53161 research outputs found
Sort by
Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array
No full textThe timing of fruit maturity is an important trait in sweet cherry production and breeding. Phenotypic variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control, but that control might be complicated by phenotypic instability across environments. Although such genotype-by-environment interaction (G × E) is a common phenomenon in crop plants, knowledge about it is lacking for fruit maturity timing and other sweet cherry traits. In this study, 1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA, thus sampling eight ‘environments’. The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic predictions. Linkage disequilibrium among marker loci declined rapidly with physical distance, and ordination of the relationship matrix suggested no strong structure among germplasm. The most parsimonious G × E model allowed heterogeneous genetic variance and pairwise covariances among environments. Narrow-sense genomic heritability was very high (0.60–0.83), as was accuracy of predicted breeding values (>0.62). Average correlation of additive effects among environments was high (0.96) and breeding values were highly correlated across locations. Results indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new environments. Limited G × E for this trait indicated that phenotypes of individuals will be stable across similar environments. Equivalent analyses for other sweet cherry traits, for which multiple years of data are commonly available among breeders and cultivar testers, would be informative for predicting performance of elite selections and cultivars in new environments
ALLIANCE: Amélioration des performances écologiques et économiques par association de plantes de services légumineuses dans des systèmes de grandes cultures.
No full textL’objectif de ce projet était de (1) quantifier les services écosystémiques rendus par les associations
« cultures de rente – Plantes de services » pour le colza d’hiver et le blé tendre d’hiver, et leurs effets
sur les cultures suivantes dans des systèmes de grandes cultures stricts (plus ou moins diversifiés) et
de polycultures élevages, en agriculture conventionnelle et biologique (2) tester différentes conduites
culturales et des outils pour accompagner cette innovation
Ce travail a démarré par une méta-analyse de résultats expérimentaux extraits de 34 articles
scientifiques couvrant 17 pays, et a montré que les plantes compagnes associées à différentes cultures
annuelles conduisent à une réduction de 56% de la biomasse d’adventices par rapport à une culture
seule non-désherbée, et 42% par rapport à une culture seule désherbée. Puis des expérimentations en
parcelles agricoles et en conditions semis controlées ont été mises en place. Concernant le colza, des
plantes de services gélives, le plus souvent choisies dans la famille des légumineuses ont été semées
en même temps que le colza pour concurrencer les adventices et perturber les insectes pendant
l’automne (Lorin et al., 2015). La plante de services ne survivant pas à l’hiver, le colza termine son cycle
sans concurrence et bénéficie d’azote restitué par les résidus de plantes. Les résultats de 79 essais
menés en France entre 2009 et 2016 ont permis de valider cette technique et d’évaluer les intérêts
multi-critères de plusieurs conduites. Les plantes légumineuses gélives associées au colza permettent à
la fois de réduire la fertilisation de 30 kg N/ha sans perdre de rendement. En agriculture biologique, en
comparaison à un semis après la récolte du blé, le semis sous couvert au printemps permet aux
légumineuses de se développer plus rapidement une fois le blé récolté. Les effets sur le blé sont
négligeables, alors que le contrôle des adventices est directement lié à la biomasse produite avant la fin
de l’été et ne sera effectif qu’après la récolte du blé, pendant l’interculture.
Un outil, permettant d’aider au choix de l’espèce à associer en fonction d’objectifs agronomiques, a été
conçu selon une démarche participative afin d’intégrer et partager les connaissances existantes sur les
associations colza – plantes de services. Le modèle développé s’appuye sur une démarche
fonctionnelle reliant les traits des espèces candidates, aux processus et aux services potentielsThe objective of this project was to (1) quantify the ecosystem services provided by the "cash crops -
service plants" associations for winter rape and soft winter wheat, and their effects on the following
crops in more or less diversified field crops and livestock systems, in conventional and organic
agriculture (2) test different cultural practices and tools to accompagny this innovation.
