This study was carried out on two rabbit lines, each selected for a feed efficiency criterion (growth on restricted feed for the AlimR line or residual consumption on an ad libitum diet for the ConsR line), introduced into a facility by adoption of newborn kits by SPF (specific pathogen free) females. Following this break in symbiotic transmission, fecal samples from females were used to study the microbiota composition of the two lines over seven generations (17 females per line and per generation). The proportion of Firmicutes was significantly higher in the AlimR line than in the ConsR line (82.22 % vs 78.21 %, p < 0.0001). Conversely, the proportion of Bacteroidota was significantly higher in the ConsR line than in the AlimR line (20.38 % vs 16.50 %, p < 0.0001). The effect of generation was also significant for the abundance of Firmicutes and Bacteroidota (p = 0.0009 and p < 0.0001, respectively). The Shannon diversity index was significantly higher in the AlimR line than in the ConsR line (5.23 vs 5.14, p = 0.02). The effect of generation was also significant for the Shannon index (p = 0.003). Finally, a discriminant principal component analysis of the microbiota composition allowed us to distinguish both the two lines and the generations, in particular the 11th selected generation (animals adopted by SPF females) and the 18th generation.

Genetic connectedness between management units quantifies the extent to which estimated breeding values (EBV) can be accurately compared across management units or subpopulations. When there is a sufficient level of genetic connectedness, best linear unbiased prediction (BLUP) of EBV enables fair comparisons across these units. Genotype-by-environment (G × E) interaction can alter an individual's expression of genetic potential across environments, thereby compromising the accuracy of selection decisions. The aim of this study was to investigate the extent of genetic connectedness and G × E interaction for a maternal pig line between countries (France, China, and Thailand) for five traits: age at 100 kg (AGE), number of functional teats (NFT), birth weight (BW), backfat thickness at 100 kg (BFT), and number of piglets born alive (NBA). We observed high connectedness across the three countries, as reflected by high coefficient of determination (CD) values (ranging from 0.61 to 0.96) across all traits and time periods. For all traits, the pair France-China had higher CD values (0.80 on average) than the pair France-Thailand (0.70 on average) between 2023 and 2024. These results were in line with Fst estimates, which were 0.015 between France and China, 0.006 between France and Thailand, and 0.020 between China and Thailand, indicating that the populations in the three countries are genetically close. Genetic correlations among the countries ranged from 0.70 to 0.79 for AGE, 0.95 to 0.98 for NFT, 0.53 to 0.83 for BW, 0.81 to 0.97 for NBA, and 0.77 for BFT. Therefore, there was no evidence of G × E interaction except for BW between France and China (0.67), and BW between China and Thailand (0.53). In conclusion, we found high genetic connectedness across countries, demonstrating that animals from different countries share sufficient genetic links to enable accurate and fair across-country genetic evaluations and comparison of EBVs. No biologically significant G × E interaction was detected (except for BW), which suggests that there is no substantial reranking of animals between the countries. Therefore, a single breeding program across these countries is appropriate and effective.

The determinism of tail biting is multifactorial and complex. The general preventive measure is tail docking of piglets shortly after birth. In recent years, a number of recommendations have been issued to limit tail biting and, consequently, tail docking. However, pigs sharing the same environment show widely varying responses to this biting phenomenon. To make progress, it is necessary to deepen our understanding of the factors specific to each individual. This review looks at the genetic and biological factors-body condition, sensitivity to stress, health and microbiota-that interact with the environment to influence the expression of tail-biting. All these factors interact with the genetic predisposition of each animal to bite or have its tail bitten. Progress is expected in the measurement of animal behaviour, working on the biting-victim-neutral typology and the characterisation of their physical and social environment to reduce tail biting. The geneticsolution has not been sufficientlyexploited to reduce tail biting. The acquisition of continuous individual data at group level and in large populations over several generations is imperative to be able to assess the genetic effects linked to social interactions between pigs. Analytical models that take into account several internal factors at the same time, their evolution overtime, and the composition of the group of individuals are now available. Their use should make it possible to improve the welfare of pigs reared in groups.

