The agroecological transition of agriculture is slow despite the wealth of knowledge produced to support it. Given the complexity and uncertainty of changing situations, the deterministic approach aimed at defining ideal transition pathways to speed up the transition seems fruitless to us. Our view is that paths are made by walking, tracing a singular route that depends on the surprises that arise. However, actors are currently not equipped to march into the unknown, a march toward greater sustainability. The challenge is to equip actors to implement agroecological principles in local, changing, complex, and uncertain situations. To this end, we propose 10 principles drawn from an argued review of pragmatic philosophy and formulated on the basis of 16 years’ experience in participatory research with French farmers in agroecological transition in the Roquefort area. Pragmatic philosophy is a theory of action rooted in a democratic ideal. It offers a universal, normative and coherent framework for conducting individual, and collective inquiries to establish what is possible, what works, and what is desirable in a situation of change. The 10 pragmatic principles we propose will enable farmers, intermediaries and consumers to create sustainable production and consumption practices. They will also be useful for those who accompany them in the transition, such as advisors, researchers, sales representatives, and employees of local authorities. Pragmatism represents a paradigm shift away from the project logic and planning that currently dominate change management. Such a shift must be accompanied by in-depth education to develop the collective skills needed to envision that another world is possible, to manage complexity and uncertainty, by being able to deliberate democratically and cooperate in action.

Genetic defects that occur naturally in livestock species provide valuable models for investigating the molecular mechanisms underlying rare human diseases. Livestock breeds are subject to the regular emergence of recessive genetic defects due to genetic drift and recent inbreeding. At the same time, their large population sizes provide easy access to case and control individuals and to massive amounts of pedigree, genomic and phenotypic information recorded for management and selection purposes. In this study, we investigated a lethal form of recessive chondrodysplasia observed in 21 stillborn calves of the Aubrac beef cattle breed. Detailed examinations of three affected calves revealed proximal limb shortening, epiphyseal calcific deposits, and other pathological signs consistent with human rhizomelic chondrodysplasia punctata, a rare peroxisomal disorder caused by recessive variants in one of five genes (AGPS, FAR1, GNPAT, PEX5, and PEX7). Using homozygosity mapping, whole genome sequencing of two affected individuals, and filtering for variants found in 1867 control genomes, we reduced the list of candidate variants to a single deep intronic substitution in GNPAT (NC_037355.1:g.4039268G > A on chromosome 28 of the ARS-UCD1.2 bovine genome assembly). For verification, we performed large-scale genotyping of this variant using a custom SNP array and found a perfect genotype–phenotype correlation in 21 cases and 26 of their parents, and a complete absence of homozygotes in 1195 unaffected Aubrac controls. The g.4039268A allele segregated at a frequency of 2.6

The need to integrate more clearly societal expectations on livestock farming has led the authors of this article to consider that livestock farming systems must be redesigned to position health and welfare at the heart of their objectives. This article proposes a vision of the advances in knowledge required at different scales to contribute to this transformation. After defining health and welfare of animals, the article emphasizes the need to consider health in a broader perspective, to deepen the question of positive emotional experiences regarding welfare, and raises the question of how to assess these two elements on farms. The positive interactions between health and welfare are presented. Some possible tensions between them are also discussed, in particular when improving welfare by providing a more stimulating and richer environment such as access to outdoor increases the risk of infectious diseases. Jointly improving health and welfare of animals poses a number of questions at various scales, from the animal level to the production chain. At the animal level, the authors highlight the need to explore: the long-term links between better welfare and physiological balance, the role of microbiota, the psycho-neuro-endocrine mechanisms linking positive mental state and health, and the trade-off between the physiological functions of production, reproduction and immunity. At the farm level, in addition to studying the relationships at the group level between welfare, health and production, the paper supports the idea of co-constructing innovative systems with livestock farmers, as well as analyzing the cost, acceptability and impact of improved systems on their working conditions and well-being. At the production chain or territory levels, various questions are raised. These include: studying the best strategies to improve animal health and welfare while preserving economic viability, the labelling of products and the consumers’ willingness to pay, the consequences of heterogeneity in animal traits on the processing of animal products, and the spatial distribution of livestock farming and the organization of the production and value chain. At the level of the citizen and consumer, one of the challenges is to better inter-relate sanitary and health perspectives on the one hand, and welfare concerns on the other hand. There is also a need to improve citizens' knowledge on livestock farming, and to develop more intense and constructive exchanges between livestock farmers, the livestock industry and citizens. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research.