This work began with a meta-analysis of experimental results from 34 scientific articles from 17
countries, and showed that companion plants associated with different annual crops lead to a 56%
reduction in weed biomass compared to a single unweeded crop, and 42% compared to a weeded crop.
Then experiments in agricultural fields and controlled sowing conditions were set up. Concerning
rapeseed, frost susceptible species, most often selected among legumes, were sown at the same time
as rapeseed to compete with weeds and disturb insects during the fall (Lorin, 2015). As the companion
plant does not survive the winter, the rapeseed ends its cycle without competition and benefits from
nitrogen released by plant residues. The results of 79 trials conducted in France between 2009 and
2016 validated this technique and assessed the multi-criteria interests of several pipes. The legume
plants associated with rapeseed make it possible to reduce fertilization by 30 kg N/ha without yield lost.
In organic farming, compared to a post-harvest sowing of wheat, sowing in spring with wheat
undercover, allows legumes to grow more quickly once the wheat is harvested. The effects on wheat
growth are negligible, whereas weed control was directly related to the biomass produced before the
end of summer and will only be effective after the wheat harvest, during intercrop cultivation.
A tool, which helps to choose the species to be associated according to agronomic objectives, has been
designed using a participatory approach in order to integrate and share existing knowledge on the
associations between rapeseed and service plants. The model developed is based on a functional
approach that links the traits of candidate species to potential processes and services
OPTIVIANDE Prédiction de la qualité technologique de la viande de poulet : apport de nouvelles approches de phénotypage et des analyses biologiques et génomiques à haut-débit.
No full textEven though meat is increasingly consumed in elaborated form, consumers are sensitive to naturality of
the products. This trend is largely taken into account by agribusiness company seeking to reduce
additives (flavor enhancers or texturizing agents) or preservatives (in particular salt). This shows the
importance of upstream control of quality of the raw material for elaborated products. This issue particularly affects chicken meat, mostly consumed in cut or processed but whose technological quality
is highly variable. The objective of the CASDAR OPTIVIANDE project was to develop new phenotyping
tools and biological or genetic markers that could be used for selection or evaluation of the impact of
breeding factors. The approaches implemented concerned the use of near-infrared spectrometry (NIRS)
as well as high-throughput biological and genomic analyzes. The study was based on an original animal
model composed of two chicken lines selected in a divergent manner on the ultimate pH of the filet and
whose technological and sensory characteristics of meat were very different. Near-infrared spectrometry
is fast to implement and makes it possible to predict several technological quality criteria such as
ultimate pH, water loss during storage and hardness after cooking. Transcriptomic and metabolomics
analyzes made it possible to develop first prediction models based on a limited number of metabolites
(blood and muscle) or muscle transcripts. At the genetic level, analyzes made possible to identify the
main regions controlling the ultimate pH of the filet and revealed several genes of interest. In
conclusion, the project led to significant advances in understanding the genetic and physiological
mechanisms involved in the establishment of quality defects in chicken. It opens perspectives of
application thanks to the development of prediction tools for selection whose genericity will have to be
validated on other populations and in conditions of productio
Gene flow across geographical barriers — scaling limits of random walks with obstacles
No full textWe study a class of random walks which behave like simple random walks outside of a bounded region around the origin and which are subject to a partial reflection near the origin. We obtain a non trivial scaling limit which behaves like reflected Brownian motion until its local time at zero reaches an exponential variable. It then follows reflected Brownian motion on the other side of the origin until its local time at zero reaches another exponential level, etc. These random walks are used in population genetics to trace the position of ancestors in the past near geographical barriers
Development and validation of an SNP-based new set of markers useful for early selection for sharka disease in apricot (P. armeniaca)
No full textA guide for ex vivo handling and storage of stool samples intended for fecal microbiota transplantation
No full textOwing to the growing recognition of the gut microbiota as a main partner of human health, we are
expecting that the number of indications for fecal microbiota transplantation (FMT) will increase.
