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Transgenerational response to an endocrine disruptor ingestion: phenotypic, genetic and epigenetic analyses in quail
No full textInternational audienceTypical prediction of an offspring’s phenotype usually focuses on the inheritance of parental alleles. However, variations across generations can also result from the transmission of non-genetic factors. Epigenetic marks such as DNA methylation offer a dynamic molecular signature of an individual’s history, as they can carry the memory of the individual’s environmental past, and probably of its ancestors. In this study, we aim to analyze in quail (Coturnix japonica) the impact of an initial supplementation with an endocrine disruptor, the genistein, on the phenotypes and epigenotypes of subsequent generations. To better disentangle the complex interplay between genetic and epigenetic effects, we designed a “mirror” breeding plan to ensure a balanced genetic structure between the group of animals issued from the treated ancestors (called epiline +) and the control group (epiline -). By recording multiple phenotypes (growth, breeding, production, behaviour) across three generations, and performing Reduced Representation Bisulfite Sequencing on blood samples for 1344 individuals, our goal is to investigate the transgenerational inheritance of an environmental effect through changes in DNA methylation profiles. Here we present the preliminary results obtained from phenotypic analysis (analysed with multiple linear regression and GLMM) and RRBS data (analysed with classical tools: BISCUIT, TrimGalore, DSS). Phenotypic analyses have shown multi and transgenerational effects for several phenotypes of interest including body weight. We are now looking to identify methylated patterns linked to phenotypic changes between generations and between groups.Funding: Région Occitanie, INRAE Animal Genetics Division, GEroNIMO (H2020 GA No 101000236)
Editorial: Emerging methodologies in genotype-phenotype models for crop improvement
No full textInternational audienceEmerging methodologies in genotype-phenotype models for crop improvementThe Research Topic on genotype-phenotype models (GPM) of crops aimed at compiling articles contributing to advance our understanding of the intricate relationship between genetic information and (eco)physiological processes in plants. We are pleased to ascertain that this Research Topic has fulfilled its objectives by successfully gathering seven diverse contributions (Table 1), reflecting a variety of approaches, disciplines, and hierarchical scales at which the models were implemented.Lu et al. presented a novel analytical framework called Differential Interaction Regulatory Equations (DIRE) to map the genetic architecture underlying trait covariation in Populus euphratica, a desert tree species. The researchers developed mathematical models based on Lotka-Volterra equations to describe cooperationcompetition patterns between paired traits and integrated these into QTL mapping to identify genetic loci regulating trait interactions, detecting 93-94 significant QTLs.Lang et al. presented a revised process-based phenology model (TPForc) that incorporates photoperiod and temperature triggers for bud growth initiation in winter deciduous forest trees across China's monsoon region. Analysing phenological data from four tree species at 102 stations, they found that photoperiod lengthening initiated bud growth in 80.8% of leaf unfolding and 77.7% of flowering time series, with a clear northsouth gradient where photoperiod dependence increases toward lower latitudes.</div
Modulating milk gel structuration by adding pre-formed whey protein aggregates.
No full textInternational audienceAim:Preheating milk before gelation is a common practice to modulate the properties of dairy products, by promoting whey protein (WP) aggregation and co-gelation with casein micelles after renneting. Another way to modify the structuration of milk curd is to incorporate pre-formed WP aggregates before renneting. While the literature on the formation and structure of WP aggregates prepared in aqueous solution is abundant, their role during casein micelle enzymatic gelation is not fully elucidated. Hence, this study aimed at understanding how pre-formed and added WP aggregates influence milk gelation. Gaining more knowledge on the underlying mechanisms would help better control dairy products processing and development of innovative functionalities.Method:WP aggregates were produced (hydrodynamic diameter of 100 ± 10 nm) and added in milk (ratio to total milk protein content: 0–15 % wt). The effect of adding WP aggregates on enzymatic gelation of milk was investigated from renneting to curd aging using Small- and Large-Angle Oscillatory Shear, particle aggregation quenching, Confocal Laser Scanning Microscopy, and Ultra Small and Small X-ray Scattering.Results:Increasing concentrations of WP aggregates extended the time required to reach the same storage modulus. However, at the same storage modulus, all milk gels displayed identical rheological behaviors in frequency and oscillation stress sweeps. The gels with WP aggregates featured smaller pores and slower structural rearrangements. Particle aggregation quenching showed the primary aggregation mechanism of casein micelles was affected by the presence of WP. As a result, gelation was delayed, but its mechanism was also modified, particularly during gel ageing involving pore formation. Conclusion:Although WP aggregates did not participate directly to the supporting structure of the curd, their presence still modified the gelation mechanisms of casein micelles and their aging. These findings provide new insights into the role of WP aggregates in enzymatic coagulation of milk, offering opportunities to modulate gel texture in dairy applications
Nanoscale whey protein aggregate ingredients modify the structuration of milk curd during enzymatic coagulation
