La peste des petits ruminants (PPR) et la Pleuropneumonie Contagieuse Caprine (PPCC) causées respectivement par un Morbillivirus (Virus de la Peste des Petits Ruminants) et un mycoplasme (Mycoplasma capricolum subsp. Capripneumoniae) sont deux maladies respiratoires très contagieuses des petits ruminants. La PPR est présente en Afrique, en Asie, au Moyen Orient, et depuis peu en Europe. Sur le continent africain, notamment en Afrique de l’Ouest, elle est en expansion et représente un facteur majeur d’insécurité alimentaire pour la population agricole. La PPCC identifiée au Niger en 1995 n’est que suspectée au Mali sur la base de résultats sérologiques.La PPR est un modèle pour l’étude des maladies transfrontalières car sa diffusion est très étroitement liée aux mouvements régionaux d’animaux vivants. La compréhension de cette diffusion est une condition essentielle à la mise en place de mesures de contrôle efficaces (vaccination, contrôle aux frontières etc.).La thèse a pour ambition de clarifier la situation épidémiologique de la PPR et de la PPCC au Mali, notamment pour savoir si ces deux maladies coexistent, afin d’en évaluer le risque pour les filières de production de caprins et de proposer des stratégies de contrôle adaptées. Nous n’avons pas réussi à mettre en évidence la présence de la PPCC au Mali. Pour la PPR, l’objectif de la thèse est de caractériser la diversité génétique de souches collectées en Afrique de l’Ouest et plus particulièrement au Mali en utilisant en première instance le gène partiel de la nucléoprotéine du virus. Nous avons ensuite estimé la diversité et le taux d’évolution du PPRV dans la région à partir de séquences génomiques complètes. Notre étude a montré qu’au Mali ainsi que dans les autres pays de l’Afrique de l’Ouest, trois lignées génétiques du PPRV circulent dont l’une d’elles, la lignée II est dominante dans la région et est caractérisée par une grande diversité génétique transfrontalière. Cette étude démontre également une progression de la lignée IV dans l’Afrique de l’Ouest et la persistance au Mali et au Niger de la lignée I (au moins jusqu’en 2001). Ces résultats reflètent par rapport aux données précédentes connues de la répartition des lignées de PPRV, une intensification des mouvements du bétail dus à l’échange et au commerce de ces animaux, flux qui n’est pas contrôlé entre tous les pays de l’ouest africain. Au Mali, il n’existe aucun moyen de contrôle, de traçabilité et d’identification animale. L’utilisation de la diversité génétique comme marqueur épidémiologique serait un moyen d’améliorer notre connaissance de la diffusion de la PPR et de là son contrôle, plus particulièrement dans les pays d’Afrique de l’Ouest. / Peste des petits ruminants (PPR) and Contagious caprine pleuropneumonia (CCPP) caused respectively by a Morbillivirus and a mycoplasma (Mycoplasma capricolum subsp. Capripneumoniae) are two highly contagious respiratory diseases of small ruminants. PPR is present in Africa, Asia, Middle East, and has just entered Europe. On the African continent, particularly in West Africa, it is emerging and is a major factor of food insecurity for low-income farmers. CCPP, identified in Niger in 1995, is only suspected in Mali on the basis of serological results.PPR is a model for the study of transboundary diseases because its diffusion is closely linked to regional movements of livestock. Understanding this diffusion is an essential condition for the implementation of effective control measures (vaccination, border control, etc.).The aims of our study is to clarify the epidemiological situation of PPR and the CCPP in Mali, including whether these two diseases coexist in order to assess the risk for goat production chains and propose appropriate control strategies.We did not succeed in confirming the presence of the CCPP in Mali. PPR has already been identified in Mali. The aim of our study for PPR is to characterize the genetic diversity and therefore the different lineages that circulate in Mali and, more generally, in the West African sub region by using at first the partial gene of Nucleoprotein of PPRV. We then estimated more accurately the diversity and rate of evolution of the virus in the region from PPRV genomic sequences. Our studies showed that three lineages of PPRV are circulating in Mali and West Africa. The lineage II is dominating and is characterized with a wide genetic diversity and extensive transboundary circulation. We also demonstrate the progression of lineage IV in West Africa and the persistence of lineage I in Mali and Niger (at least until 2001). These results reflect the large flow of uncontrolled livestock trade between all West African countries. In Mali, there is no means of control, traceability and animal identification. The use of genetic diversity as an epidemiological marker is an effective means of controlling the spread of PPR in these West African countries.