Thus, there is an urgent need for standardization of the entire process of fecal transplant production.
This study provides a complete standardized procedure to prepare and store live and ready-to-use
transplants that meet the standard requirements of good practices to applied use in pharmaceutical
industry. We show that, if time before transformation to transplants would exceed 24hours, fresh
samples should not be exposed to temperatures above 20°C, and refrigeration at 4°C can be a safe
solution. Oxygen-free atmosphere was not necessary and simply removing air above collected samples
was sufcient to preserve viability. Transplants prepared in maltodextrin-trehalose solutions, stored
in a -80°C standard freezer and then rapidly thawed at 37°C, retained the best revivifcation potential
as proven by 16S rRNA profles, metabolomic fngerprints, and fow cytometry assays over a 3-month
observation period. Maltodextrin-trehalose containing cryoprotectants were also efcient in preserving
viability of lyophilized transplants, either in their crude or purifed form, an option that can be attractive
for fecal transplant biobanking and oral formulation.
Te human intestinal microbiota ensures several essential functions that support maintenance of health and
well-being. One of them is the prevention of colonization with allochtonous microbes including pathogens, also
known as barrier efect or competitive exclusion. Tis is dependent on the maintenance of ecological homeostasis of the gut ecosystem1 . Another well-established function of the intestinal microbiota is its contribution to
immune maturation and maintenance of a balanced immune tolerance and reactivity. It is mediated by a constant
and intimate crosstalk between intestinal microbiota and the gut associated lymphoid tissues2
. Here again, a balanced microbiota-host crosstalk is dependent on the maintenance of ecological homeostasis of the gut ecosystem. In healthy adults, microbiota composition is individual specifc and for a given person, it remains fairly stable over time3 . Upon mild stress such as exposure to specifc nutrients or diverse conditions of modern daily life or clinical practices, including antibiotics, the intestinal microbiota can be temporarily altered but will eventually return to its original composition; it is resilient4 . Nonetheless, marked alterations of dietary habits, environmental exposures, drug therapy or surgical interventions will induce alterations of the intestinal microbiota that may exceed the resilience capacity5,6 and lead to onset of dysbiosis, i.e. distorted intestinal microbiota composition. Dysbiosis is now acknowledged as a common feature of numerous non-infectious diseases of modern societies, which have had a constant increase in incidence since the middle of the past century. Obesity is one of these
The kisspeptin analog C6 is a possible alternative to PMSG (pregnant mare serum gonadotropin) for triggering synchronized and fertile ovulations in the Alpine goat
No full textIn temperate regions goat's reproduction is seasonal. To obtain year-round breeding, hormonal treatments are currently applied. These treatments usually combine a progesterone analog with the pregnant mare serum gonadotropin (PMSG). However, their use has significant ethical and environmental drawbacks. Therefore, alternative methods to manage reproduction are needed. The discovery that in mammals the neuropeptide kisspeptin is a major positive regulator of hypothalamo-pituitary gonadal axis offered an attractive alternative strategy to control reproduction. We have previously designed a kisspeptin analog, called C6, which offers pharmacological advantages over endogenous kisspeptin. These include a longer lasting effect and enhanced activity following intramuscular injection. In the present work, we evaluated C6 effect on LH and FSH plasma concentrations in the Alpine goat breed and tested whether C6 could replace PMSG to trigger ovulation. An intramuscular injection of C6 (15 nmol/doe) given 24 hours after the end of progestogen treatment induced a surge-like peak of both LH and FSH. This was followed by an increase of progesterone, a hallmark of ovulation induction and corpus luteus formation. These results were obtained at three different time of the year: during the breeding season, the non-breeding season and at the onset of the breeding season. Furthermore, we compared the efficacy of C6 and PMSG to induce fertile ovulations when these treatments are given at the onset of the breeding season and are followed by artificial insemination. The results of this first attempt were extremely promising with gestation rates of 45% and 64% for C6 and PMSG respectively. Pending optimization of the treatment procedure in order to improve efficacy, kisspeptin analogs could be the long sought-after alternative to PMSG