Pigs in intensive production systems encounter various stressors that negatively impact their productivity and welfare. The primary aim of this study was to estimate the genetic correlations of the slope (indicator of sensitivity of the animals to environmental challenges) of the daily feed intake (DFI) across different environmental gradients (probability of the occurrence of a challenge on a given day) with growth, feed efficiency, carcass, and meat quality traits using a single-step reaction norm animal model (RNAM) in Piétrain pigs. In addition, genetic correlations of DFI (its total breeding value) with the same traits were also estimated. The probabilities of the occurrence of an unrecorded environmental challenge, inferred via a Gaussian mixture model, were taken as a reference and used in the genetic analysis as an environmental descriptor. Variance components were estimated via restricted maximum likelihood using the single-step genomic best linear unbiased prediction method, using a series of multivariate RNAM with two phenotypes (DFI and each of the traits of economic importance), with the probability of an unrecorded challenge on a given day included as an environmental descriptor for DFI only, because DFI is recorded daily but the other traits are not. Genetic correlations of the slope of DFI were 0.15 with age at 100 kg, 0.04 with backfat thickness, − 0.29 with loin muscle thickness, 0.05 with feed conversion ratio, − 0.07 with lean meat percentage, − 0.13 with pH of the ham at 24 h postmortem, 0.06 with drip loss percentage, and 0.15 with boneless ham weight. Complementary results showed that genetic correlations of DFI with other economic traits varied across the environmental gradients. Estimates of genetic correlations of DFI with other traits of economic importance varied across the environmental gradients, especially for growth rate, which suggests the presence of genotype-by-environment interactions. The slope of DFI is an indicator of sensitivity of the animals to environmental challenges. Most traits of economic importance exhibited weak genetic correlations with the slope of DFI, indicating that selection for resilience based on the environmental sensitivity (slope of DFI) can be performed without adversely affecting these other traits. Our results demonstrate the feasibility of improving resilience through genetic selection.

Le déterminisme de la morsure de queue est multifactoriel et complexe. La mesure préventive généralisée est la coupe de queue des porcelets peu après la naissance. Depuis quelques années, de nombreuses recommandations invitant à agir sur l’environnement de l’animal ont été émises pour limiter la morsure de queue et donc la caudectomie. Cependant, les porcs qui partagent le même environnement peuvent montrer des réponses largement variables vis-à-vis de ce phénomène de morsure. Pour progresser, il est nécessaire d'approfondir notre compréhension des facteurs propres à chaque individu. Cette synthèse s’intéresse aux facteurs génétiques et biologiques – l’état corporel, la sensibilité au stress, la santé et le microbiote – qui interviennent en interaction avec l’environnement sur l’expression de la caudophagie. Tous ces facteurs interagissent avec la prédisposition génétique de chaque animal à mordre ou se faire mordre la queue. Des progrès sont attendus sur la mesure du comportement des animaux, pour travailler sur la typologie mordeur-victime-neutre et la caractérisation de leur environnement physique et social. L’acquisition de données individuelles en continu au niveau du groupe et dans de grandes populations sur plusieurs générations est impérative pour pouvoir évaluer les effets génétiques liés aux interactions sociales entre les porcs. Des modèles analytiques qui tiennent compte de plusieurs facteurs internes à la fois, de leur évolution dans le temps, et de la composition du groupe d’individus sont maintenant disponibles. Leur utilisation devrait permettre d’utiliser le levier de la sélection génétique pour améliorer le bien-être des porcs élevés en groupe.

In facing the challenge of sustainability, animal breeding provides the option to improve animal robustness. In the search for new selection criteria related to robustness, the hypothalamic–pituitary–adrenocortical (HPA) axis is studied as a major neuroendocrine system involved in metabolic regulations and adaptive responses. Indeed, HPA axis activity is strongly influenced by genetic factors acting at several levels of the axis. The adrenocorticotropic hormone (ACTH) stimulation test has long been used to analyze interindividual and genetic differences in HPA axis activity in several species, including pigs. To uncover the genetic determinism of HPA activity and its influence on functional traits and robustness, a divergent selection experiment was carried out for three generations in a Large White pig population based on plasma cortisol levels measured one hour after injection of ACTH. In the present study the response to selection was very strong (confirming our previous studies), with a heritability value of cortisol level after ACTH injections reaching 0.64 (±0.03). The difference between the two divergent lines was around five genetic standard deviations after three selection steps. A genome-wide association study pointed out the importance of the glucocorticoid receptor gene (NR3C1) in this response. The measurement of plasma corticosteroid-binding globulin (CBG) binding capacity excluded any significant role of CBG in this selection process. The phenotypic effect of selection on body weight and growth rate was modest and/or inconsistent across generations. The HPA axis, a major neuroendocrine system involved in adaptation processes is highly heritable and responsive to genetic selection. The present experiment confirms the importance of glucocorticoid receptor polymorphism in genetic variation of HPA axis activity–in addition to the previously demonstrated role of CBG gene polymorphism. Further studies will explore the effect of this divergent selection on production and robustness.

Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits. We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively. We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation.

French organic pig production is very diverse. This results from differences in pig farming systems, in terms of the size of the farms, with many small farms; from differences in pork market, with a long chain well established in the west of France, and more territorialized short chains; and from the multiplicity of its actors that are specific to organic farming (OF) or mixed. Although the number of sows certified in OF has doubled between 2016 and 2021, it represents only 1.9% of the total French pig production. In view of this, the ORIGAMI consortium (INRAE-METABIO) has conducted a study to analyse the brakes and levers to the development of this production. Interviews with 21 stakeholders of the pork sector identified 164 obstacles and 231 levers. Multiple component analyses followed by a classification revealed seven types of brakes and six types of levers according to their level of organisation (from the animal to the territory) and the position within the food chain (from agri-supply to consumption). Interpretation of these typologies allows us to identify research themes to meet the main challenges. These concern the acquisition of technical references specific for OF, the deepening connection between sectors and territories, the promotion of pork product markets, but also the training of current and future actors and the communication with the general public. These topics provide research and development actors with thoughts for the construction of transdisciplinary projects.

In organic farming (AB) systems, animals may be more vulnerable because they are raised in less controlled environments. Rearing animals from breeding schemes designed for animals in conventional systems in less intensive systems may prove inadequate if they are unable to cope with fluctuations in the availability and quality of feed resources. AB specifications make little mention of breeds or lines, and current AB livestock production might suffer from a lack of suitable genetic resources. AB breeders tend to formulate genetic needs specific to their breeding systems, with a major interest in robustness, which implies that geneticists and breeders should be able to provide an offer that is different and more diversified. Few studies have focused on breeding objectives for organic farming systems, and the genetic offer desired by AB farmers is often expected of as a break with that used in conventional systems. It is necessary to rethink the use of animal selection methods for the AB context. This article presents the current state of knowledge and the genetic resources that can be mobilized to adapt animals from selected populations to organic systems.

Dans les systèmes d’élevage sous cahier des charges agriculture biologique (AB), les animaux peuvent être plus vulnérables car ils sont élevés dans des environnements moins contrôlés. Élever des animaux issus de programmes de sélection conçus pour les systèmes conventionnels dans des systèmes moins intensifs peut s’avérer inadéquat s’ils ne savent pas composer avec les fluctuations de la disponibilité et de la qualité des ressources alimentaires. Les cahiers des charges en AB font peu mention de races ou de lignées et les productions animales AB actuelles peuvent souffrir d’un manque de ressources génétiques adaptées. Les éleveurs AB tendent à formuler des besoins génétiques spécifiques à leurs systèmes d’élevage avec un intérêt majeur pour la robustesse, ce qui suppose pour les généticiens et les sélectionneurs d’être en mesure de fournir une offre somme toute différente et plus diversifiée. Peu de travaux portent sur les objectifs de sélection spécifiques au cahier des charges AB, et l’offre génétique attendue par les éleveurs concernés est souvent réfléchie en rupture avec les systèmes conventionnels. Il est nécessaire de repenser l’utilisation des méthodes de sélection animale dans le cadre de l’AB. Cet article présente l’état des connaissances et les moyens génétiques qui sont mobilisables pour adapter les animaux issus de populations sélectionnées aux systèmes biologiques.