This paper presents the work and research to be conducted to place health and welfare at the heart of the agroecological transition of livestock systems. It highlights the need to consider health in a broader perspective than today and the question of positive emotional experiences in terms of welfare. The positive interactions between health and welfare as well as the possible tensions between these two dimensions are discussed. The joint improvement of animal health and welfare raises questions at different scales. At the animal level, the trade-offs between the physiological functions of production, reproduction and immunity, the role of the microbiota as well as the psycho-neuro-endocrine mechanisms that link mental state and health need to be explored. At the farm level, it would be appropriate to consider the expertise of breeders and to assess the effect of changes in practices on their well-being at work. On production chain and territory levels strategies to improve animal health and welfare while preserving economic viability are to be studied, such as the possibility of labeling, consumers' willingness to pay, the consequences of the phenotypic heterogeneity of animals for the processing of products and the spatial distribution of farms. On the citizens level, a challenge is to better link their concerns regarding animal welfare and health. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research.

Cet article présente les travaux et les recherches à conduire pour placer la santé et le bien-être au cœur de la transition agroécologique des systèmes d’élevage. Il souligne la nécessité de considérer la santé dans une perspective plus large qu’aujourd’hui et la question des expériences émotionnelles positives en matière de bien-être. Les interactions positives entre santé et bien-être mais aussi les tensions possibles entre ces deux dimensions sont discutées. L'amélioration conjointe de la santé et du bien-être des animaux pose des questions à différentes échelles. Au niveau de l'animal, sont à explorer les compromis entre les fonctions physiologiques de production, de reproduction et d'immunité, le rôle du microbiote ainsi que les mécanismes psycho-neuro-endocriniens qui relient l'état mental et la santé. Au niveau de l'exploitation, il conviendrait de considérer l’expertise des éleveurs et d’évaluer l’effet des changements de pratiques sur leur bien-être au travail. Au niveau de la filière de production comme du territoire, les stratégies pour améliorer la santé et le bien-être des animaux tout en préservant la viabilité économique sont à étudier, comme la possibilité d’étiquetage et de labellisation des produits, le consentement à payer des consommateurs, les conséquences de l'hétérogénéité phénotypique des animaux pour la transformation des produits et la répartition spatiale des exploitations. Au niveau des citoyens, un défi consiste à mieux relier leurs préoccupations en matière de bien-être des animaux et de santé. Ces nombreuses questions plaident en faveur d'une approche interdisciplinaire et transdisciplinaire sur de nombreux sujets, associant l’ensemble des acteurs, y compris les décideurs publics, dans une démarche de recherche participative.

L’agroécologie est un concept dynamique, dont le périmètre et les définitions ont évolué au cours du temps. Dans son acception la plus récente, l’agroécologie se définit comme « l’écologie des systèmes alimentaires durables ». Elle vise à promouvoir des systèmes viables, respectueux des animaux, des humains et de leur environnement, à les transformer en s’attaquant aux causes profondes des problèmes et en apportant des solutions globales et de long terme fondées sur la co-création de connaissances, le partage et l’innovation. Elle est à la fois une science, un ensemble de pratiques et un mouvement social, ces trois éléments étant indispensables pour créer la dynamique nécessaire à la transformation des systèmes. La transition agroécologique mobilise un ensemble de principes. Treize ont été définis à l’échelle des systèmes alimentaires globalement. Un sous-ensemble de ces principes peut être mis en œuvre pour penser l’évolution des systèmes d’élevage spécifiquement : 1) réaliser une gestion intégrée de la santé animale ; 2) potentialiser l’utilisation des ressources naturelles et des coproduits pour diminuer les intrants nécessaires à la production ; 3) optimiser le fonctionnement métabolique des systèmes et réduire les pollutions ; 4) gérer la diversité des ressources et la complémentarité des animaux pour renforcer la résilience des systèmes d’élevage ; 5) adapter les pratiques d’élevage de manière à préserver la biodiversité et à assurer les services écosystémiques associés.

Les systèmes agricoles et alimentaires ont connu de profondes transformations durant les dernières décennies dans l’ensemble des pays industrialisés. Les territoires et exploitations agricoles se sont fortement spécialisés. L’usage d’intrants de différentes natures s’est intensifié. La part des produits animaux et des produits ultra-transformés dans nos assiettes a fortement augmenté. Cette dynamique de « modernisation » a induit une augmentation de la productivité des systèmes agricoles, permettant de réduire, puis de maintenir, la part de l’alimentation dans le budget des ménages. Mais les coûts associés à ces systèmes alimentaires sont très importants. L’alimentation représente aujourd’hui le quart des émissions de gaz à effet de serre dans notre pays. Le modèle de développement agricole « productiviste » adopté depuis plus d’un demi-siècle est à l’origine de perturbations majeures des cycles de l’azote, du phosphore, de l’eau. Il a fortement contribué à l’effondrement massif et brutal de la biodiversité, à la dégradation importante de la santé des sols. Par ailleurs, la part de valeur ajoutée captée par les agriculteurs n’a cessé de s’éroder au cours du temps. La durabilité sociale et économique d’un nombre important d’exploitations agricoles est aujourd’hui menacée. Face à ce constat, une transformation importante de nos systèmes agricoles et alimentaires doit être envisagée. L’agroécologie offre un cadre pertinent pour penser et mettre en œuvre cette transformation.

