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Transgenerational response to endocrine disruptor : phenotypic, genotypic and epigenotypic analyses in quail
No full textInternational audienceWhile the typical evaluation of an offspring’s phenotypic traits usually focuses on the inheritance of parental alleles, variations across generations can also result from the transmission of non-genetic factors. Epigenetic marks like DNA methylation offer a dynamic molecular signature of an individual’s history, as they can carry a memory of the individual’s environmental past, and also of its parents. A recent study in quail (Coturnix japonica) found that alterations in the embryonic environment can have an impact on subsequent generations, resulting in significant reduction of the offspring’s body weight. To better disentangle the complex interplay between genetic and epigenetic effects, a specific quail breeding plan was designed. Twenty initial founder families were crossed to generate two epilines with similar genetic backgrounds. In the first generation, one epiline received a genistein supplementation whereas the other was only provided with regular feed. After this initial diet disruption, the groups were maintained under standard breeding conditions, and animals from the next two generations were mated following a mirrored design to ensure a balanced genetic structure in both groups. By recording multiple phenotypes (production, breeding, behaviour), genotypes and epigenotypes of both epilines, this approach aims to investigate the transgenerational inheritance of an environmental effectthrough changes in DNA methylation profiles
Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers
No full textData is deposited in the European Nucleotide Archive (ENA) with the accession number PRJEB58821 and PRJEB71464.International audienceWhole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens. Until now, breeding companies have been using or developing SNP chips. Nevertheless, alternatives methods based on sequencing have been developed. Among these, reduced representation sequencing approaches can offer sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability of double digested Restriction site Associated DNA sequencing (ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CR SNP ) and mean depth of sequencing per SNP (DP SNP ) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CR SNP of 0.55, a DP SNP of 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CR SNP and DP SNP values were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CR SNP (0.25) and DP SNP (1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CR SNP , DP SNP , genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a minimum of 40% of the SNPs with a CcR of 98%. Then, ddRAD-seq was defined as a suitable method for variant calling and genotyping in layers
Quels défis et opportunités des approches grassroots pour transformer le métabolisme urbain ?
No full textInternational audienceLe colloque visera à examiner de manière interdisciplinaire et pluridisciplinaire les défis et les opportunités que les innovations circulaires urbaines rencontrent pour créer, maintenir et étendre leurs solutions pour des transitions durables et inclusives à partir d’une approche grassroots (social, communautaire, populaire et de terrain).Les recherches sur les métabolismes urbains montrent que les villes sont des espaces de surconsommation, de production à forte intensité de déchets et d'empreintes environnementales élevées, mais aussi des centres de créativité et d'innovation. Les citoyens expérimentent une multitude d'innovations pour relever le défi d'une croissance constante de la consommation et d'une surexploitation des ressources.Malgré leurs contributions, des recherches supplémentaires interdisciplinaires sont nécessaires pour étudier les défis et les opportunités de diffusion de ces pratiques en termes : de dimension spatiale (scalabilité, montée en échelle, expansion spatiale, foncier), d'arènes collaboratives, d’organisation multi-acteurs et de structuration de filières, d'inclusivité et d'évolutivité des initiatives des communautés. Ce colloque qui présentera notamment les travaux menés au sein de l’ axe de recherche CODIUM (Combining Disciplines for Urban Metabolism) de la FR CNRS IRSTV, prendra la forme d’une demi-journée de discussion en matière d'économie circulaire et de développement local portés par les acteurs eux-mêmes, pouvant prendre la forme d'organisations collectives, réseaux, associations, coopératives, etc.Une première table ronde portera sur la question de l'aménagement urbain (conflits d'usage, délaissés urbains, etc.) et une seconde autour de l'alimentation (microfilière coopérative, organisations collectives...).Deux grands témoins interviendront pour partager leur expertise sur le sujet des mobilisations collectives et de l’économie circulaire
La jachère urbaine : point d'acupuncture pour une ville résiliente
