Servin
Laurence Lamothe
TeamsDavi Savietto
Annabelle Meynadier
Ingrid David
TeamsDominique Hazard
Catherine Larzul
Martin Beaumont
TeamsChristelle Knudsen
Stéphane Fabre
Sylvain Foissac
TeamsAlain Pinton
Guillaume Devailly
Kamila Canale-Tabet
Diversity and selection
Genomic tools (genotyping chips, sequencing) enable large-scale characterization of the genetic diversity of animal populations. The Diversity and Selection division develops research to understand how this diversity was historically established, to promote its future conservation, and to characterize its influence on the response to the selection of increasingly varied phenotypes.
Thus, part of our work focuses on characterizing the structure of population diversity, from a global scale (worldwide and continental diversity) to delimited scales (national and regional breeds, herds). We aim to understand how the evolutionary history of populations (demography, domestication, geo-climatic adaptation, agricultural selection) has led to the diversity observed today.
We also contribute to optimizing the genetic improvement of animal populations through research aimed at finely describing the contributions of genetic diversity to phenotypic variability (the genetic architecture of traits) and predicting the response to selection. In a context of rapidly changing farming conditions, due to climate change and the agroecological transition, we aim to develop methods that allow to conserve and enhance the genetic diversity of populations to promote their resilience.
Keywords: Quantitative genetics; Population genomics; Evolutionary genetics; Statistics; Selection; Conservation; Population management; Genetic evaluation; Genetic diversity; Recombination.
The CHAMADE team develops methodological research for the statistical analysis of genetic and genomic data to understand the links between genetic diversity and the evolution of animal populations. To achieve this, we heavily rely on data from genetic improvement programs and research programs (experimental lines, diversity panels, etc.) provided by our professional and academic partners.
The team conducts population genomics research to reconstruct the evolutionary history of domestic animal species. This involves developing and applying models to analyze large genomic data sets to describe domestication, continental colonization, hybridization with wild species, and the genes involved in responses to natural and artificial selection.
The team also undertakes quantitative genetics research to build statistical models of the genetic architecture of traits and their interactions with the environment. This work aims to better predict the genetic characteristics of individuals, thereby improving genetic selection in livestock species.
Finally, we combine these two approaches to understand the evolution of complex traits and their genetic architecture in the context of populations under selection by modeling the evolution of genetic diversity in response to polygenic selection.
You can access all the highlights of this division, classified by year, by following this link.
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Design and assessment of farming practices and systems
Agricultural systems, including farming systems, must contribute to meeting the challenge of a more sustainable food supply and to better satisfying societal demands, particularly those concerning animal welfare. In this context, the aim of our work is to contribute to the design of farming systems and practices based on the principles of agroecology, and to propose management tools. Our objectives are to evaluate, understand and even predict the influence of the living environment, animal management and feeding practices on production performance, animal health, behavior and mental states, and/or on the sustainability of farming systems. Our study models are ruminants, pigs and rabbits, with levels of analysis ranging from the individual animal (including its microbiota) to the agroecosystem.
Our scientific disciplines are nutrition, ethology and animal physiology, veterinary science and systemic zootechnics. The division 2 brings together staff from INRAE, ENVT, AgroToulouse and EI Purpan, mainly attached to the Animal Physiology and Livestock Systems or Animal Genetics division.
Keywords: Digestive microbiota; Biomarkers; Animal behavior; Animal cognition; Emotions; Animal welfare; Animal health; Animal nutrition; Feed efficiency; Product quality; Resources; Grazing; Living environment; Agroecology; Farming practices; Environmental impact; Sustainable farming systems; Crop-livestock integration; Agroforestry.
The scientific project of SYSÆ aims to contribute to the design of livestock farming systems based on the principles of agroecology. Our research activities cover levels of analysis ranging from the animal (rabbits and sheep) to the agroecosystem.
At the animal level, our research aims to understand the influence of the environment on animal welfare: health, behaviour, positive mental states, etc. To this end, our work focuses on the comprehension and promotion of cognitive processes in animals (perception, memory, learning) and the development of welfare indicators.
