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Mining microbiome data to identify antagonists of grapevine downy mildew (Plasmopara viticola)
No full textInternational audienceLes vignes sont colonisées par une myriade de micro-organismes qui interagissent entre eux et avec leur hôte. L’ensemble de ces micro-organismes constitue le microbiote de la vigne et comprend des bactéries, des champignons et des oomycètes. Certains sont des phytopathogènes comme l'oomycète Plasmopara viticola, qui provoque le mildiou de la vigne. Lorsque ce pathogène arrive sur la feuille de vigne, il entre en contact avec le microbiome résident, qui peut agir comme une barrière à sa croissance. Notre objectif est d’identifier les membres de ce microbiote qui régulent naturellement le mildiou. Afin de cibler au mieux ces taxons microbiens bénéfiques, nous avons adopté une approche de caractérisation des communautés microbiennes par metabarcoding à l’échelle du tissu foliaire (sain versus infecté) et de la parcelle (résistante versus sensible). Grâce à des analyses d’abondances différentielles, nous avons identifié des candidats microbiens potentiels pour le biocontrôle du mildiou de la vigne. Cette approche est prometteuse pour mettre en évidence des consortiums microbiens d'intérêt, dont la dynamique et les interactions devront ensuite être étudiées expérimentalement pour développer le biocontrôle microbien du mildiou et faire évoluer la viticulture vers une viticulture sans pesticides
Méthodes et outils utilisés pour accompagner les agriculteurs à la transition agroécologique en systèmes irrigués : Revue Systématique de la Littérature
No full textInternational audienceIrrigated agricultural systems are threatened by climate change, necessitating their agroecological transition with adequate farmer support. While existing reviews explore methods and tools to support farmers in agroecological transition, none address the specific challenges of irrigated systems. Our study pursued two goals: (i) describe the diversity of ways used to support farmers in irrigated systems, and (ii) assess the outcomes of these supports in terms of learnings, practices changes, and contributions to agroecology. Guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, we analysed 41 peer-reviewed articles by constructing a support typology based on their objectives. For each type, we described methods and tools mobilised and analysed outcomes. We identified four types of support. Sustained support over several years is crucial for practice change. Top-down approaches reach more farmers through simpler methods and tools but often promote isolated plot-level changes. In contrast, bottom-up approaches employ more complex methods and tools, enabling systemic changes at both plot and farm scales. Within farm-level transitions, irrigation is treated as a context, with methods and tools similar to those in rainfed systems. At the territorial scale, scenario-based approaches involving stakeholders from food and water sectors are specific to irrigated systems. However, there is no evidence of these approaches driving concrete practice changes. This review confirmed the complexity of supporting farmers in agroecological transition. By focusing on irrigated systems, and by proposing a new typology of support and linking methods and tools with outcomes, this review is taking the debate on support a step further. Finally, it highlights a scientific gap in assessing the real impact of support
Parental phenotypes and breeding performance: a review of non-experimental investigation in well-studied Western Palearctic tits and flycatchers
No full textInternational audienceNumerous hypotheses predict associations between phenotype-associated breeder traits and reproductive success. In secondary cavity-nesting passerine birds, which have been investigated most, up to more than 90 parental characteristics have been linked to at least one field measure of breeding performance. However, within study populations, different parental traits, such as clutch size, first-egg date, egg size, nest architecture, plumage colour, adult morphometry, or song performance, are often weakly correlated across female and/or male breeders. Furthermore, many of these studies have been conducted outside the theoretical framework of the 'Individual Optimisation Hypothesis' of clutch size (IOH). IOH predicts that: (i) females with larger clutches will have larger broods at hatching and fledging compared to those with smaller clutches; and (ii) clutch size, which is adaptively adjusted to the parents' ability to rear nestlings, should always maximize the percentage of eggs producing fledglings so that variation in clutch size becomes disconnected from variation in breeding success. In this paper, we present the first detailed review of implications of IOH for parental characters other than clutch size. Our review covered 188 non-experimental studies and 1074 statistical results that examined how parental traits influence breeding success in Western Palearctic Great Tits (Parus major), Blue Tits (Cyanistes spp.), and flycatchers (Ficedula spp.). Clutch size explained one third of the variation in brood size at hatching and fledging within study populations. However, most parental characteristics associated weakly with the number of hatchlings or fledglings, likely because they did not correlate with clutch size. Overall, parental traits were poorly correlated with the proportion of hatchlings and fledglings per egg. We discuss why intraspecific variation in phenotype-associated breeder traits is often disconnected from interindividual differences in breeding success, and highlight the importance of underexplored research problems in avian breeding biology
Chapitre 24. Le méthane agricole : un levier de réduction des émissions de gaz à effet de serre pour respecter l'accord de Paris
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/614795/)International audienc
Quelles solutions pour la gestion de l'eau agricole face au changement climatique ?
