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Genotyping-by-sequencing reveals marker-based genome stability in tetraploid clementines for triploid breeding
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/616541/) * Autres projets (id;sigle;titre): PID2021-128115OR-I00;;(ESP) Estrategias geneticas y biotecnologicas para la mejora de variedades de mandarino// IVIA-GVA 52201;AgroAlimVal;(ESP) Mejora genómica de frutales tradicionales y emergentes de interés para la Comunidad Valencina// ;AgroAlimVal;//International audienceTetraploid non-apomictic citrus genotypes are key female parents for 4x × 2x hybridizations aimed at producing seedless triploid hybrids. However, the extent to which different tetraploidization methods affect genome integrity remains insufficiently characterized at a genome-wide scale. In this study, genotyping-by-sequencing (GBS) was used to evaluate marker-based genomic stability in ten tetraploid plants of 'Clemenules', 'Fina', and 'Marisol' clementines obtained via colchicine treatment, in vitro adventitious organogenesis, or somatic cybridization. Diploid parental plants, two haploid plants of 'Clemenules' and 'Fina' clementines, and one doubled haploid plant of 'Clemenules' clementine were included, being the haploid and double haploid essential to resolve allelic phases. After quality filtering, 3333 SNP (Single Nucleotide Polymorphism) markers distributed across the nine citrus chromosomes were identified and used to compare allele dosage patterns along the genome. Across all GBS-covered regions, no major marker-based genomic gains or losses were detected in any tetraploid plant. These results indicate that, at the resolution provided by GBS, all three tetraploidization methods largely preserve chromosome structure, supporting their suitability for citrus triploid breeding programs based on 4x × 2x sexual hybridizations
Quelles salamandres tachetées trouve-t-on dans le sud-ouest de la France ?
No full textInternational audienceThe taxonomy and diversity of French populations of the fire salamander (Salamandra salamandra) have recently regained scientific interest, due to advances in genetic methods that help identify and define taxa. This study reanalyzes molecular data from two recent studies to clarify the distribution of S. salamandra subspecies in southwestern France. First, genome-wide RAD sequencing of 30 samples confirms the existence of two highly divergent genetic groups in the Pyrenees: one in the central and western parts, corresponding to S. s. fastuosa, and another in the eastern Pyrenees and the rest of France. This second group actually includes three distinct phylogeographic lineages that diverged during the Pleistocene: S. s. terrestris, and two others (in the Spanish Pyrenees and Montseny Mountains) linked to the debated S. s. “hispanica”, whose genetic traces also appear in France. Second, mitochondrial DNA sequencing of 98 individuals using minibarcoding refines the distribution boundaries of S. s. fastuosa and S. s. terrestris/“hispanica”, particularly identifying a transition zone in the central Pyrenees in the area where RAD data suggest genetic introgression. The findings support the intraspecific status of S. s. fastuosa and suggest that S. s. “hispanica” is absent from France in its pure form. This work lays the foundation for better understanding subspecies distributions and gene flow in French S. salamandra.La systématique et la diversité des populations françaises de Salamandre tachetée (Salamandra salamandra) a récemment reçu un regain d'intérêt scientifique, principalement en raison de nouvelles opportunités offertes par les méthodes génétiques pour mieux identifier et définir les taxons. Cet article propose une analyse des données moléculaires issues de deux récentes études afin de clarifier la distribution des sous-espèces de S. salamandra supposées dans le sud-ouest de la France. Premièrement, les analyses de milliers de marqueurs génomiques obtenus sur une trentaine d' échantillons par une approche RAD (Restriction Associated DNA) confirment l' existence de deux groupes génétiques très divergents dans les Pyrénées, l'un distribué sur la partie centrale et occidentale du massif, correspondant à S. s. fastuosa, l'autre occupant la partie orientale et s' étendant sur le reste de la France. Ce deuxième groupe consiste en trois lignées phylogéographiques distinctes ayant récemment évolué pendant le Pléistocène, l'une correspondant à S. s. terrestris, et les deux autres, restreintes aux Pyrénées espagnoles et au massif du Montseny, associées à la controversée S. s. "hispanica", dont des traces génétiques se retrouvent également en France. Deuxièmement, le séquençage d'un fragment d' ADN mitochondrial chez une centaine d'individus Pyrénéens par une approche de minibarcoding (génotypage de marqueurs code-barres) confirme et affine les aires respectives de S. s. fastuosa et S. s. terrestris/"hispanica" dans le sud-ouest français, notamment la présence d'une transition dans les Pyrénées centrales, là où les données RAD suggèrent de l'introgression génétique. Cette synthèse, qui soutient le statut intraspécifique de S. s. fastuosa et l'absence de S. s. "hispanica" en France, du moins sous sa forme pure, constitue un point de départ pour approfondir les connaissances sur la distribution géographique des sous-espèces de Salamandre tachetée et pour examiner les processus qui régulent le flux de gènes entre elles