At the agroecosystem level, we evaluate the services of provisioning, regulation and support. These different ecosystem services are assessed in innovative systems: crop-livestock integration (e.g. grasslands and herbivores) or agroforestry (arboriculture and livestock).
We also consider societal demand and the farmer's personal aspirations and professional goals in designing innovative systems.
Our research involves innovative design workshops and participatory approaches, as well as experiments with animals in experimental units and on farms. We use multi-criteria evaluation, modelling tools as well as serious games.
In order to support the transition of livestock farming towards multi-efficient and sustainable systems in a context of climate change, the PILOTE team (piloting the holobiont for the transition of livestock farming) proposes to invest in 4 major fields of application:
Its aim is to provide tools for assessing and improving these 4 areas, which also ccorrespond to the one-health concept.
To meet this objective, our team is interested in the animal and its digestive microbiota, defined as the holobiont, and the effect of alternative and innovative practices on it. The two areas developed by the team are:
The PILOTE team consits of INRAE researchers and teacher-researchers from Toulouse's leading agro-veterinary schools (EIPurpan, AgroToulouse, ENVT), supported by laboratory staff with expertise in molecular biology and chemistry analyses.
You can access all the highlights of this division, classified by year, by following this link.
Savietto, D., Fillon, V., Temple-Boyer--Dury, A., Derbez, F., Aymard, P., Pujol, S., Rodriguez, A., Borne, S., Simon, S., Grillot, M., Lhoste, E., Dufils, A., Drusch, S. 2023. Design of a functional organic agroforestry system associating rabbits and apple trees. Animal - Open Space, 2, 100051. ⟨10.1016/j.anopes.2023.100051⟩. ⟨hal-04224414⟩
Fetiveau, M., Savietto, D., Janczak, A.M., Bannelier C., Plagnet A-S., Tauveron M., Fortun-Lamothe, L. 2023. Time budget of two rabbit genotypes having access to different-sized pasture areas. Applied Animal Behaviour Science, 260, 105872. ⟨10.1016/j.applanim.2023.105872⟩. ⟨hal-04123096⟩
Fortun-Lamothe, L., Collin, A., Combes, S., Ferchaud, S., Germain, K., Guilloteau, L., Gunia, M., Lefloc’h, N., Manoli, C., Montagne, L., Savietto, D. 2023. Principes, cadre d'analyse et leviers d'action à l’échelle de l’élevage pour une gestion intégrée de la santé chez les animaux monogastriques. INRAE Productions Animales, 35 (4), 307-326. ⟨10.20870/productions-animales.2022.35.4.7225⟩. ⟨hal-03947496⟩
Gidenne, T., Savietto, D., Fortun-Lamothe L., Huang Y. 2022. Cuniculture au pâturage et sous certification agriculture biologique en France : fonctionnement des systèmes, performances et règlementation. INRAE Productions Animales, 35 (3), 201-216. ⟨10.20870/productions-animales.2022.35.3.7257⟩. ⟨hal-03948372⟩
Leterrier C., Petit, O., Fillon, V. 2022. Améliorer le bien-être des animaux d'élevages intensifs, est-ce vraiment possible ? France-Inter. La Terre au carré. ⟨ Podcast⟩
Fetiveau, M., Savietto, D., Gidenne, T., Pujol, S., Aymard, P., Fortun-Lamothe, L. 2021. Effect of access to outdoor grazing and stocking density on space and pasture use, behaviour, reactivity, and growth traits of weaned rabbits. Animal, 15 (9), 100334. ⟨10.1016/j.animal.2021.100334⟩. ⟨hal-03365288⟩
Tiphaine Blanchard, Quentin Le Graverand, Annabelle Meynadier. 2024. Le rumen : un atout pour la transition agroécologique et un levier pour la gestion intégréede la santé des élevages de ruminants. NPV élevages & santé | n° 54 | Volume 15. ⟨10.1051/npvelsa/2024011⟩
Enjalbert Francis , Zened Asma , Cauquil Laurent , Meynadier Annabelle. 2023. Integrating data from spontaneous and induced trans-10 shift of ruminal biohydrogenation reveals discriminant bacterial community changes at the OTU level. Frontiers in Microbiology. ⟨10.3389/fmicb.2022.1012341⟩. ⟨hal-04029019⟩
Mozduri Zohre, Lo Bara, Marty-Gasset Nathalie, Masoudi Ali Akbar, Arroyo Julien, Morisson Mireille, Canlet Cécile, Bonnet Agnès, Bonnefont Cécile. 2021. Application of Metabolomics to Identify Hepatic Biomarkers of Foie Gras Qualities in Duck. Frontiers in Physiology. ⟨10.3389/fphys.2021.694809⟩. ⟨hal-03285768⟩