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/614783/)International audienc
Spatialized and Prospective LCA of Agrivoltaism in the Mediterranean basin under Climate Change
No full textInternational audienceMediterranean agriculture will face significant challenges from climate change throughout the 21st century, necessitating adaptation tosustain production. Without such measures, reduced efficiency and yields will further increase agriculture’s environmental footprint tomaintain output levels. Among the options for adaptation and mitigation, agrivoltaics—the integration on the same land of photovoltaicenergy production and crop cultivation—offers a promising solution by mitigating climate impacts on crops while promoting renewableenergy production.However, the environmental performance of agrivoltaic systems depends on complex interactions among technological, agronomic, andmeteorological factors, all of which are expected to evolve. Anticipating these systems’ future performances is essential to identify contextsand scenarios where agrivoltaics maximize environmental benefits. Such projection also helps prevent suboptimal deployment, whereconventional photovoltaic and agricultural systems might outperform agrivoltaics.Our study thus supports decision-making by conducting a prospective, consequential life cycle assessment (LCA) of agrivoltaics, whetherdriven by crop or energy demand. We integrate a parameterized LCA model with prospective databases using PREMISE and simulateyields and environmental flows with the ORCHIDEE land surface model, tailored for agrivoltaic and conventional systems. The analysisfocuses on the Mediterranean coasts of France, Spain, and Italy, considering local soil carbon and water dynamics. Substantial attention isgiven to addressing the uncertainty and the sensitivity of the results in relation to the three components of the model, i.e., foreground,background and land surface model.Our work thus provides an insightful mapping of where, when, to what extent and under which scenarios agrivoltaic impacts outperform theconventional ones by studying a large scope of possibilities for socio-economic patways (SSP), climate trajectories, technological and methodological choices. This comprehensive approach provides actionable insights for planning agrivoltaic deployment under diversescenarios for the 21st century
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community
No full textInternational audiencePopulation growth and the impacts of climate change are placing increasing pressure on global agriculture and breeding programmes. Recent advancements in phenotyping techniques, genotyping technologies, and predictive modelling are accelerating genetic gains in breeding programmes, helping researchers and breeders develop improved crops more efficiently. However, these advancements have also led to an overwhelming torrent of fragmented data, creating significant challenges in data integration and management. To address this issue, the Breeding Application Programming Interface (BrAPI) project was established as a st andardized dat a model for breeding data. BrAPI is an international, community-driven effort that facilit ates interoperabilit y among dat abases and tools, improving the sharing and interpretation of breeding-related data. This open-source standard is software-agnostic and can be used by anyone interested in breeding , phenot yping , germplasm, genot yping , and agronomy data management. This manuscript provides an overview of the BrAPI project, highlighting the significant progress made in the development of the data standard and the expansion of its community. It also presents a showcase of the wide variety of BrAPI-compatible tools that have been built to enhance breeding and research activities, demonstrating how the project is advancing agricultural innovation and data management practices.</div
Insights into the genomic and phenotypic diversity of Monosporozyma unispora strains isolated from anthropic environments
No full textInternational audienceFood microorganisms have been employed for centuries for the processing of fermented foods, leading to adapted populations with phenotypic traits of interest. The yeast Monosporozyma unispora (formerly Kazachstania unispora) has been identified in a wide range of fermented foods and beverages. Here, we studied the genetic and phenotypic diversity of a collection of 53 strains primarily derived from cheese, kefir, and sourdough. The 12.7-Mb genome of the type strain CLIB 234T was sequenced and assembled into near-complete chromosomes and annotated at the structural and functional levels, with 5639 coding sequences predicted. Comparison of the pangenome and core genome revealed minimal differences. From the complete yeast collection, we gathered genetic data (diversity, phylogeny, and population structure) and phenotypic data (growth capacity on solid media). Population genomic analyses revealed a low level of nucleotide diversity and strong population structure, with the presence of two major clades corresponding to ecological origins (cheese and kefir vs. plant derivatives). A high prevalence of extensive loss of heterozygosity and a slow linkage disequilibrium decay suggested a predominantly clonal mode of reproduction. Phenotypic analyses revealed growth variation under stress conditions, including high salinity and low pH, but no definitive link between phenotypic traits and environmental adaptation was established
Assessing fruit tree vigor in peach and apple orchards through wood segmentation in ground-based RGBimages
No full textInternational audienc
Toward an interdisciplinarity approach to explore the local embedding of organic pig farming systems in France
No full textSession 52- Poster 19International audienceAlthough currently weak, the organic pig farming sector under Organic Farming (OF) specifications offers potential for development and for the agroecological transition of livestock farming systems in Europe. This project is based on the main barriers and levers identified in French pig production. It aims to promote a systemic approach to adding value in pork chain, and to consider the complementarities between animal and plant production at farm level, and between organic and non-organic farming sectors at regional level. The question addressed is how the local anchoring of organic pig farming contribute to the transition of local agri-food systems. The objectives of the project are to establish a method for analysing the role of organic pigs in localized food systems, integrating both the farm and regional levels and to test it in contrasted French territories. The project brings together researchers and academic staff with expertise in technical sciences as well as human and social sciences. Different dimensions will be emphasized, such as natural environments, interaction and cooperation between stakeholders, territorial resources, valorisation of products and coproducts and the link between animal and plant production for human nutrition. Three stages will be followed: (1) definition of conceptual and theoretical frameworks to build interdisciplinarity, (2) design and testing of the approach in three regions of France, and (3) synthesis and dissemination of the results. The approach will be communicated to students, stakeholders from both organic and non-organic sectors, policymakers and scientists