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Characterization of Worldwide Olive Germplasm Banks of Marrakech (Morocco) and Córdoba (Spain): Towards management and use of olive germplasm in breeding programs
No full textOlive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites
The rhizobial type III effector ErnA confers the ability to form nodules in legumes
No full textSeveral Bradyrhizobium species nodulate the leguminous plant Aeschynomene indica in a type III secretion system-dependent manner, independently of Nod factors. To date, the underlying molecular determinants involved in this symbiotic process remain unknown. To identify the rhizobial effectors involved in nodulation, we mutated 23 out of the 27 effector genes predicted in Bradyrhizobium strain ORS3257. The mutation of nopAO increased nodulation and nitrogenase activity, whereas mutation of 5 other effector genes led to various symbiotic defects. The nopM1 and nopP1 mutants induced a reduced number of nodules, some of which displayed large necrotic zones. The nopT and nopmutants induced uninfected nodules, and a mutant in a yet-undescribed effector gene lost the capacity for nodule formation. This effector gene, widely conserved among bradyrhizobia, was named ernA for "effector required for nodulation-A." Remarkably, expressing ernA in a strain unable to nodulate A. indica conferred nodulation ability. Upon its delivery by Pseudomonas fluorescens into plant cells, ErnA was specifically targeted to the nucleus, and a fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy approach supports the possibility that ErnA binds nucleic acids in the plant nuclei. Ectopic expression of ernA in A. indica roots activated organogenesis of root- and nodule-like structures. Collectively, this study unravels the symbiotic functions of rhizobial type III effectors playing distinct and complementary roles in suppression of host immune functions, infection, and nodule organogenesis, and suggests that ErnA triggers organ development in plants by a mechanism that remains to be elucidated
Minéraux, cycles thermiques de faibles intensités et coagulation du lait
No full textQuestions de recherche
Q1 : Les itinéraires thermiques affectent ils les propriétés fonctionnelles des laits?
Q2 : Si oui, quelles en sont les bases physicochimiques ?
Q3 : Les modifications physicochimiques et technofonctionnelles sont elles réversibles et quelles sont les cinétiques de « réversibilité »
Emplois précaires en agriculture
No full textLa question, ancienne, de la précarité des emplois en agriculture reste particulièrement importante aujourd'hui. Si la précarité est complexe et multifactorielle, le statut des employés en constitue un facteur central. En 2016, la moitié du travail salarié dans les exploitations agricoles était effectuée sous des statuts intrinsèquement précaires (CDD, travail saisonnier, apprentis). Compte tenu de la durée plus courte des périodes d'emploi sous statut précaire, 80 % des 756 000 salariés agricoles employés cette année-là évoluaient sous ces statuts. Cet article étudie les populations de salariés agricoles, que ce soit en exploitation, dans les groupements d'employeurs, les entreprises de travaux agricoles et l'intérim en France métropolitaine. Il présente également les éléments du débat sur les facteurs de précarité de ces travailleurs, qu'ils soient démographiques, économiques, sociologiques ou juridiques.The long-standing issue of the precariousness of salaried jobs in agriculture remains particularly important today. While precariousness is complex and multifactorial, the occupational status of the employees is a key factor. This article describes the populations of employees working on the farms in metropolitan France, whether hired by the farms, by employer groups, by agricultural work companies or by temporary employment agencies. In 2016, half of all paid work on agricultural holdings was carried out under inherently precarious status (fixed-term contracts, seasonal work, apprentices). Given the short duration of precarious employment, 80% of the 756,000 farm workers employed that year were hired under these occupational status. It also presents the debates regarding the drivers of the precariousness of these workers, whether demographic, economic, sociological or legal
Peer-Reviewed Literature on Grain Legume Species in the WoS (1980–2018): A Comparative Analysis of Soybean and Pulses