Lisanne M G Verschuren, Mario P L Calus, Alfons J M Jansman, Rob Bergsma, Egbert F Knol, Hélène Gilbert, Olivier Zemb. 2018. Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex. Journal of Animal Science, Volume 96, Issue 4, April 2018, Pages 1405–1418. ⟨10.1093/jas/sky060⟩. ⟨hal-02626161⟩
Genetics for multi-performance
Agricultural production systems, including livestock systems, are faced with the constraints imposed by climate change and new societal demands. In this context, our research explores genetic levers for adapting populations to new economic, environmental and social performance requirements for small ruminants, pigs and rabbits.
Our quantitative genetics work focuses on the study of new traits to be improved and on new selection strategies to be implemented in order to embark on the agro-ecological transition and contribute to mitigating the impact of livestock farming on the environment. To this end, we study different scales (animal, batch, herd, breeding, system, etc.), with a particular focus on the interactions and interrelationships that exist within them, and their evolutionary dynamics over time.
Keywords: Genetic improvement, Quantitative genetics, Sheep, Goats, Pigs, Rabbits.
Studies developed in the team MAGE is organized through 3 mains axes:
Three axes are developed taking into account, at the animal scale, economic, environmental and social components of sustainability.
The SESAME team's research focuses on the modeling and design of new selection strategies for adapting animal populations to changes in breeding conditions under the influence of climate change and social expectations.
Selecting for multi-performance means integrating a multitude of traits into a selection objective to meet economic, environmental and social expectations.
We are interested in multi-trait integration models, exploring the modalities of selection, at animal level, on compromises and parsimonious selection, or at system level on modular selection modalities, selection for different scales taking into account emergence properties. We are initiating research into the non-additive construction of multi-criteria selection objectives. We aim to develop dynamic selection strategies adapted to the diversity and future evolution of production systems. We are interested in non-additive transmission mechanisms, in particular genotype x environment interactions, and are refining transmissibility models.
You can access all the highlights of this division, classified by year, by following this link.
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Interactions in traits development
The goal of our work is to acquire knowledge useful for controlling the early development of animals, their health and their adaptability to the environment. Our strategy is based on understanding the biological interactions involved in the construction, variability and transmission of traits of interest. In particular, we study interactions within and between genomes and epigenomes, as well as between the microbiota and the intestinal barrier. These phenomena are deciphered considering interactions with environmental factors such as diet and climate. Our disciplines include molecular genetics, epigenetics, bioinformatics, animal physiology, immunology and microbiology.
The two teams in division 4 are affiliated to the INRAE departments Animal Genetics (GENESIS) and Animal Physiology and Livestock Systems (MUSE).
Keywords: Early development; Health; Gut barrier; Environmental adaptation; Nutrition; Microbiota; Metabolites; Genetics; Epigenetics; Metagenomics; Variability; Multi-generational transmission; Maternal effects.
The work of the MUSE (Microbiota, Nutrition and Gut Health) team focuses on preserving the health of young farm animals (pig and rabbit models), which are particularly susceptible to digestive disorders. The intestinal barrier function is immature at birth, and plastic during the postnatal period. Nutritional and non-nutritional compounds ingested during the postnatal period may therefore play a critical role in the maturation of this barrier.