Intra-wet season variation in rangeland fodder quality influences feed conversion, growth and methane emissions in West African zebu cattle
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/616495/) * Autres projets (id;sigle;titre): FOOD/2019/410-169;CaSSECS;(EU) Carbon Sequestration and Greenhouse Gas Emissions in (Agro) Sylvopastoral Ecosystems in the Sahelian CILSS States// ;DeSIRA;(EU) Development Smart Innovation through Research in Agriculture//International audienceLivestock in sub-Saharan Africa is a major contributor to greenhouse gas emissions, particularly enteric methane (eCH4), with emissions intensities and yield often elevated. In this region, wet-season rangeland fodder is the primary feed source for livestock. This study evaluated the effects of fodder growth stage and feed allowance on feed intake, digestibility, average daily gain (ADG), feed conversion ratio (FCR), and eCH4 emissions in cattle. Over a 112-day period, including a 14-day adaptation and a 98-day data collection phase, ten Sudanese Fulani zebu bulls (52 ± 1.2 months of age, 195 ± 14.6 kg body weight) were fed green rangeland fodder. They were divided into two groups of five animals each: one received fodder at a high allowance level of 4.5 % of body weight (BW) dry matter (DM) basis (4.5ING), while the other received 2.5 % of BW (2.5ING). Voluntary intake, digestibility, and eCH4 (GreenFeed®) were measured daily across three fodder growth stages: vegetative stage (VeS), reproductive stage (ReS), and mature stage (MaS). ADG and FCR were assessed fortnightly. DM intake decreased progressively from VeS to MaS with the highest values recorded for 4.5ING (P < 0.05). Digestibility was affected only by growth stage, decreasing from VeS to MaS (P < 0.05). Both ADG and FCR were influenced by fodder growth stage and feed level. The lowest eCH4 yield and intensity were observed in VeS (P < 0.05). Fodder level influenced eCH4 intensity (P < 0.05). Intra-wet season fodder growth stage significantly affected intake, digestibility, growth, and eCH4 emissions in cattle, while feed allowance influenced performance and eCH4 intensity. Significant interactions effects were observed between fodder growth stage and feed allowance for all parameters except digestibility. The best animal performance, along with the lowest eCH4 yield and intensity were observed in 4.5ING animals during VeS. These findings suggest that optimizing feed availability at the beginning of the wet season is an effective feeding strategy to enhance productivity while mitigating methane emissions in extensive livestock systems
Validation of a representative sampling protocol for studying grape berry microbiota at the plot scale
No full textData availability: Raw sequences have been deposited at NCBI under the BioProject accession number PRJNA1327833.International audienceIn viticulture, a comprehensive understanding of the grape microbiota is crucial, as it influences various aspects of the winemaking process, from vine health and grape development to fermentation dynamics and the final sensory profile of the wine. Monitoring these communities helps optimize vineyard practices and ensure product authenticity. Metagenetics is a fast culture-independent approach that allows identification of the microorganisms present in grape berries' microbiota at the genus or species level. In this context, it is crucial to assess the quality of sampling methods in terms of their representativeness of the diversity of microbial communities on grape berries at the plot level. In this study, the microbiota of the variety Artaban was examined. This variety is resistant to powdery mildew and tolerant to downy mildew. Two sampling methods for studying microbiota were investigated by forming two groups: one that pooled the microbiota of 10 vines, and another that studied the microbiota of each vine separately.</div
Bisexual releases are as effective as male‐only releases to control <i>Drosophila suzukii</i> with the sterile insect technique