No full textGrain-legume crops are important for ensuring the sustainability of agrofood systems. Among them, pulse production is subject to strong lock-in compared to soya, the leading worldwide crop. To unlock the situation and foster more grain-legume crop diversity, scientific research is essential for providing new knowledge that may lead to new development. Our study aimed to evaluate whether research activity on grain-legumes is also locked in favor of soya. Considering more than 80 names grouped into 19 main grain-legume species, we built a dataset of 107,823 scholarly publications (articles, book, and book chapters) between 1980 and 2018 retrieved from the Web of Science (Clarivate Analytics) reflecting the research activity on grain-legumes. We delineated 10 scientific themes of interest running the gamut of agrofood research (e.g., genetics, agronomy, and nutrition). We indexed grain-legume species, calculated the percentage of records for each one, and conducted several analyses longitudinally and by country. Globally, we found an unbalanced research output: soya remains the main crop studied, even in the promising field of food sciences advanced by FAO as the “future of pulses”. Our results raise questions about how to align research priorities with societal demand for more crop diversity
Hierarchical variance decomposition of fish scale growth and age to investigate the relative contributions of readers and scales
No full textCorrect estimation of interindividual variability is of primary importance in models aiming to quantify population dynamics. In a fisheries context, individual information such as age and growth is often extracted using scales; however, the rationale for using a given scalimetric method (i.e. number of scales per individual and number of readers) is rarely discussed, but different sources of variance may affect the results. As a case study, we used scale growth and age of brown trout (Salmo trutta) caught in the Kerguelen Islands. Based on a nested design (readings of four scales per fish by two independent readers), we decomposed variance in growth and age according to fish (interindividual level), scales (intraindividual level) and readers by using repeatability analysis. The results highlight that most variation is attributable to fish. Readers and scales contribute little to interindividual variance, suggesting that inference was insensitive to intraorganism biological variation. Using additional scales or readers was an inefficient use of sampling resources. We argue that variance decomposition should be widely used for studies aimed at modelling natural variability in life history traits. This would improve our knowledge of the implications of measurement error, helping rationalise and define appropriate sampling strategie
In-vitro evaluation of the antibacterial activity of the essential oils of Micromeria barbata, Eucalyptus globulus and Juniperus excelsa against strains of Mycobacterium tuberculosis (including MDR), Mycobacterium kansasii and Mycobacterium gordonae
No full textBackground: Mycobacterium spp. are responsible for several diseases, particularly in immunocompromised populations. The spreading of the resistance to antimycobacterial drugs is a significant problem to the public health and requires to find out a new and innovative alternative for the treatment of drug resistant mycobacterial strains. In this study, the antimycobacterial activity of Micromeria barbata, Eucalyptus globulus and Juniperus excelsa essential oils extracted from Lebanese plants was investigated against selected Mycobacterium spp. strains. Methods: Several dilutions of the three aforementioned essential oils were studied for antimycobacterial activity against four Mycobacterium spp. strains: Mycobacterium tuberculosis subsp. tuberculosis (ATCC (R) 27294 (TM)), multidrug-resistant M. tuberculosis (CMUL 157), Mycobacterium kansasii Hauduroy (ATCC (R) 12478 (TM)) and Mycobacterium gordonae Bojalil et al. (ATCC (R) 14470 (TM)). Results: Even with high dilutions, all tested essential oils showed a high antimycobacterial activity against targeted strains. Our data showed that M. barbata, E. globulus and J. excelsa essential oils totally inhibit the mycobacterial growth whatever the tested strains for the dilution 1/250, 1/100 and 1/250, respectively. Conclusion: To our knowledge, this is the first study regarding the antimycobacterial activity of essential oils in Lebanon. Our data show promising results, and encourage to investigate more on these medicinal plants, especially M. barbata
Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model
No full textDetecting genomic regions under selection is an important objective of population genetics.
Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but
rapid advances in DNA sequencing have increased the availability of time series genomic data. A common
approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain.