The work of the MUSE team aims to understand and optimize the postnatal development of all components of the intestinal barrier function, namely the microbiota, epithelium and immune cells, and their interactions. Our strategy is based on early-life nutrition as a lever to strengthen the intestinal barrier, in particular via the metabolites derived from the microbial degradation of nutrients. The team's work focuses both on the impact of milk constituents (oligosaccharides, immunoglobulin A) or solid foods (fibers, polyphenols, etc.) and on the temporality in the succession of food intakes (beginning of solid food intake, end of milk intake).
To achieve these objectives, and to study the effects of diet on the microbiota and its metabolites, as well as on the intestinal mucosa, the MUSE team uses a combination of in vivo and in vitro approaches (culture of commensal bacteria, intestinal organoids, primary culture of intestinal immune cells). Bacteria from the microbiota and host cells are studied using high-throughput techniques (metagenomics, metabolomics, transcriptomics), molecular biology (bacterial genetic engineering) and biochemistry. These laboratory approaches are combined with a strong expertise in bioinformatics and biostatistics, based on the development of tools adapted to the changes in sequencing technologies, such as FROGS and metagWGS.
The GENESIS team is interested in the molecular determinants of phenotypic variability in livestock species, monogastrics and small ruminants, and their transmission between generations, for traits of agronomic interest, particularly in relation to health, well-being and adaptation to environmental conditions.
We develop our research around three main axes:
You can access all the highlights of this division, classified by year, by following this link.
Demars J, Labrune Y, Iannuccelli N, Deshayes A, Leroux S, Gilbert H, Aymard P, Benitez F, Riquet J. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities. Genomics. 2022 May;114(3):110361. ⟨10.1016/j.ygeno.2022.110361⟩. Epub 2022 Apr 1. ⟨hal-03665709⟩
Hazard D, Plisson-Petit F, Moreno-Romieux C, Fabre S, Drouilhet L. Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep. Front Genet. 2020 Dec 23;11:616960. ⟨10.3389/fgene.2020.616960⟩. eCollection 2020. ⟨hal-03137552⟩
Leroux S, Gourichon D, Leterrier C, Labrune Y, Coustham V, Rivière S, Zerjal T, Coville JL, Morisson M, Minvielle F, Pitel F. Embryonic environment and transgenerational effects in quail. Genet Sel Evol. 2017 Jan 26;49(1):14. ⟨10.1186/s12711-017-0292-7⟩. ⟨hal-01479143⟩
Mussard E, Lencina C, Gallo L, Barilly C, Poli M, Feve K, Albin M, Cauquil L, Knudsen C, Achard C, Devailly G, Soler L, Combes S, Beaumont M. The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids. Front Cell Dev Biol. 2022 Aug 29;10:983031. ⟨10.3389/fcell.2022.983031⟩. eCollection 2022. ⟨hal-03788364⟩
Paës C, Gidenne T, Bébin K, Duperray J, Gohier C, Guené-Grand E, Rebours G, Barilly C, Gabinaud B, Cauquil L, Castinel A, Pascal G, Darbot V, Aymard P, Debrusse AM, Beaumont M, Combes S. Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions. mSystems. 2022 Jun 28;7(3):e0024322. ⟨10.1128/msystems.00243-22⟩. Epub 2022 Jun 8. ⟨hal-03699002⟩
Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics. 2018 Apr 15;34(8):1287-1294. ⟨10.1093/bioinformatics/btx791⟩. ⟨hal-02626808⟩
Structural and functional genomics
Within the cell nucleus, an animal's genome holds all the genetic information that defines the organism and its species. Fundamental and complex mechanisms, like DNA replication or gene expression for instance, drive the genome's function and underpin all life on Earth.
To understand how the genome works, we meticulously examine (1) its linear organization, including its DNA sequence and the positions of functional elements along the chromosomes, (2) its three-dimensional structure, including DNA loops and chromatin compartments, and (3) the dynamic interactions between these players in relation with gene expression.
In this context, we harness high-throughput "omics" data generation and analysis, employing comparative and integrative approaches within a highly interdisciplinary and multi-species framework.
Keywords: Sequencing; Annotation; Structural variations; Pangenomics; Diversity; Polymorphism; Genic expression; Transcriptomics; Epigenetics; Metabolomics; Molecular and cellular genomics; Comparative genomics; Bioinformatics; Omics data analysis; 3D genomics; Chromosomes.