No full textInternational audiencePreheating milk before gelation is a common practice to increase the yield of dairy products, since it promotes whey protein (WP) aggregation and co-gelation with casein micelles after renneting. While the literature on the formation and structure of WP aggregates prepared in aqueous solution is abundant, their role during casein micelle enzymatic gelation, especially when incorporated as pre-formed ingredients is not fully elucidated. Hence, this study aimed at understanding how pre-formed and added WP aggregates influence milk gelation. Gaining more knowledge on the underlying mechanisms would help better control dairy products making and development of innovative functionalities. WP aggregates were produced (hydrodynamic diameter of 100 ± 10 nm) and added in milk (ratio to total milk protein content: 0–15 % wt). The effect of adding WP aggregates on enzymatic gelation of milk was investigated from renneting to curd aging using Small- and Large-Angle Oscillatory Shear, Confocal Laser Scanning Microscopy, particle aggregation quenching, and Ultra Small and Small X-ray Scattering. Increasing concentrations of WP aggregates extended the time required to reach the same storage modulus. However, at the same storage modulus, all milk gels displayed identical rheological behaviors in frequency and oscillation stress sweeps. The gels with WP aggregates featured smaller pores and slower structural rearrangements. Particle aggregation quenching shows the primary aggregation mechanism of casein micelles is affected by the presence of WP. As a result, gelation was delayed, but its mechanism was also modified, particularly during gel ageing involving pore formation. Even if WP aggregates did not participate directly to the supporting structure of the curd, their presence still modified the gelation mechanisms of casein micelles and their aging.These findings provide new insights into the role of WP aggregates in enzymatic coagulation of milk, offering opportunities to modulate gel texture in dairy applications
Pour la circularité et l'ancrage territoriale des élevages porcins biologiques
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From Chaos to Clarity: Deriving Meaningful Biology from Big Data in Plant Pathology
No full textInternational audienceThis Focus Issue was inspired by the vast volumes of data now being generated from both laboratory experiments and field studies. These complex, high dimensional data sets demand new analytic approaches. We invited contributions that apply novel statistical, machine learning, or artificial intelligence methods, or that integrate multiple ‘omics approaches to reveal new aspects of pathogen biology, host interactions, or emergent system-level properties. The Focus Issue contains 13 articles falling into five broad themes and drawing upon a diverse range of data types, from disease imaging to meta-barcoding data to optical sensing to genetic data to expert knowledge. Together, these papers show how integrating technology, data, and biology is already transforming plant pathology. We hope this Focus Issue inspires new collaborations, new methods, and a continued commitment to turning data into understanding and chaos into clarity
Mesurer la contribution de l’écopâturage au cadre de vie
No full textInternational audienceMethods for assessing the social and environmental performance of agricultural systems often overlook their impacts on the living environment. Based on the case study of the Nantaise Cow’s local chain and on interviews with local stakeholders, we develop a set of indicators that integrates social and landscape amenities generated by urban pasture practices. This framework broadens impact assessment to include territorial socio-environmental sustainability.Les méthodes d’évaluation sociale et environnementale des systèmes agricoles négligent souvent leurs impacts sur le cadre de vie. En nous appuyant sur le cas de la filière locale de la Vache Nantaise et à partir d’enquêtes auprès d’acteurs du territoire, nous construisons un tableau de bord intégrant les aménités sociales et paysagères issues de l’écopâturage. Ce cadre permet d’élargir l’analyse des impacts à la durabilité socio-environnementale du territoire
Individual cows responses to climatic perturbations using VAR models
No full textInternational audienceWithin a dairy herd, response to climatic challenges may differ between cows and analysing the impact of heat stress for example on an animal basis is then of importance. In traditional approaches, animal responses to such a challenge are assessed against a reference value, based on thresholds or periods prior to this challenge. But post-disturbance response, may not return back to pre-disturbance level, questioning the relevance of a single, fixed cut-off over the time for considering the impact of a climate challenge. To address this limitation, a dynamic approach using VAR (Vector Autoregressive) models was used to assess individual animal responses to climatic perturbations (heat stress in this case) over time without assuming predefined thresholds or periods. Data were collected from June 16th to September 15th 2024, on 158 Holstein dairy cows (parity 1–5), across 2 commercial farms in western France. The cows were housed indoors year-round and monitored through behavioral data (standing, holding area time, drinking, eating detected by AIherd® device) and environmental data (temperature, humidity, wind speed, Wet Bulb Globe Temperature). Data were aggregated on a 4 hours basis. VAR models combined with Impulse Response Analysis (IRF) were used to analyze animal response dynamics, focusing on intensity (response magnitude) and lag, e.g. the delay between a temperature shock and the peak response. Results indicated a strong predictive performance (R² > 0.7, p-value < 0.05). The IRF diagnostic test revealed significant responses of cows to increased temperature, especially in drinking behavior. For instance, an increase of 7% (Farm 1) and 5% (Farm 2) was observed after 24-hours (lag 6 : 6x4h). Cumulative effects of temperature reached peaks of 44% at lag 13 (Farm 1) and 59% at lag 21 (Farm 2) for drinking, and 36% at lag 21 (Farm 1) and 9.7% at lag 13 (Farm 2) for standing behavior. In contrast, eating and lying behaviors showed minimal effects (<1.5%), indicating a limited response to the thermal shock. To fully assess this original approach and its perspectives, a comparison with commonly used methods will be performed