Based on this principle, several methods have been proposed to infer selection intensity. One of their
differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-
Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so
approximations to this model based on parametric distributions have been proposed. Here, we compared
the performance of some of these approximations with respect to their power to detect selection and their
estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood
calculator and applied it on genetic time series simulated under various evolutionary scenarios. The
Beta with spikes approximation, which combines discrete fixation probabilities with a continuous Beta
distribution, was found to perform consistently better than the others. This distribution provides an almost
perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does
not increase with population size. We further evaluated this model for population sizes not accessible to
the Wright-Fisher model and illustrated its performance on a dataset of two divergently selected chicken
populations
ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra
No full textMotivation: In metabolomics, the detection of new biomarkers from NMR spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses, in a reproducible way. Results: We present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independent datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketing. It also found new relevant metabolites involved in
metabolic pathways related to risk factors associated with the condition. Availability: ASICS is distributed as an R package, available on Bioconductor
Rôle de l'environnement précoce dans la variabilité des phénotypes et l’adaptation des animaux d’élevage à leur milieu
No full textLes animaux d’élevage sont confrontés à de multiples contraintes environnementales auxquelles ils doivent s’adapter. De plus en plus d’études s’intéressent à l’impact de l’environnement précoce sur les phénotypes des animaux et leurs capacités à s’adapter aux différents challenges rencontrés ultérieurement. Dans cette revue, nous nous intéressons aux connaissances actuelles sur l’influence de l’environnement précoce sur la construction et la variabilité des phénotypes et de l’adaptation des animaux d’élevage à leur milieu, en prenant des exemples dans différentes espèces. Nous nous focalisons sur les rôles de trois contributeurs importants de la construction des phénotypes : les mécanismes épigénétiques, le microbiote et les processus comportementaux. Les mécanismes épigénétiques, qui modulent l’expression du génome sous l’effet de perturbations environnementales intervenues pendant le développement, peuvent induire une variété de phénotypes dont les caractéristiques peuvent perdurer jusqu’à l’âge adulte, voire se transmettre à la génération suivante. La constitution du microbiote digestif est elle aussi très dépendante de l’environnement précoce, et joue un rôle important dans l’expression des phénotypes, notamment dans le domaine de la santé. Enfin, l’expérience précoce influence considérablement le comportement de l’animal, en particulier ses capacités d’apprentissage, qui peuvent lui conférer une meilleure adaptation à des situations nouvelles ultérieures. Les études menées
dans ces domaines permettent de définir de nouveaux leviers d’action pour tenter d’optimiser les capacités d’adaptation de nos animaux, notamment par les voies de l’alimentation des animaux jeunes ou de leurs parents voire de leurs grands-parents, de l’acclimatation pendant le développement, ou plus généralement par des modifications de l’environnement, en particulier de l’environnement social.Farm animals face multiple environmental constraints to which they must adapt. More and more studies are investigating the impact of the early environment on animal phenotypes and their ability to adapt to the various challenges encountered later. Here we review current knowledge on the influence of the early environment on the construction and variability of phenotypes and adaptation of farm animals to their environment, taking examples from different species. We focus on the roles of three major contributors to the construction of phenotypes: epigenetic mechanisms, microbiota, and behavioural processes. Epigenetic mechanisms, which modulate genome expression under the influence of environmental disturbances during development, can induce a variety of phenotypes whose characteristics can persist into adulthood, or even be transmitted to the next generation. The constitution of the digestive microbiota is also highly dependent on the early environment, and plays an important role in the expression of phenotypes, especially in the field of animal health. Finally, early experiences greatly influence an animal’s behaviour, especially its learning abilities, which can give it a better chance of adapting to new situations later on. The studies carried out in these fields make it possible to define new levers for action to try to optimise the adaptability of our animals, in particular through the feeding of young animals or their parents or even grandparents, acclimatisation during development, or more generally through changes in the environment, in particular the social environment