In pig breeding, environmental challenges can affect the welfare and productivity of animals. Resilient animals have the capacity to be minimally affected by these environmental challenges. Understanding the genetic basis of sensitivity to these environmental challenges is crucial for selecting more resilient animals, thereby enhancing welfare and productivity. The aims of this study were to 1) estimate the probability of the occurrence of an unrecorded environmental challenge on a given day using daily feed intake (DFI) data and 2) evaluate the genetic determinism of environmental sensitivity in three pig lines bred in real selection conditions. Data comprised of 100,799, 186,247, and 304,826 DFI records from 1,618, 2,517, and 3,788 Landrace (LA), Large White (LW), and Pi & eacute;train (PI) male pigs, respectively. The pedigree included 3,730, 5,649, and 9,293 animals for LA, LW, and PI, respectively. The probabilities of the occurrence of an unrecorded environmental challenge on a given day were estimated via a mixture model. The probabilities (p) of being "high coefficient of variation days" were then taken as reference and used in genetic analysis as an environmental descriptor to describe the environment. DFI records were analyzed using two linear models: a linear reaction norm animal model (RNAM) and the animal model. (Co)variance components were estimated using average-information restricted maximum likelihood (AI-REML). The means of the probabilities of the occurrence of an environmental challenge for LA, LW, and PI were 0.24, 0.10, and 0.22, respectively, indicating that the probability of an environmental challenge was low for most of the days. The genetic correlations between the intercept and the slope obtained from the RNAM for LA, LW, and PI were -0.52, 0.06, and -0.36, respectively. These findings suggest that selecting hypothetically for decreased DFI in nonstressful conditions would result in pigs with increased DFI in stressful conditions in the LA and PI lines, whereas it would have a minor impact on the environmental sensitivity of LW. The proportion of resilient animals for LA, LW, and PI was 75.0, 74.2, and 72.2%, respectively, implying that most of the animals were resilient. The study demonstrated that the slope of DFI is heritable and can effectively be used as an indicator of sensitivity to environmental challenges. These results are valuable in improving the resilience of livestock species to environmental challenges through genetic selection. This study evaluated the genetic basis of pigs' sensitivity to unrecorded environmental challenges, which can be used in genetic selection to improve livestock resilience, resulting in improved welfare and productivity. Selecting resilient animals, those minimally affected by disturbances or able to quickly recover, is vital for improving pig welfare and productivity. While pigs in selection farms benefit from monitored and more stable environmental conditions, they still face potential challenges that are unrecorded and of unknown origin. Hence, resilience in pigs remains important. Using daily feed intake data, we estimated the probability of occurrence of an unrecorded environmental challenge and evaluated the genetic determinism of sensitivity to these challenges. In our study, the probability of being a stressful day was low for all the studied pig lines. Most animals in all the lines were less sensitive to environmental challenges. These results can be utilized in the genetic selection of resilient animals.

La production porcine française en AB est très diversifiée de par ses élevages, notamment en termes de taille avec de nombreux ateliers à faibles effectifs ; de par la commercialisation des produits, avec une filière longue bien implantée dans le grand ouest de la France, et des filières courtes plus territorialisées ; et de par la multiplicité de ses acteurs spécifiques à l’AB ou mixtes. Bien que le nombre de truies certifiées en AB ait doublé entre 2016 et 2021, il ne représente que 1,9 % du cheptel français. Face à ce constat, une étude a été réalisée par le consortium ORIGAMI (INRAE-Métabio) pour comprendre les freins et leviers au développement de cette production. Des entretiens de 21 porteurs de projets ont permis d’identifier 164 freins et 231 leviers. Des analyses en composantes multiples suivies d’une classification ont mis en évidence sept types de freins et six types de leviers en fonction de leur niveau d’organisation (de l’animal au territoire) et du maillon de la filière qu’ils concernent (de l’agrofourniture à la consommation). L’interprétation de ces typologies permet d’identifier des thèmes de recherche pour relever les principaux défis identifiés. Ces thèmes concernent l’acquisition de références techniques spécifiques pour l’AB, la meilleure articulation entre filières et territoires, la promotion des débouchés des produits, mais aussi la formation des acteurs actuels et futurs et la communication auprès du grand public. Ces sujets sont des pistes de réflexion pour la construction de projets transdisciplinaires de recherche ou recherche-action avec les acteurs des filières.

The present research has estimated the additive and dominance genetic variances of genic and intergenic segments for average daily gain (ADG), backfat thickness (BFT) and pH of the semimembranosus dorsi muscle (PHS). Further, the predictive performance using additive and additive dominance models in a purebred Piétrain (PB) and a crossbred (Piétrain × Large White, CB) pig population was assessed. All genomic regions contributed equally to the additive and dominance genetic variations and lead to the same predictive ability that did not improve with the inclusion of dominance genetic effect and inbreeding in the models. Using all SNPs available, additive genotypic correlations between PB and CB performances for the three traits were high and positive (> 0.83) and dominance genotypic correlation was very inaccurate. Estimates of dominance genotypic correlations between all pairs of traits in both populations were imprecise but positive for ADG-BFT in CB and BFT-PHS in PB and CB with a high probability (> 0.98). Additive and dominance genotypic correlations between BFT and PHS were of different sign in both populations, which could indicate that genes contributing to the additive genetic progress in both traits would have an antagonistic effect when used for exploiting dominance effects in planned matings.

In addition to DNA, non-genetic information, that can cause phenotypic differences between animals (microbiota, epigenetic), can be transmitted physically from one generation to the next, thus contributing to the inheritance of a trait. The path coefficients of transmission of these non-genetic inherited factors are unknown. We propose a method to estimate them from the similarity matrix between individuals. This matrix can be derived from the direct measurements of the transmitted factors. The method provided consistent estimates on simulated and real data.