Hiérarchisation des médicaments vétérinaires susceptibles de contaminer les eaux destinées à la consommation humaine en Bretagne
No full textInternational audienceThe continuous use of veterinary pharmaceuticals can represent diffuse and pseudo-persistent pollution in the environment. This is confirmed by the fact that veterinary pharmaceutical residues (VPRs) have been quantified in natural waters at concentrations ranging from ng/L to μg/L, thanks to improvements in analytical methods. In order to perform a monitoring study in Brittany, a region subject to high husbandry pressure, a ranking of veterinary pharmaceutical residues was carried out to select the veterinary pharmaceuticals that would be the most likely to reach the aquatic environment. A preliminary list of 70 veterinary drugs was considered based on the results of interviews conducted with veterinarians during the REMEDES project and on the results of the study of the Regional Health and Environment Plan Working Group 2. The ranking methodology developed aims to reflect the potential of VPRs to enter natural waters. Criticality groups have been established on the basis of three criteria: 1) the potential for entry into the environment, divided into animal targets, route of administration and veterinary practices in Brittany; 2) the mobility of molecules from soil to water; and 3) the persistence of compounds in natural waters. Metabolites were integrated when relevant. Fifty-four compounds out of the 70 studied were classified according to this methodology. Establishing a ranking method is currently a complex task for VPRs. There is still a significant lack of experimental data conducted under homogeneous conditions on the environmental fate of these compounds. Some families have been studied in depth, such as antibiotics like sulfonamides and tetracycline families, but data in the literature is scarce for others, such as antiparasitic drugs and anticoccidians, despite the fact that these veterinary drugs are widely used in breeding areas such as Brittany.L’utilisation continue de médicaments vétérinaires peut représenter une pollution diffuse et pseudo-persistante dans l’environnement. Ceci est confirmé par le fait que des résidus de médicaments vétérinaires (RMV) ont été quantifiés dans les eaux naturelles à des concentrations allant du ng/L au μg/L, grâce aux progrès des méthodes analytiques. Afin de réaliser une étude de suivi en Bretagne, région soumise à une forte pression d’élevage, une priorisation des médicaments vétérinaires a été réalisée pour sélectionner les médicaments vétérinaires les plus susceptibles d’atteindre le milieu aquatique. Une liste préliminaire composée de 70 médicaments vétérinaires, basée sur des enquêtes d’usage chez les vétérinaires (Projet REMEDES) et les résultats d’un Groupe de travail du Plan régional santé environnement 2 (GDT PRSE 2), ont été considérés. La méthodologie de hiérarchisation développée a pour objectif de refléter le potentiel d’entrée dans les eaux naturelles des RMV étudiés. Des groupes de criticités ont été établis sur la base de trois critères : 1) le potentiel d’entrée dans l’environnement, décomposé en fonction des cibles animales, de la voie d’administration et des pratiques vétérinaires en Bretagne ; 2) la mobilité des molécules du sol vers l’eau ; 3) la persistance des composés dans les eaux naturelles. D’autre part, les métabolites ont été intégrés quand cela était pertinent.Sur les 70 étudiés, 54 composés ont pu être hiérarchisés par cette méthodologie. L’établissement d’une méthode de priorisation est, à ce jour, une tâche complexe. Il y a encore un manque notable de données expérimentales menées en conditions homogènes sur le devenir environnemental de ces composés. Certaines familles ont fait l’objet d’études approfondies, comme les antibiotiques, dont les sulfonamides ou les tétracyclines, mais les données de la littérature sont rares pour d’autres familles comme les antiparasitaires ou les anticoccidiens. Pourtant, ces médicaments vétérinaires sont largement utilisés dans les zones d’élevage en Bretagne
The environmental benefits of grassroots cooperatives in agriculture
No full textInternational audienceThis paper analyses the environmental benefits of grassroots cooperation in agriculture. Specifically, it focuses on the French context, which is characterised by a heavy reliance on pesticides and by strong inter-farmer interactions structured within farm machinery sharing cooperatives (CUMAs). We theorise that these social interactions are strategically complementary in the sense that the agroecological practices of farmers involved in the CUMA network, in a given spatial unit, are influenced by the presence and actions of CUMA members in their vicinity. At the extensive margin, increased peer-to-peer interactions, driven by a higher density of CUMA members, foster sociotechnical exchanges conducive to reducing pesticide use. At the intensive margin, if members individually make greater use of their CUMA, they collectively gain access to technologically advanced machinery assets, which leads to a reduction in pesticide use through improvements in technical efficiency. Our econometric analysis, based on a dataset provided by the National Federation of CUMAs covering 5793 individual cooperatives, fully supports the extensive-margin mechanism. The intensive-margin mechanism, however, is only observed for greater use of agroecological equipment by CUMA members, suggesting a rebound effect when it comes to conventional equipment. Overall, these results point to the idea of a ‘hidden agroecological transition.