Gastrointestinal nematode parasites cause great losses in the production of small ruminants through reduced productivity and the cost of preventive and curative treatments. Because of the threat of anthelmintic resistance, biological control of sheep nematodes has been identified as an alternative to anthelmintic drugs. Bacillus thuringiensis (Bt) (Berliner) and Clonostachys rosea (Schroers) have been widely studied as biocontrol agents. B. thuringiensis has been used for the biocontrol of insects and C. rosea has been successfully used as biocontrol agent of Botrytis cinera (De Bary) in plants. B. thuringiensis and C. rosea strains were isolated from soil collected from the Livestock Section at Ukulinga Research Farm, University of KwaZulu Natal, Pietermaritzburg. Twenty-five strains of Bt and 10 strains of C. rosea were successfully isolated. The Bt colonies were identified by their circular, white, flat and undulate character, and the gram-positive and rod-shaped endospores. C. rosea was identified by white colonies on Potato-dextose agar and the characteristic conidiophores, which were branched and showed phialides at the tips. In vitro screening of the isolates was undertaken to select the best isolates. The isolates that caused significantly greater mortality were Bt isolate B2, B10 and B12 and C. rosea isolates P1, P3 and P8. These isolates caused substantial nematode mortality in both faeces and water bioassay. Nematode counts were reduced by 28.5% to 62% and 44% to 69.9% in faecal bioassay for Bt and C. rosea, respectively. In the water bioassay, nematode counts were reduced by 62% to 85% for Bt and by 62.7% to 89.3% for C. rosea. The best inoculum level at which the best isolates were most effective, and the optimum frequency of application were determined. The trial was conducted using bioassays with faeces and water. Inoculum levels of 10(6), 10(8), 10(10), 10(12) spores ml-1 for Bt and 10(6), 10(8) and 10(10) conidia ml-1 for C. rosea was used in the faecal bioassay. The inoculum levels tested in water bioassay were 10(6), 10(8), 10(10) and 10(12) spores ml-1 for Bt and 10(9), 10(10), 10(11), 10(12) conidia ml-1 for C. rosea. In the faecal bioassay, B2 was the most effective Bt isolate at an inoculum level of 10(10) spores ml-1. Isolate P3 was the best C. rosea isolate at 10(8) conidia ml-1. In the water bioassay, Isolate P3 caused a mortality of 85% at inoculum levels of 10(9), 10(10) and 10(11) conidia ml-1. The performance of biological control agents in the field is sometimes inconsistent. Combining different biocontrol agents may be a method of improving their reliability and performance. However, the combination of most of the isolates was antagonistic, with efficacy less than that of either individual biocontrol agent. In particular, Isolate P3 was more effective when used alone than when combined with any other isolates. Therefore, the combination of biocontrol agents does not always result in synergistic interaction. There were some additive interactions between two bacterial isolates, and with one bacterial and fungal combination. The effect of feeding the best of the biocontrol agents, or diatomaceous earth (DE), was evaluated in sheep. Two doses of Bt (1g and 2g kg-1BW) and C. rosea (1g kg-1BW) reduced the numbers of L3 nematode larvae in sheep faeces. The DE product (at 15% of feed) also reduced L3 numbers but it was less effective than either the Bt or the C. rosea products. Nematode counts were reduced by 74.6%, 75.1%, 84.6%, 68.5% and 27.5% for Bt 1g kg-1BW, Bt 2g kg-1BW, C. rosea (1g kg-1 BW), DE and control, respectively. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

The growing demand for meat worldwide by the increasing human population (6.8 billion) calls for an increase in livestock production as well as attention to environmental sustainability. Production increases are critical especially in Africa with the highest annual population growth rate (2.5%), where most communities rely on livestock for protein supply. Attempts by intensive livestock farming to optimize production are limited by fibrous quality feeds (roughages) and their unavailability in both developed and developing countries. The overall objective of this study was to scan both domestic and wild herbivores in search for microbial ecosystems with superior fibrolytic potential that can be used as feed additives. It was hypothesized that microbes from wild herbivore can improve fibrous feed breakdown in domesticated ruminants. Experiment 1 evaluated the use of fresh or in vitro cultured faecal inoculum (FF) from two Jersey cows as a potential substitute for rumen fluid (RF). Cultured FF was a better substitute for fresh RF as demonstrated by percentage differences in exocellulase activity (0.4%) and true degradability (TD) (7%), compared to the differences observed between fresh RF and FF for exocellulase activity (33%) and TD (14%). It was applied in subsequent experimentation because it was cost effective (no surgery and reduced sample collection time). The second experiment compared the fibrolytic competence of cultured faecal