Direct observation of the cell-wall remodeling in adhering Staphylococcus aureus 27217: An AFM study supported by SEM and TEM
No full textWe took benefit from Atomic Force Microscopy (AFM) in the force spectroscopy mode to describe the time evolution–over 24 h–of the surface nanotopography and mechanical properties of the strain Staphylococcusaureus 27217 from bacterial adhesion to the first stage of biofilm genesis. In addition, Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM) experiments allowed identifying two types of self-adhering subpopulations (the so-called “bald” and “hairy” cells) and revealed changes in their relative populations with the bacterial culture age and the protocol of preparation. We indeed observed a dramatic evanescing of the “hairy” subpopulation for samples that underwent centrifugation and resuspension processes. When examined by AFM, the “hairy” cell surface resembled to a herringbone structure characterized by upper structural units with lateral dimensions of∼70 nm and a high Young modulus value (∼2.3 MPa), a mean depth of the trough between them of∼15 nm and a resulting roughness of∼5 nm. By contrast, the “bald” cells appeared much softer (∼0.35 MPa) with a roughness one order of magnitude lower. We observed too the gradual detachment of the herringbone patterns from the “hairy” bacterial envelope of cell harvested from a 16 h old culture and their progressive accumulation between the bacteria in the form of globular clusters. The secretion of a soft extracellular polymeric substance was also identified that, in addition to the globular clusters, may contribute to the initiation of the biofilm spatial organization
Parathyroid hormone initiates dynamic NHERF1 phosphorylation cycling and conformational changes that regulate NPT2A-dependent phosphate transport
No full textNa+-H+ exchanger regulatory factor-1 (NHERF1) is a PDZ protein that scaffolds membrane proteins, including sodium-phosphate co-transport protein 2A (NPT2A) at the plasma membrane. NHERF1 is a phosphoprotein with 40 Ser and Thr residues. Here, using tandem MS analysis, we characterized the sites of parathyroid hormone (PTH)-induced NHERF1 phosphorylation and identified 10 high-confidence phosphorylation sites. Ala replacement at Ser(46), Ser(162), Ser(181), Ser(269), Ser(280), Ser(291), Thr(293), Ser(299), and Ser(302) did not affect phosphate uptake, but S290A substitution abolished PTH-dependent phosphate transport. Unexpectedly, Ser(290) was rapidly dephosphorylated and rephosphorylated after PTH stimulation, and we found that protein phosphatase 1 (PP1), which binds NHERF1 through a conserved VxF/W PP1 motif, dephosphorylates Ser(290). Mutating (VPF259)-V-257 eliminated PP1 binding and blunted dephosphorylation. Tautomycetin blocked PP1 activity and abrogated PTH-sensitive phosphate transport. Using fluorescence lifetime imaging (FLIM), we observed that PTH paradoxically and transiently elevates intracellular phosphate. Added phosphate blocked PP1-mediated Ser(290) dephosphorylation of recombinant NHERF1. Hydrogen-deuterium exchange MS revealed that -sheets in NHERF1's PDZ2 domain display lower deuterium uptake than those in the structurally similar PDZ1, implying that PDZ1 is more cloistered. Dephosphorylated NHERF1 exhibited faster exchange at C-terminal residues suggesting that NHERF1 dephosphorylation precedes Ser(290) rephosphorylation. Our results show that PP1 and NHERF1 form a holoenzyme and that a multiprotein kinase cascade involving G protein-coupled receptor kinase 6A controls the Ser(290) phosphorylation status of NHERF1 and regulates PTH-sensitive, NPT2A-mediated phosphate uptake. These findings reveal how reversible phosphorylation modifies protein conformation and function and the biochemical mechanisms underlying PTH control of phosphate transport