No full textUrban leftover spaces tend to be integrated into urban strategy as an opportunity to prefigure the city of the future. Public decision makers are now encouraging inhabitants to take ownership of these spaces. On the model of the traditional agricultural fallow, which consists in working the land to prepare for future crops, we introduce the notion of urban fallow to qualify these spaces made available to the initiatives of local players to develop a transitional project. In any complex system, it is the sub-systems, through their diversity and capacity for creation/innovation, that give the whole (the system) a capacity for adaptation, enabling it to re-produce itself over time. It is thus at the level of its neighborhoods (of its sub-systems) that the city will draw the springs of its resilience. Urban fallows will enable the innovative and experimental capacities present in neighborhoods to express themselves in temporary projects. The aim of urban fallows is to take targeted action on specific points and locations in the area, in order to extend its effects and ultimately respond more broadly to problems diagnosed on the wider scale of the district. Five main issues that will guide the nature of the projects to be prioritized on these urban fallow lands: 1) enhancing and restoring an identity to the site, 2) revitalizing social and cultural life, 3) improving biodiversity and the quality of life, 4) revitalizing the local economic fabric, and 5)strengthening urban cohesion. Planned and thought out as part of an urban acupuncture strategy, these urban fallows will reinforce the dynamism of the city's various territories and, in so doing, contribute to the city's resilience.Hier symbole de la désindustrialisation et de l’échec de la politique urbaine, l’espace vacant urbain est aujourd’hui de plus en plus considéré comme une opportunité pour la fabrique de la ville. L’appropriation de ces espaces par les habitants-citoyens est ainsi désormais encouragée par les acteurs publics. Sur le modèle de la jachère agricole traditionnelle qui consiste à travailler la terre pour préparer les cultures à venir, nous introduisons la notion de jachères urbaines pour qualifier ces espaces mis à disposition des initiatives des acteurs. Les jachères urbaines vont permettre aux capacités d’innovation, d’expérimentation présents dans les quartiers de s’exprimer dans des projets temporaires. Planifier et penser dans une stratégie d’acupuncture urbaine, ces jachères urbaines vont ainsi renforcer le dynamisme des différents territoires de la ville et, ce faisant, contribuer à la résilience de la ville
Change of support for heavy-tailed zero inflated data: application to spatially aggregated ecological data for fine-scale species distribution inference
No full textIn environmental sciences, available data are often available at a coarse resolution. This can result in a mismatch between the data resolution and the resolution at which process inferences should be made. This misalignment, usually named as change of support (COS) issue, can lead to biased inferences if not addressed in the models.Yet, solutions to the COS issue have only been proposed for a limited number of simple observational processes (e.g. Poisson or Gaussian processes), which narrows their range of application. Motivated by a fisheries science case study, we introduce a hierarchical method addressing COS issue for zero-inflated data with highly skewed tails. Such data are common in environmental sciences but are not handled by existing COS methods. Our approach requires to know the spatial locations of point-level data and considers that aggregated available data are convolutions of these point-level data.We assess the accuracy of our method through a simulation study, describing different scenarios of COS. Subsequently, we apply our model to a motivating case study, focusing on the distribution of the common sole in the Bay of Biscay. Our findings illustrate that our approach provides better estimates and predictions than the ad hoc methods used to geoprocess aggregated data and refine their resolution
Envirotyping within a multi-environment trial allowed identifying genetic determinants of winter oilseed rape yield stability
No full textInternational audienceAbstract Key message A comprehensive environmental characterization allowed identifying stable and interactive QTL for seed yield: QA09 and QC09a were detected across environments; whereas QA07a was specifically detected on the most stressed environments. Abstract A main challenge for rapeseed consists in maintaining seed yield while adapting to climate changes and contributing to environmental-friendly cropping systems. Breeding for cultivar adaptation is one of the keys to meet this challenge. Therefore, we propose to identify the genetic determinant of seed yield stability for winter oilseed rape using GWAS coupled with a multi-environmental trial and to interpret them in the light of environmental characteristics. Due to a comprehensive characterization of a multi-environmental trial using 79 indicators, four contrasting envirotypes were defined and used to identify interactive and stable seed yield QTL. A total of four QTLs were detected, among which, QA09 and QC09a, were stable (detected at the multi-environmental trial scale or for different envirotypes and environments); and one, QA07a, was specifically detected into the most stressed envirotype. The analysis of the molecular diversity at QA07a showed a lack of genetic diversity within modern lines compared to older cultivars bred before the selection for low glucosinolate content. The results were discussed in comparison with other studies and methods as well as in the context of breeding programs
Protein ingredient quality within infant formulas impacts plasma amino acid concentrations in neonatal minipiglets