inocula from three hindgut fermenters (miniature horse (mH), horse (H) and Zebra (ZB)) in summer and winter grazing in their natural environment. Both cellulase enzyme assays (exocellulase, endocellulase and hemicellulase) and in vitro maize stover digestibility study ranked the herbivores according to their fibrolytic competence as ZB > H > mH. The effect of cultured faecal inocula from H, ZB and wildebeest (WB) and its combined systems (N1=H+WB, N2=H+ZB, N3=WB+ZB and N4=H+WB+ZB) on the fermentation of maize stover were also evaluated in vitro. Both enzyme assays and MS degradability studies showed that the combined systems were higher (P<0.01) in fibrolytic activities compared to the individual systems. The microbial ecosystems were ranked as N1 > N2 > N4 > H > ZB > WB >N3; and N3 > N1 > N4 > WB > N2 > ZB >H by their exocellulase activity and degradability parameters, repetitively. The diversity of microbial ecosystems was confirmed by numerous active carboxymethyl cellulase bands present on a carboxymethy cellulose zymograms in experiment 4. The combined microbial ecosystems contain more active and variable bands of cellulases than in the individual microbial ecosystems. Systems N3 and N1 were considered as the best inocula for rumen transinoculation studies. Experiment 5 assessed the in vivo effect of direct-fed microbials from N1 and N3 on MS degradation, ruminal fermentation characteristics and cellulase enzyme profile in sheep. Feed dry matter intake increased (P<0.03) in N1 but tended to increase when inoculated with N3. The treatments, N1 and N3 increased (P<0.05) rumen exocellulase (9.4 and 33.2%, respectively) and endocellulase (82.1 and 47.1%, respectively) specific activities but not hemicellulase activity. Maize stover degradability parameters for N3 (TD, degradability of the insoluble fraction of MS, effective degradability, total SCFA and propionate) measured after 96 h of incubation tended (P>0.05) to be numerically different (1.1, 5.4, 7.1 and 7.9%, respectively). Increase in propionate for N3 was accompanied by higher total SCFA and lower CH4. A decrease in CH4 and no difference in CO2 allow both systems to be environmentally friendly since they have been associated with global warming. These studies showed that direct-fed microbials from N1 and N3 inocula have the potential of improving the utilization of maize stover feeds in ruminants, particularly in view of its simplicity and availability which allows it to be implemented at a relatively lower cost compared to other specific strains or microbial cultures. However, more research is required to identify, purify and classify the superior fibrolytic microbes in the most active ecosystems. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

The aim of this study was to determine firstly if there exist variations in fibrolysis among herbivore microbial ecosystems and secondly, the effect on fibre hydrolysis of compositing the most active systems with ruminal microbial ecosystem harvested from a Jersey cow. A literature review pointed to the complexity of carbohydrate (fibre) and how the physical and chemical nature of the forage carbohydrate can present barriers that hinder digestion in the rumen, especially its association with hemicelluloses, pectin, lignin and tannins. Fresh rumen fluid was collected from fistulated herbivores (Jersey cow and sheep) and faecal samples from non-fistulated herbivores (buffalo, horse, impala, camel, elephant, llama, sheep, wildebeest and elephant). Crude protein samples were precipitated with 60% ammonium sulfate. Sample activities were monitored and optimised by incubating with carboxymethyl cellulose (CMC) for 2 h at 39°C. The crude protein samples precipitated from the 11 herbivore microbial ecosystems were active. This was confirmed by an increase in enzyme specific activity with a decrease in total crude protein concentration. In vitro pH optimisation showed a broad range of activity for all ecosystems (4.5-8.0) but for the zebra, horse and elephant which peaked at pH 5. In experiment two (Chapter 4), seasonal variation of the enzymes (exocellulase, endocellulase, cellobiase and xylanase) were monitored through winter and summer. Enzyme specific activity of exocellulase, endocellulase, cellobiase and xylanase were determined by incubation with the specific substrates, crystalline cellulose, CMC, pNPG and xylan, respectively. The amount of reducing sugar released was used to determine the enzyme specific activity. Exocellulase analysis was suitable in winter while summer was preferred for carboxymethyl cellulase and xylanase due to their relative abundance. Cellobiase analysis did not depend on any particular season. Eleven herbivore microbial ecosystems were characterised according to their fibrolytic enzyme specific activities. Enzyme catalytic activities were calculated from kinetic parameters (Km and Vmax) obtained from Eisenthal and Cornish-Bowded plots (Chapter 5). Fibrolytic enzyme expression as well as their activities differed among the 11 ecosystems (P<O.OOOI). They were classified into three groups based on fibrolytic enzyme