The GENOME3D team studies the 3D organization of the genome within the nucleus. Our work specifically focuses on this organization in livestock species. The folding of chromosomes into active and inactive nuclear compartments and DNA loops allows the compaction of the long DNA fiber within the nucleus and plays a crucial role in genome function, particularly its expression. We aim to understand the molecular mechanisms involved in chromosome folding and how the 3D organization of chromatin affects genome function.
A significant part of our work is dedicated to the question of individual variability in this organization and its conservation across species. We are developing several research projects on the impact of structural variability on 3D organization and its potential consequences on genome function. This involves the characterization of structural variants in populations (using bioinformatics and cytogenetic approaches), constructing Hi-C maps for animals carrying these variants, and functional studies of the observed modifications using dedicated methods (ChIPseq, RNAseq, RCMC, 3D FISH). We are also conducting computational approaches to characterize the structural variability in populations (construction of pangenome graphs).
The REGLISS team is interested in the regulation of animal gene expression by analysing "-omics" data associated with biological variations of interest. We study several types of genes (protein-coding, short or long non-coding RNA, circular RNA, retrogenes), several mechanisms of regulation (tissue-specific or developmental expression, genetic control of gene expression, regulation by DNA methylation, distal regulatory elements), in several tissues (muscle, digestive tissues, blood) and species of interest (pigs, small ruminants, rabbits).
Our aim is to move from descriptive approaches of gene annotation and expression to a functional approaches, establishing causal regulatory links. A bit like moving from the "anatomy" to the "physiology" of the genome. To achieve this, we employ both whole-genome and targeted approaches, comparing several conditions, races, species, or experimentally triggering perturbations in cell models.
The BeeGees team works on genome diversity with a focus on the honey bee Apis mellifera. Our interest is on specific features of the genome and the study of Apis mellifera populations used for honey production. From a genomics point of view, specific interests of the model are the small genome size (228 Mb), enabling low-cost sequencing, and the fact that males (drones) are haploid, allowing direct access to phased data and facilitating the study of long tandem repeat elements.
In continuation of our past work, we are still obtaining high quality reference genomes from different subspecies, including for French native black bee Apis mellifera mellifera, as well as performing genome-wide population genomics studies of honey bee populations used by French and non-French beekeepers. The team contributes to different breeding programs for resistance against the parasitic mite Varroa destructor or for improving honey bee resilience to climate change.
Current and future work focuses on two main axes: :
You can access all the highlights of this division, classified by year, by following this link.
Sonia Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, et al.. The black honey bee genome: insights on specific structural elements and a first step towards pan-genomes. 2024. ⟨hal-04473386⟩
Guillaume Devailly, Katia Feve, Safia Saci, Julien Sarry, Sophie Valière, et al.. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles. Physiological Genomics, 2024, ⟨10.1152/physiolgenomics.00123.2023⟩. ⟨hal-04528954⟩
Cyril Kurylo, Cervin Guyomar, Sylvain Foissac, Sarah Djebali. TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data. NAR Genomics and Bioinformatics, 2023, 5 (4), pp.lqad089. ⟨10.1093/nargab/lqad089⟩. ⟨hal-04278708⟩
Jeanlin Jourdain, Harmonie Barasc, Thomas Faraut, Anne Calgaro, Nathalie Bonnet, et al.. Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets. Genome Research, 2023, 33 (6), pp.957-971. ⟨10.1101/gr.277787.123⟩. ⟨hal-04170739⟩
David Wragg, Sonia Eynard, Benjamin B. Basso, Kamila Canale-Tabet, Emmanuelle Labarthe, et al.. Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones. Molecular Ecology Resources, 2022, 22 (8), pp.3068-3086. ⟨10.1111/1755-0998.13665⟩. ⟨hal-03807491⟩
Nicolas Mary, Nathalie Iannuccelli, Geoffrey Petit, Nathalie Bonnet, Alain Pinton, et al.. Genome‐wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig. Evolutionary Applications, 2022, 15 (7), pp.1115-1128. ⟨10.1111/eva.13432⟩. ⟨hal-03740011⟩