No full textInternational audienceBACKGROUND: The sterile insect technique (SIT) suppresses insect reproduction by repeatedly releasing sterile insects and allowing them to mate with insects of the same species in the wild. While the classical SIT relies on sterile males mating with wild females, there is a debate regarding the risks and benefits of releasing sterile females along with the sterile males (i.e. bisexual releases). In a replicated cage experiment, we compared the effect of unisexual and bisexual sterile releases of Drosophila suzukii on induced sterility. To ensure field-realism, fertile females -wild-F0 freshly emerged from field-collected sweetcherries -were placed in cages with artificial vegetation and plastic berries.RESULTS: The proportion of fertile females that produced offspring was not significantly different in unisexual and bisexual treatment (45% and 46%, respectively). Excluding females that had not mated (i.e. no sperm in the spermathecae) from the analysis had no influence.CONCLUSION: These results suggest the release of sterile females does not always affect the efficacy of the SIT. Even though additional phenomena may arise when scaling up from cages to the field, we conclude that sorting females with genetic constructs or robotic systems is probably dispensable in D. suzukii SIT, at least when deployed in confined farming systems.</div
Chemical composition and aphicidal activity of Santolina africana essential oil: a new opportunity in Aphis gossypii management?
No full textData availability statement: All sequences that confirm the molecular identity of the studied material are available on GenBank under the Accession numbers indicated in the text (PV738052-PV738059). All DNA extracts are stored at the Centre de Biologie pour Gestion des Populations (CBGP), Montferrier sur Lez (France) under the authority of Nathalie Gauthier. All phytochemical profiles and aphicidal results are stored at the Universite Djillali Liabes, Sidi Bel Abbes (Algeria) under the authority of Radouane Zaid.International audienceThe cotton aphid (Aphis gossypii), is a polyphagous species that transmits phytoviruses. It is one of the most damaging and widespread insect pests in pomegranate orchards worldwide, including countries of the Mediterranean basin such as Algeria. The control of its populations mainly relies on synthetic pesticides although safer alternatives, such as botanical insecticides, warrant further exploration. This study investigated the aphicidal potential of the essential oil (EO) of Santolina africana leaves (Asteraceae), widespread North African shrub, against A. gossypii populations under laboratory conditions. The EO phytochemical profile was determined by GC/MS. The 49 compounds identified were mainly oxygenated sesquiterpenes and monoterpenes, with artemisia ketone (22.69%) and longiverbenone (16.55%) as the dominant compounds. The toxicity of the EO was tested at five concentrations (0.1–1.6%, v/v) through topical contact and fumigation bioassays across seven exposure times (2–72 h). Each bioassay involved a population of 25 aphids with five replicates, totalling 750 individuals per method. Mortality was both concentration- and time-dependent, reaching 100% within 12 h under fumigation. After 24 h, fumigation required EO concentrations 3.6 and 36 times lower than topical application to achieve LC₅₀ and LC₉₀ values, respectively. This study provides the first evidence of the strong biocidal activity of S. africana leaf EO against A. gossypii populations, highlighting its potential for pest populations and for reducing the spread of the phytoviruses transmitted by this aphid
Synthèse des connaissances sur les fourmis (Hymenoptera, Formicidae) du Parc national des Écrins (SE France)
No full textInternational audienceSynthesis of knowledge on the ants (Hymenoptera, Formicidae) of the Écrins national park (SE France). The synthesis of 1686 occurrence data of ants (family Formicidae, Hymenoptera) identified to the species level, distributed across the entire Écrins National Park (core zone and adhesion zone) revealed 83 species, i.e. more than one third of the myrmecofauna of metropolitan France. The species ac- cumulation curve shows, however, that the completeness of the inventory is moderate. Although the first data date back to 1984, more than 90% of the data have been obtained since 2018. To remedy to the knowledge deficit, the park adopted a strategy in 2018 which consisted in: first mobilizing park agents for opportunistic collections throughout the territory and an association of ant specialists for identification, and second occasionally involving ant specialists in field surveys. This sampling effort allowed exploring the distribution of diversity and species according to the type of environment and to elevation, and to reveal the presence of species that could represent an issue for the park. In particular, Formica paralugubris Seifert, 1996, a species