Industrial livestock systems faces a major crisis of legitimacy and animal breeding contributes to this situation. Worldwide, breeding goals focus on economic performance and rarely consider the environmental and social impacts. Agroecology offers a conceptual framework to think alternative solutions to face this crisis and to guide the transition of livestock farming towards nature-based systems. Animal genetics, as an essential component of animal husbandry, should contribute to this evolution. Based on the agroecological principles applied to animal farming and the efficiency-substitution-redesign (ESR) framework, we showed that animal breeding mainly focused on the E-S levels of the ESR framework and few on the redesign of animal farming. We then present some perspectives for the redesign of breeding goals, the use of the G×E interaction information in the evaluation of animals, and the benefits of managing the available genetic diversity of livestock species to fit to the needs of nature-inclusive systems.

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub-species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the "hybrid" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 "outliers" (3.6%), for which the proportion of the genome of "domestic" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of "wild" origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.

Depuis les débuts de la domestication, les humains ont cherché à améliorer les animaux avec lesquels ils vivent, travaillent, et dont ils font commerce. Restée empirique pendant des millénaires et devenue méthodique au XVIIIe siècle, cette activité bénéficie des apports scientifiques de la génétique depuis le milieu du XXe siècle. Cela a entraîné des évolutions spectaculaires de la morphologie, du comportement et de la physiologie des animaux, sur des pas de temps de plus en plus courts. L’intensification de la sélection dans les dernières décennies a répondu aux attentes des filières mais au prix d’évolutions non désirées, comme une certaine dégradation des aptitudes fonctionnelles. Les questions qui se posent au secteur de la sélection animale concernent (i) la préservation de la biodiversité domestique ; (ii) les objectifs de sélection, en lien avec les conditions environnementales et les types de systèmes que l’on souhaite promouvoir, et les limites à poser à la modification du vivant ; (iii) les outils et méthodes à employer ; (iv) la place respective des différents opérateurs. Les réponses relèvent moins de choix techniques que de choix de société.

The "genetic purity" of French wild boar populations has been monitored since the 1980s based on a cytogenetic difference between wild boars and domestic pigs (36 and 38 chromosomes, respectively). This difference makes it possible to identify any boar with 37 or 38 chromosomes as "hybrid", without however being able to determine the origin (recent or ancient) of the hybridization, nor guarantee the "purity" of an animal with 36 chromosomes. Analysis of results of more than 4,600 tests performed over the last 12 years reveals an average "hybrid" rate of 15.8%, with high variability between populations. To analyse hybridization in greater detail and overcome inherent limitations of the cytogenetic approach, 362 wild boars recently collected in different regions of France were genotyped on a 70K SNP (GeneSeek GGP Porcine HD) chip. This study showed that for 96.4% of the wild boars analysed, includingmost of those with 37 or 38 chromosomes, the percentage of the genome of "domestic pig" origin varied from 0 to 18%. This suggests that hybridization is a fairly common phenomenon but of moderate intensity, and often ancient. Nevertheless, higher rates of hybridization have been observed in some regions such as Ard{\`e}che, and several cases of recent hybridization with domestic pigs were found in 3.6% of the wild boars analysed, most of them with pigs of Asian origin.

Carriers of balanced constitutional reciprocal translocations usually present a normal phenotype, but often show reproductive disorders. For the first time in pigs, we analyzed the meiotic process of an autosome–autosome translocation associated with azoospermia. Meiotic process analysis revealed the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body. Additionally, γH2AX signals were observed on apparently synapsed autosomes other than the SSC1 or SSC15, as previously observed in Ataxia with oculomotor apraxia type 2 patients or knock-out mice for the Senataxin gene. Gene expression showed a downregulation of genes selected on chromosomes 1 and 15, but no upregulation of SSCX genes. We hypothesized that the total meiotic arrest observed in this boar might be due to the silencing of crucial autosomal genes by the mechanism referred to as meiotic silencing of unsynapsed chromatin (MSUC).