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Interest in the serum color as an indirect criterion of selection of digestive efficiency in chickens
No full textImproving the digestive efficiency of birds is becoming increasingly important with the diversification of feedstuffs used in poultry diets. Compared with time-consuming chemical analyses that were previously used to measure digestive efficiency, near-infrared spectroscopy has been a great advance as it was fast and thus allowed measurements to be taken from a large number of animals, as required for genetic studies. However, it still implies to rear the birds in cages to collect feces, which is questionable in terms of welfare. The purpose of this study was thus to establish whether the serum color could be used as a biomarker of digestive efficiency that would be easy and fast to measure on floor-reared animals. We first compared the serum color of 2 lines of chickens divergently selected for high or low digestive efficiency when fed with a wheat-based diet. Digestive efficiency was assessed by nitrogen-corrected apparent metabolizable energy. Color was assessed by the absorbance of the serum between 300 and 572 nm. Color differed between the 2 lines between 430 and 572 nm, which corresponds to the absorption zone of carotenoids such as lutein and zeaxanthin. In a second step, we estimated the heritability of serum color measurements and their genetic correlations with digestive efficiency. Taking these parameters into account, in our experimental conditions the best trait among those tested that can be used as a biomarker of digestive efficiency is serum absorbance at 492 nm, with a heritability estimate of 0.31+0.09 and a genetic correlation with digestive efficiency of 0.84+0.28
Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species
No full textRecent interest for microgeographic adaptation, i.e. adaptation at spatial scales compatible with substantial amount of gene dispersal, offers to reconsider the scale at which evolution occurs (Richardson et al. 2014). Whether gene flow is constraining or facilitating local adaptation at this fine spatial scale remains an unresolved question. Too important gene flow would overwhelm the effects of natural selection and decrease local adaptation along environmental gradients. Conversely, gene flow, and particularly long-distance dispersal events, could play a major role in resupplying the genetic variation of populations and favouring the spread of beneficial alleles (Kremer et al. 2012). Hence, the high dispersal capacities of trees are often assumed to be the main process maintaining the large levels of genetic variation measured in their natural populations. However, evidences for microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited in most temperate trees.
Here, we sampled 60 open-pollinated families of European beech (Fagus sylvatica L.) from three natural plots, spreading along a short elevation gradient (∼1.5 km) at the warm margin of this species distribution. We analysed the phenotypic and genotypic data of ∼2,300 seedlings grown in a common garden. We focused on 11 potentially adaptive traits with significant heritabilities (Gauzere et al. 2016) and tested for signature of local selection on quantitative trait differentiation. We then identified the offspring likely originating from local or distant pollen immigration events and quantified the role of gene flow in increasing locally the additive variance of traits under selection.
We found a significant signal of adaptive differentiation among plots separated by less than one kilometre, with local selection acting on growth and phenological traits. We found that trees in the plots at high elevation, experiencing the lowest temperature conditions, flushed earlier and had a higher height and diameter growth in our common garden than trees from the plot at low elevation. Beech populations originating from higher longitude or elevation have also been shown to be genetically earlier in provenance tests, suggesting that these populations evolved phenological traits promoting a longer vegetation period. At this southern margin of the species, the reduced allocation to stem growth at the low elevation plot is likely an adaptive response to drought, which has previously been described by comparing marginal vs central beech populations. Consistently with theoretical expectations, our results suggest a beneficial effect of pollen dispersal by increasing the genetic diversity for these locally differentiated traits. These effects were quantitatively high, with more than twice higher genetic variance for immigrant than local offspring, although with large standard errors around estimates.
Our results highlight that local selection is an important evolutionary force in natural tree populations, and provide a strong evidence that adaptive genetic differentiation can occur despite high gene flow. For the two genetically differentiated traits, our analyses suggested a beneficial effect of pollen dispersal by increasing genetic diversity after one episode of reproduction. The findings suggest that conservation and management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and thereby enhance their adaptive potential
ATR-FTIR Microspectroscopy Brings a Novel Insight Into the Study of Cell Wall Chemistry at the Cellular Level
No full textWood is a complex tissue that fulfills three major functions in trees: water conduction,
mechanical support and nutrient storage. In Angiosperm trees, vessels, fibers and
parenchyma rays are respectively assigned to these functions. Cell wall composition
and structure strongly varies according to cell type, developmental stages and
environmental conditions. This complexity can therefore hinder the study of the
molecular mechanisms of wood formation, underlying the construction of its properties.
However, this can be circumvented thanks to the development of cell-specific
approaches and microphenotyping. Here, we present a non-destructive
microphenotyping method based on attenuated total reflectance–Fourier transformed
infrared (ATR-FTIR) microspectroscopy. We applied this technique to three types of
poplar wood: normal wood of staked trees (NW), tension and opposite wood of artificially
tilted trees (TW, OW). TW is produced by angiosperm trees in response to mechanical
strains and is characterized by the presence of G fibers, exhibiting a thick gelatinous extralayer,
named G-layer, located in place of the usual S2 and/or S3 layers. By contrast, OW
located on the opposite side of the trunk is totally deprived of fibers with G-layers. We
developed a workflow for hyperspectral image analysis with both automatic pixel
clustering according to cell wall types and identification of differentially absorbed
wavenumbers (DAWNs). As pixel clustering failed to assign pixels to ray S-layers with
sufficient efficiency, the IR profiling and identification of DAWNs were restricted to fiber
and vessel cell walls. As reported elsewhere, this workflow identified cellulose as the main
component of the G-layers, while the amount in acetylated xylans and lignins were shown
to be reduced. These results validate ATR-FTIR technique for in situ characterization of G
layers. In addition, this study brought new information about IR profiling of S-layers in TW,
OW and NW. While OW and NW exhibited similar profiles, TW fibers S-layers combined
characteristics of TW G-layers and of regular fiber S-layers. Unexpectedly, vessel S-layers
of the three kinds of wood showed significant differences in IR profiling. In conclusion,
ATR-FTIR microspectroscopy offers new possibilities for studying cell wall composition at
the cell level
Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily
No full textThe Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period
The synergistic triad between microcin, colibactin, and salmochelin gene clusters in uropathogenic Escherichia coli
No full textA functional synergy was previously demonstrated between microcin, salmochelin and colibactin islands
in Escherichia coli strains from B2 phylogroup. We aimed to determine this association prevalence in
uropathogenic E. coli, and whether it was predictive of the infection severity in a collection of 225 E. coli
strains from urinary samples. The high prevalence of this triad, even if it wasn’t correlated with infection
severity, suggested that it might not be a virulence factor per se within the urinary tract, but would
promote its colonization. This triad would enable the strain to dominate the rectal reservoir with a
minimal genetic cost
Effective Catalytic Delignification and Fractionation of Lignocellulosic Biomass in Water over Zn3V2O8 Mixed Oxide
No full textThe conversion of poplar wood biomass to highly value-added chemicals and molecular building blocks was achieved by using the dispersed mixed oxide Zn3V2O8 (ZVO) in water under 100 kPa of 10% O-2/N-2 at 160, 180, and 200 degrees C for 4 h. This nanostructured mixed oxide was prepared via the precipitation process and then characterized by several techniques. The results showed that this mixed oxide has interesting catalytic properties and is a versatile catalyst for biomass delignification and lignin and hemicellulose depolymerization. ZVO exhibited high activity on poplar biomass delignification and fractionation (degree delignification > 97%) and lignin and holocellulose conversion with high yield into aromatic and furan compounds (80 mg/g initial wood at 200 degrees C), with high selectivities for 5-hydroxymethylfurfural (HMF) (25 mg/g of initial wood), vanillin, and syringaldehyde
Conceptual basis, formalisations and parameterization of the STICS crop model, second edition
No full textExposition des travailleurs en élevages de porcs et de volailles de chair à l’ammoniac et aux particules
No full textL'air des bâtiments porcins et avicoles contient de l’ammoniac et des particules. Pour caractériser l'exposition des travailleurs à ces polluants, des données ont été collectées dans des exploitations agricoles. Les mesures ont été effectuées dans 20 exploitations porcines pendant des tâches considérées comme exposantes : les soins aux porcelets, le sevrage, l'alimentation des porcelets et le tri des porcs. 21 exploitations avicoles ont également été suivies pendant la surveillance en fin de bande, le ramassage, le curage du fumier et le paillage du bâtiment. En général, les particules et l'ammoniac ne sont pas considérés comme des risques professionnels par les travailleurs. Le risque est souvent minimisé mais les mesures montrent que l'exposition aux particules et à l'ammoniac impacte leur santé (augmentation des symptômes respiratoires et diminution de la capacité respiratoire). En outre, 15% des exploitations porcines ont une teneur en ammoniac supérieure à la limite d'exposition professionnelle (20 ppm pendant 15 minutes) pour au moins une des tâches contrôlées. En aviculture, 17% des mesures d'ammoniac au cours des tâches suivies sans paillage et 3% de toutes les mesures de particules effectuées dépassent la valeur maximale recommandée (5 mg/m3 de particules alvéolaires). Il est nécessaire de sensibiliser les acteurs du terrain aux risques respiratoires. À cette fin, une chaîne YouTube AIR Eleveur a été créée, ainsi que 2 brochures (équipement de protection et résultats AIR Eleveur).The air of pig and poultry farms contains ammonia and dust. To characterize the exposure of workers to these pollutants, data were collected on farms. Measurements were carried out in 20 pig farms during piglet care, weaning, feeding of piglets and sorting pigs and in 21 poultry farms during inspection of animals, catching birds, the manure disposal and litter distribution in the building. In general, particulate matter and ammonia are not considered as occupational hazards by workers. The risk is often minimized but measurements showed that exposure to particulate matter and ammonia poses a risk to their health (increased respiratory symptoms and decreased respiratory capacity). In addition, 15% of pig farms had an ammonia content above the occupational exposure limit (20 ppm for 15 minutes) on at least one of the tasks monitored. In poultry farming, 17% of the ammonia measurements during the tasks followed without mulching, and 3% of all the measurements of particles carried out exceeded the maximum recommended value (5 mg / m3 of cellular particles). It is necessary to sensitize the actors of the field on the respiratory risks. For this purpose, an AIR Eleveur YouTube channel was created as well as 2 brochures (protection equipment and AIR Eleveur results)
The quail genome: insights into social behaviour, seasonal biology and infectious disease response
No full textBackground The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. Conclusions We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species
Inference of breed structure in farm animals: empirical comparison between SNP and microsatellite performance
No full textKnowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, F-ST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise F-ST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number