of redwood ant endemic to the western Alps and the Jura, very little known in France, was detected in several sites. This species being difficult to distinguish from Formica lugubris Zetterstedt, 1838 – a very common boreomontane species – the identification was based on a double diagnosis: morphological and molecular. The inventory revealed other remarkable species such as Leptothorax gredleri Mayr, 1855, a species from central and northern Europe whose only known station in France is the one in the park, and Leptothorax pacis (Kutter, 1945), a very rare species occurring mainly in the Alps and the Pyrenees. A conservation value analysis relying on a method specific to the park revealed Formica paralugubris as a species with a particularly high conservation value within the territory of the park.La synthèse de 1686 données d’occurrence de fourmis (famille des Formicidae, Hymenoptera) identifiées à l’espèce réparties sur l’ensemble du parc national des Écrins (zone cœur et zone d’adhésion) a permis de recenser 83 espèces, soit plus du tiers de la myrmécofaune de France métropolitaine. La courbe d’accumulation des espèces montre cependant que la complétude de l’inventaire des espèces est modérée. Bien que les premières données datent de 1984, plus de 90 % des données ont été obtenues depuis 2018. Face au déficit de connaissance d’avant 2018, la stratégie du parc, qui s’est avérée efficace, a d’abord été de mobiliser les agents du parc pour des collectes opportunistes sur l’ensemble du territoire et une association spécialiste des fourmis pour l’identification, puis de faire intervenir ponctuellement des spécialistes sur le terrain. Cette pression d’échantillonnage a permis d’explorer la distribution de la diversité et des espèces en fonction du type de milieu et de l’altitude, et de révéler la présence d’espèces pouvant constituer un enjeu pour le parc. En particulier, Formica paralugubris Seifert, 1996, une espèce de fourmis rousse des bois endémique de l’ouest des Alpes et du Jura, très peu connue en France, a été détectée dans plusieurs stations. Cette espèce étant difficile à distinguer de Formica lugubris Zetterstedt, 1838, une espèce boréo-montagnarde très commune, l’identification a porté sur un double diagnostic, morphologique et moléculaire. L’inventaire a révélé d’autres espèces remarquables telles que Leptothorax gredleri Mayr, 1855, une espèce d’Europe centrale et du nord dont la seule station connue en France est celle du parc, et Leptothorax pacis (Kutter, 1945), une espèce très rare présente essentiellement dans les Alpes et les Pyrénées. L’évaluation de patrimonialité selon une méthode propre au parc n’a révélé qu’une seule espèce à considérer comme patrimoniale pour le parc : Formica paralugubris
Legal Repair: Domesticating European Legislation on Pig Welfare
No full textInternational audienceOur daily activities rely on a proliferating number of things that are subject to decay. As stressed in a growing body of literature, repair is critical to the smooth functioning of material infrastructure. However, this scholarship has overlooked a crucial dimension: things become fragile not only due to material degradation but also as a result of regulatory change. This article introduces the notion of “legal repair” to describe how, in the face of legal change, certain actors reassemble the material world. We elaborate on this concept through an analysis of the domestication of European Union (EU) animal welfare legislation by the French pig sector. While it was feared that stricter pig housing standards would fragilize the existing farms, pig farmers complied using technical systems that failed to significantly improve animal welfare. We analyze this domestication of EU legislation as a process of legal repair. Alongside the political work of the leaders of the pig sector, agricultural advisers also played a key role. Their work reveals the relational nature of legal repair: in the production of “local specifications” matching the demands of existing farming systems, in the negotiation of the finer points of the legislation, and in the redefinition of farming performance
Comportement quasi-limite du processus de branchement bi-sexué multi-type de Galton-Watson sous-critique
No full textInternational audienceWe investigate the quasi-limiting behaviour of bisexual subcritical Galton-Watson branching processes. While classical subcritical Galton-Watson processes have been extensively analyzed, bisexual Galton-Watson branching processes present unique difficulties because of the lack of the branching property. To prove the existence of and convergence to one or several quasi-stationary distributions, we leverage on recent developments linking bisexual Galton-Watson branching processes extinction to the eigenvalue of a concave operator