No full textInternational audienceBackground: Infant formulas (IFs), the only adequate substitute to human milk, are complex matrices that require numerous ingredients and processing steps that may impact protein digestion and subsequent amino acid (AA) absorption. Objectives: The objective was to understand the impact of the protein ingredient quality within IFs on postprandial plasma AA profiles. Methods: Four isonitrogenous and isocaloric IFs were produced at a semi-industrial scale using whey proteins from different origins (cheese compared with ideal whey) and denaturation levels (IF-A, -B, -C), and caseins with different supramolecular organizations (IF-C, -D). Ten Yucatan minipiglets (12- to 27-d-old) were used as a human infant model and received each IF for 3 d according to a Williams Latin square followed by a 2-d wash-out period. Jugular plasma was regularly sampled from 10 min preprandial to 4 h postprandial on the third day to measure free AAs, urea, insulin, and glucose concentrations. Data were statistically analyzed using a mixed linear model with diet (IFs), time, and sex as fixed factors and piglet as random factor.Results: IFs made with cheese whey (IF-A and -B) elicited significantly higher plasma total and essential AA concentrations than IFs made with ideal whey (IF-C and -D), regardless of the pre- and postprandial times. Most of the differences observed postprandially were explained by AA homeostasis modifications. IFs based on cheese whey induced an increased plasma concentration of Thr due to both a higher Thrcontent in these IFs and a Thr-limiting degrading capability in piglets. The use of a nonmicellar casein ingredient led to reduced plasma content of AA catabolism markers (IF-D compared with IF-C).Conclusions: Overall, our results highlight the importance of the protein ingredient quality (composition and structure) within IFs on neonatal plasma AA profiles, which may further impact infant protein metabolism
Mise au point d'un système innovant de production de plantes horticoles compactes et ramifiées pour mieux répondre aux marchés urbains émergents -Projet IRRADIANCE
No full textCe numéro traite de résultats de projets lauréats en 2017 et 2018 de l'appel à projet CASDAR (Compte d'Affectation Spéciale Développement Agricole et Rural), "Innovation et Partenariat" et "Recherche Technologique. Ces projets sont financés par le ministère de l'Agriculture et de la Souveraineté Alimentaire.National audienceUrban space devoted to plants is becoming increasingly limited (balconies, terraces, etc.), and this is accompanied by an increasing demand for compact and branched plants by the consumer. As part of the STRATège Joint Technology Unit program, the IRRADIANCE project (2018-2022), carried out by ASTREDHOR in partnership with the Institute of Research in Horticulture and Seeds (IRHS-INRAE, Institut Agro, Angers University), aimed to develop a new production system to meet this demand. To achieve this objective, the first phase, carried out in a climatic chamber, enabled compact, branched young plants to be produced more rapidly, thanks to the addition of far-red light (FR). However, in rose, used as a model plant in this project, a genotype-specific response to FR was shown, with some varieties showing no response at all. This insensitivity might result from the accumulation of abscisic acid in the stems and the leaves, inhibiting the stimulating effect of FR on photosynthesis. The young plants, produced in climatic chamber by the IRHS, were grown in greenhouse at ASTREDHOR stations until they reached the commercial stage. A favourable effect of this new cultivation system was demonstrated on rose architecture, with more compact plants, compared with a traditional cultivation system. A genotypespecific response was also shown, justifying the choice of varieties for this cultivation system. In collaboration with a growers’ cooperative, this new cultivation system was evaluated on other horticultural species and demonstrated its genericity.L’espace urbain consacré au végétal est de plus en plus réduit (balcons, terrasses, …), et s’accompagne d’une demande croissante de plantes compactes et ramifiées par le consommateur. Intégré au programme de l’Unité Mixte Technologique STRATège, le projet IRRADIANCE (2018-2022), réalisé par ASTREDHOR en partenariat avec l’Institut de Recherche en Horticulture et Semences (IRHS), avait pour objectif de développer un nouveau système de production, pour répondre à cette attente. Pour atteindre cet objectif, la première phase, réalisée en enceinte climatique, a permis de produire plus rapidement des jeunes plants compacts et ramifiés, grâce à l’ajout de lumière rouge sombre (Rs). Cependant, chez le rosier, utilisé comme plante modèle dans ce projet, une réponse génotype-spécifique au Rs a été mise en évidence, allant chez certaines variétés jusqu’à l’absence de réponse. Cette insensibilité résulterait de l’accumulation d’acide abscissique dans les tiges et les feuilles et inhiberait l’effet stimulant du Rs sur la photosynthèse. La culture des jeunes plants, produits en enceinte climatique par l’IRHS, a été poursuivie en serre, au sein des stations ASTREDHOR, jusqu’au stade commercial. Un effet favorable de ce nouveau système de culture a été mis en évidence sur l’architecture du rosier, avec des plantes plus compactes, comparé à un système de culture traditionnel. Une réponse génotype-spécifique a été également mise en évidence, justifiant de raisonner le choix variétal pour ce système de culture. En collaboration avec une coopérative de producteurs, ce nouveau système de culture a été évalué sur d’autres espèces horticoles et a permis de démontrer sa généricité
Genetic control of root morphology in response to nitrogen across rapeseed diversity
No full textInternational audienceRapeseed (Brassica napus L.) is an oil‐containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root‐to‐shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype‐by‐nitrogen interactions. Genome‐wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co‐localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed
