Systèmes d’élevage méditerranéens et tropicaux

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Agroecology and industrial ecology can be viewed as complementary means for reducing the environmental footprint of animal farming systems: agroecology mainly by stimulating natural processes to reduce inputs, and industrial ecology by closing system loops, thereby reducing demand for raw materials, lowering pollution and saving on waste treatment. Surprisingly, animal farming systems have so far been ignored in most agroecological thinking. On the basis of a study by Altieri, who identified the key ecological processes to be optimized, we propose five principles for the design of sustainable animal production systems: (i) adopting management practices aiming to improve animal health, (ii) decreasing the inputs needed for production, (iii) decreasing pollution by optimizing the metabolic functioning of farming systems, (iv) enhancing diversity within animal production systems to strengthen their resilience and (v) preserving biological diversity in agroecosystems by adapting management practices. We then discuss how these different principles combine to generate environmental, social and economic performance in six animal production systems (ruminants, pigs, rabbits and aquaculture) covering a long gradient of intensification. The two principles concerning economy of inputs and reduction of pollution emerged in nearly all the case studies, a finding that can be explained by the economic and regulatory constraints affecting animal production. Integrated management of animal health was seldom mobilized, as alternatives to chemical drugs have only recently been investigated, and the results are not yet transferable to farming practices. A number of ecological functions and ecosystem services (recycling of nutrients, forage yield, pollination, resistance to weed invasion, etc.) are closely linked to biodiversity, and their persistence depends largely on maintaining biological diversity in agroecosystems. We conclude that the development of such ecology-based alternatives for animal production implies changes in the positions adopted by technicians and extension services, researchers and policymakers. Animal production systems should not only be considered holistically, but also in the diversity of their local and regional conditions. The ability of farmers to make their own decisions on the basis of the close monitoring of system performance is most important to ensure system sustainability.

BACKGROUND: Common variable immunodeficiency (CVID) is a primary immune deficiency defined by defective antibody production. In most series, a small proportion of patients present with opportunistic infections (OIs). METHODS: The French DEFI study has enrolled patients with primary hypogammaglobulinemia and allows a detailed clinical and immunologic description of patients with previous OIs and/or at risk for OIs. RESULTS: Among 313 patients with CVID, 28 patients (8.9%) presented with late-onset combined immune deficiency (LOCID), defined by the occurrence of an OI and/or a CD4(+) T cell count <200 x 10(6) cells/L, and were compared with the remaining 285 patients with CVID. The patients with LOCID more frequently belonged to consanguineous families (29% vs 8%; P = .004). They differed from patients with CVID with a higher prevalence of splenomegaly (64% vs 31%), granuloma (43% vs 10%), gastrointestinal disease (75% vs 42%), and lymphoma (29% vs 4%). Even on immunoglobulin substitution, they required more frequent antibiotics administration and hospitalization. Lymphocyte counts were lower, with a marked decrease in CD4(+) T cell counts (158 x 10(6) vs 604 x 10(6) cells/L; P < .001) and a severe defect in naive CD45RA(+)CCR7(+)CD4(+) T cell counts (<20% of total CD4(+) T cells in 71% of patients with LOCID vs 37% of patients with CVID; P = .001). The CD19(+) B cell compartment was also significantly decreased (20 x 10(6) vs 102 x 10(6) cells/L; P < .001). CONCLUSIONS: LOCID differs from classic CVID in its clinical and immunologic characteristics. Systematic T cell phenotype may help to discriminate such patients from those with CVID. Identification of this phenotype should result in a more fitted diagnostic and therapeutic approach of infections and could provide insights for genetic diagnosis.

Abstract: A rich theory has been developed to explain the evolution of populations at equilibrium conditions of gene flow, inbreeding, and selection. There are, however, few empirical examples of the effects of gene flow into recently isolated, small populations under nonequilibrium conditions, such as are expected following population fragmentation. We studied the effects of inbreeding and gene flow in small, experimental populations of the mustard Brassica campestris ( rapa ). Replicate populations of five individuals randomly mated in a growth room received treatments of 0, 1, or 2.5 migrants each generation. Plants from the sixth experimental generation were planted in an outdoor common garden to evaluate the effects of the treatments on fitness and the distribution of phenotypic variation. Regression of six fitness components on inbreeding coefficients indicated a negative effect of inbreeding on fitness for five of these components. The 0‐migrant treatment had significantly lower fitness than the migrant treatments for four of six fitness components, but fitness did not differ between the 1‐migrant and 2.5‐migrant treatments. Phenotypic divergence among populations decreased with an increased number of migrants. These data provide empirical evidence of the beneficial fitness effects of a small number of migrants for recently fragmented populations.

Abstract Improving feed efficiency ( FE ) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30–70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE . Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.

Ongoing intensification and specialisation of livestock production lead to increasing volumes of manure to be managed, which are a source of the greenhouse gases (GHGs) methane (CH4) and nitrous oxide (N2O). Net emissions of CH4 and N2O result from a multitude of microbial activities in the manure environment. Their relative importance depends not only on manure composition and local management practices with respect to treatment, storage and field application, but also on ambient climatic conditions. The diversity of livestock production systems, and their associated manure management, is discussed on the basis of four regional cases (Sub-Saharan Africa, Southeast Asia, China and Europe) with increasing levels of intensification and priorities with respect to nutrient management and environmental regulation. GHG mitigation options for production systems based on solid and liquid manure management are then presented, and potentials for positive and negative interactions between pollutants, and between management practices, are discussed. The diversity of manure properties and environmental conditions necessitate a modelling approach for improving estimates of GHG emissions, and for predicting effects of management changes for GHG mitigation, and requirements for such a model are discussed. Finally, we briefly discuss drivers for, and barriers against, introduction of GHG mitigation measures for livestock production. There is no conflict between efforts to improve food and feed production, and efforts to reduce GHG emissions from manure management. Growth in livestock populations are projected to occur mainly in intensive production systems where, for this and other reasons, the largest potentials for GHG mitigation may be found.

La peste des petits ruminants (PPR) est une maladie très contagieuse, fréquemment associée à une forte mortalité. Dans les pays où elle sévit, la PPR représente un frein important à l'amélioration de la productivité des moutons et des chèvres. Jusqu'à présent, le seul moyen de lutte contre ce fléau a été l'utilisation du vaccin hétérologue anti peste bovine, toutes les tentatives pour développer un vaccin homologue ayant échoué. Cet article décrit l'atténuation de la souche nigériane du virus PPRV Nig. 75/1 par passages en série sur cellules Vero. Le virus avirulent obtenu a les mêmes caractéristiques que le vaccin bovipestique de Plowright et Ferris. Il constitue donc un vaccin homologue potentiel contre la PPR.

A two-step strategy, named exclusive PCR or E-PCR, has been developed to overcome the main limitation of PCR, which is the detection of already-known sequences only. This strategy allows the ability to detect and further clone and sequence genes for which no specific primers are available and in which a variable region exists between two conserved regions. This approach has been applied to Bacillus thuringiensis cryI genes by the use of mixtures of degenerate and specific primers recognizing well-known sequences. The first step allows the accurate identification of already-characterized cryI genes by the use of three primers. During the second step, the same sets of primers are used to exclude known sequences and to positively detect cryI genes unrecognized by any specific primer. The method, as well as its application to detect, clone, and sequence a novel cryIB gene, is described in this article.

ABSTRACT Amylose content is a parameter that correlates with the cooking behavior of rice. It is measured at the earliest possible stages of rice improvement programs to enable breeders to build the foundations of appropriate grain quality during cultivar development. Amylose is usually quantified by absorbance of the amylose‐iodine complex. The International Network for Quality Rice (INQR) conducted a survey to determine ways that amylose is measured, reproducibility between laboratories, and sources of variation. Each laboratory measured the amylose content of a set of 17 cultivars of rice. The study shows that five different versions of the iodine binding method are in use. The data show that repeatability was high within laboratories but reproducibility between laboratories was low. The major sources of variability were the way the standard curve was constructed and the iodine binding capacity of the potato amylose used to produce the standard. Reproducibility is much lower between laboratories using a standard curve of potato amylose alone compared with those using calibrated rice cultivars. This study highlights the need to standardize the way amylose is measured, and presents research avenues for doing so.

The consistent monitoring of trees both inside and outside of forests is key to sustainable land management. Current monitoring systems either ignore trees outside forests or are too expensive to be applied consistently across countries on a repeated basis. Here we use the PlanetScope nanosatellite constellation, which delivers global very high-resolution daily imagery, to map both forest and non-forest tree cover for continental Africa using images from a single year. Our prototype map of 2019 (RMSE = 9.57%, bias = -6.9%). demonstrates that a precise assessment of all tree-based ecosystems is possible at continental scale, and reveals that 29% of tree cover is found outside areas previously classified as tree cover in state-of-the-art maps, such as in croplands and grassland. Such accurate mapping of tree cover down to the level of individual trees and consistent among countries has the potential to redefine land use impacts in non-forest landscapes, move beyond the need for forest definitions, and build the basis for natural climate solutions and tree-related studies.

Old World camels have served humans in cross-continental caravans, transporting people and goods, connecting different cultures and providing milk, meat, wool and draught since their domestication around 3000-6000 years ago. In a world of modern transport and fast connectivity, these beasts of burden seem to be out-dated. However, a growing demand for sustainable milk and meat production, especially in countries affected by climate change and increasing desertification, brings dromedaries (Camelus dromedarius) and Bactrian camels (Camelus bactrianus) back onstage and into the focus of animal breeders and scientists. In this review on the molecular genetics of these economically important species we give an overview about the evolutionary history, domestication and dispersal of Old World camels, whereas highlighting the need for conservation of wild two-humped camels (Camelus ferus) as an evolutionarily unique and highly endangered species. We provide cutting-edge information on the current molecular resources and on-going sequencing projects. We cannot emphasise enough the importance of balancing the need for improving camel production traits with maintaining the genetic diversity in two domestic species with specific physiological adaptation to a desert environment.

Abstract Identifying homozygous‐by‐descent (HBD) regions in individual genomes is highly valuable to infer the recent history of populations and to provide insights into trait architecture. Here, we present the RZooRoH R ‐package that implements an efficient and accurate model‐based approach to identify HBD segments. The underlying hidden Markov model partitions the genome‐wide individual autozygosity into different age‐related HBD classes while accounting for genotyping errors and genetic map information. The RZooRoH package is user‐friendly and versatile, accepting either genotyping or sequencing (including low‐coverage) data in various formats. Through numerical maximization and parallelization, computational performances were improved compared to our initial Fortran implementation of the model. The package allows to evaluate and compare various models defined by their number of HBD classes and it also provides several graphical functions that help interpretation of the results. RZooRoH is an efficient tool that proves particularly suited for sub‐optimal datasets (e.g. low marker density, individual low‐coverage sequencing, uneven marker spacing) and for individuals from populations with complex demographic histories. RZooRoH is available from CRAN: https://CRAN.R-project.org/package=RZooRoH .

Deep-fat frying is a popular process that has been studied essentially to clarify the complex mechanisms of fat decomposition at high temperatures and to assess their effects on human health. The aim of this paper is to show how the application of process engineering methods has recently improved our understanding of the basic principles and mechanisms involved at different scales and different times during the process: pretreatment, frying, and cooling. New results concerning the understanding of the frying process have been obtained as a result of major breakthroughs in on-line instrumentation (heat, steam flux, and local pressure sensors), in the methodology of microstructural and imaging analysis (NMR, MRI, SEM) and in software tools for the simulation of coupled transfer and transport phenomena. Such advances have opened up the way for the creation of a major database of the behavior of various materials and to the development of new tools to control frying operations via final product quality in real conditions. Lastly, this paper promotes an integrated approach to the frying process including various competencies such as those of chemists, engineers, toxicologists, nutritionists, and materials scientists as well as of the catering and industrial sectors.

Abstract In recent decades, in the South of France some young people from urban backgrounds have chosen to become shepherds and to learn to reconnect with the herding practices that many livestock breeders had abandoned under the pressure of agricultural modernization policies. In some cases they have found themselves entrusted with sheep that are as naive about herding as they themselves were. Before their introduction to transhumance—seasonal movement between pastures—these animals were primarily confined and fed indoors or in small fenced areas. The shepherds had to learn how to lead, how to understand other modes of living, how to teach their sheep what is edible and what is not, and how to form a flock; the sheep had to learn how to “compose with” dogs and humans, to acquire new feeding habits, a new ethos, and moreover, new ways of living in an enlarged world. These practices cannot be reduced to a livestock economy: shepherds consider herding a work of transformation and ecological recuperation—of the land, of the sheep, of ways of being together. Learning the “arts of living on a damaged planet,” as Anna Tsing has termed it, humans and animals are making their own contributions to a new cosmoecology, creating cosmoecological connections and contributing to what Ghassan Hage has called alter-politics.

Abstract At world level, the current official number of large camelids cannot be determined exactly (it is estimated to be more than 35 million heads), and the role of camels in the livestock economy is highly variable. The only reliable statistics are provided by FAO since 1961. According to these data, five different patterns of demographic changes have been observed. In countries marked by a regular or drastic decline of their camelid population, a tendency to re-increase has been in force since the beginning of the century, except in India. Generally, countries marked by a sharp recent increase in their large camelid population have implemented a census and readjusted their data. Many inconsistencies occur in available data, most notably cases arising from changes occurring in state status (for example secession of Eritrea, Soviet Union collapse). Moreover, large camelid stocks in Australia, in countries of new camel establishment (Western countries) and those related to the expansion of camel farming, notably in Africa, are not recorded in the international database. In addition, there is no distinction between dromedary and Bactrian data. The present large camelid population in the world is probably more than 40 million and could reach 60 million after 25 years from now if the current demographic trend is maintained.

Camel milk is a newcomer to domestic markets and especially to the international milk market. This recent emergence has been accompanied by a diversification of processed products, based on the technologies developed for milk from other dairy species. However, technical innovations had to be adapted to a product with specific behavior and composition. The transformation of camel milk into pasteurized milk, fermented milk, cheese, powder, or other products was supported, under the pressure of commercial development, by technological innovations made possible by a basic and applied research set. Some of these innovations regarding one of the less studied milk sources are presented here, as well as their limitations. Technical investigations for an optimal pasteurization, development of controlled fermentation at industrial scale, control of cheese technology suitable for standardized production, and improvements in processes for the supply of a high-quality milk powder are among the challenges of research regarding camel milk.

1. Regional above-ground biomass estimates for tropical moist forests remain highly inaccurate mostly because they are based on extrapolations from a few plots scattered across a limited range of soils and other environmental conditions. When such conditions impact biomass, the estimation is biased. The effect of soil types on biomass has especially yielded controversial results. 2. We investigated the relationship between above-ground biomass and soil type in undisturbed moist forests in the Central African Republic. We tested the effects of soil texture, as a surrogate for soil resources availability and physical constraints (soil depth and hydromorphy) on biomass. Forest inventory data were collected for trees ≥20 cm stem diameter in 2754 0.5 ha plots scattered over 4888 km2. The plots contained 224 taxons, of which 209 were identified to species. Soil types were characterized from a 1:1 000 000 scale soil map. Species-specific values for wood density were extracted from the CIRAD’s data base of wood technological properties. 3. We found that basal area and biomass differ in their responses to soil type, ranging from 17.8 m2 ha−1 (217.5 t ha−1) to 22.3 m2 ha−1 (273.3 t ha−1). While shallow and hydromorphic soils support forests with both low stem basal area and low biomass, forests on deep resource-poor soils are typically low in basal area but as high in biomass as forests on deep resource-rich soils. We demonstrated that the environmental filtering of slow growing dense-wooded species on resource-poor soils compensates for the low basal area, and we discuss whether this filtering effect is due to low fertility or to low water reserve. 4. Synthesis. We showed that soil physical conditions constrained the amount of biomass stored in tropical moist forests. Contrary to previous reports, our results suggest that biomass is similar on resource-poor and resource-rich soils. This finding highlights both the importance of taking into account soil characteristics and species wood density when trying to predict regional patterns of biomass. Our findings have implications for the evaluation of biomass stocks in tropical forests, in the context of the international negotiations on climate change.

Mass transfer phenomena were qualitatively investigated during osmotic dehydration of fresh apple in concentrated solutions using response‐surface methodology. the influence of the main process variables (solute concentration, solute molecular weight, temperature and processing time) were thus determined. Osmotic phenomena, such as plant cell plasmolysis, only had a marked effect on dehydration at moderate temperatures (T &gt; 50°C) and when low molecular weight solutes that could easily penetrate tissues were used. More generally, basic dehydration mechanisms were diffusive and seemed to be closely correlated with the formation of dense solute barrier at the surface of the product. the formation of this barrier layer, which was promoted by high molecular weight solutes and/or high solute content, could reduce loss of natural fruit solutes.

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.

The Shea tree (Vitellaria paradoxa) is a major tree species in African agroforestry systems. Butter extracted from its nuts offers an opportunity for sustainable development in Sudanian countries and an attractive potential for the food and cosmetics industries. The purpose of this study was to develop near-infrared spectroscopy (NIRS) calibrations to characterize Shea nut fat profiles. Powders prepared from nuts collected from 624 trees in five African countries (Senegal, Mali, Burkina Faso, Ghana and Uganda) were analyzed for moisture content, fat content using solvent extraction, and fatty acid profiles using gas chromatography. Results confirmed the differences between East and West African Shea nut fat composition: eastern nuts had significantly higher fat and oleic acid contents. Near infrared reflectance spectra were recorded for each sample. Ten percent of the samples were randomly selected for validation and the remaining samples used for calibration. For each constituent, calibration equations were developed using modified partial least squares (MPLS) regression. The equation performances were evaluated using the ratio performance to deviation (RPD(p)) and R(p)(2) parameters, obtained by comparison of the validation set NIR predictions and corresponding laboratory values. Moisture (RPD(p) = 4.45; R(p)(2) = 0.95) and fat (RPD(p) = 5.6; R(p)(2) = 0.97) calibrations enabled accurate determination of these traits. NIR models for stearic (RPD(p) = 6.26; R(p)(2) = 0.98) and oleic (RPD(p) = 7.91; R(p)(2) = 0.99) acids were highly efficient and enabled sharp characterization of these two major Shea butter fatty acids. This study demonstrated the ability of near-infrared spectroscopy for high-throughput phenotyping of Shea nuts.