concentrations; group A with high enzyme concentrations (horse, impala, zebra, wildebeest and the elephant), group B with intermediate (cow, llama, camel, buffalo and giraffe) and group C with low enzyme concentrations (sheep). Exocellulase activity was reasonably correlated with endocellulase activity (r = 0.8978). Xylanase activity was also correlated with carboxymethyl cellulase actvity (r = 0.7104). Enzyme kinetic studies revealed that crude protein samples from the horse, zebra, wildebeest and elephant had the highest enzyme catalytic activities. Microbial or enzyme composite systems were created from the most active ecosystems (horse, wildebeest and zebra) in an attempt to improve the Jersey cow system. These systems were B (cow and horse), C (cow and wildebeest), D (cow and zebra) and E (cow, horse, zebra and wildebeest). The specific activities and enzyme efficiencies of these new systems were determined and compared with system A (cow). Microbial synergism of these systems was also investigated by measuring the amount of gas produced and true degradability (TD) after 72 h of incubation. The composite systems Band E were the most active fibrolytic enzyme systems while C and D were intermediate when compared to that of A. In vitro microbial synergism assays showed that systems B, D, and E had the highest potential of improving milky maize stover (MM) and nutral detergent fibre (NDF) fermentation and degradability in Jersey cows. It was concluded that: (i) fibrolytic and hemicellulolytic enzyme concentrations vary from one season to another with the changing forages; (ii) microbial fibrolytic activities vary among animals grazing on the same field or different geographical regions; and (iii) lastly microbial synergisms of active ecosystems have the potential of improving fibre hydrolysis. However, there is a need to conduct in vivo experimentation to determine the real potential of these in vitro observations. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Les progrès technologiques récents nous permettent d'accéder à la variation des génomes complets ce qui nous ouvre la porte d'une meilleure compréhension de leur diversification via des approches de génomique des populations et de génomique du paysage. Ce travail de thèse se base sur l'analyse des données de génomes complets (WGS) pour caractériser la diversité génétique des petits ruminants (chèvre et moutons) et rechercher les bases génétiques d'adaptations locales.Dans un premier temps, ce travail appréhende un aspect méthodologique et examine la précision et le biais de différentes approches d'échantillonnage des génomes pour caractériser la variabilité génétique, en les comparant aux données WGS. Nous mettons en évidence un fort biais des approches classiques (i.e. puces à ADN, capture de l'exome) ainsi que des séquençages de génomes à faibles taux de couverture (1X et 2X), et nous suggérons des alternatives basées sur un échantillonnage aléatoire de marqueurs dont la densité est variable selon les objectifs d'étude (évaluation de la diversité neutre, déséquilibre de liaison, signatures de sélection). Le jeu de données produit a permis d'évaluer l'état des ressources génétiques de différentes populations domestiques (races locales marocaines, iraniennes, races industrielles) et sauvages (aegagre, mouflon asiatique). Nous relevons une très forte diversité génétique dans les populations indigènes et sauvages qui constituent des réservoirs d'allèles et peuvent jouer un rôle important pour préserver le potentiel adaptatif des petits ruminants domestiques dans un contexte de changement climatique. L'étude plus approfondie des populations de chèvres du Maroc montre une forte diversité génétique faiblement structurée géographiquement, et met en évidence des portions de génome présentant des signaux de sélection. Leur étude montre l'existence de mécanismes adaptatifs potentiellement différents selon les populations (e.g. transpiration/halètement dans l'adaptation probable à la chaleur).Enfin, nous explorons les bases génétiques de l'adaptation locale à l'environnement chez les moutons et chèvres via une approche de génomique de paysage. En scannant les génomes de 160 moutons et 161 chèvres représentant la diversité éco-climatique du Maroc, nous identifions de nombreux variants et gènes candidats qui permettent d'identifier les voies physiologiques potentiellement sous-jacentes à l'adaptation locale. En particulier, il apparait que les mécanismes respiratoires et les processus cardiaques joueraient un rôle clé dans l'adaptation à l'altitude. Les résultats suggèrent que les chèvres et moutons ont probablement développé différents mécanismes adaptatifs pour répondre aux mêmes variations environnementales. Cependant, nous identifions plusieurs cas probables de voies adaptatives communes à plusieurs espèces. Par ailleurs, nous avons caractérisé les patrons de variations du niveau de différenciation de régions chromosomiques sous sélection en fonction de l'altitude. Cela nous permet de visualiser la diversité des réponses adaptatives selon les gènes (par exemple, sélection de variants à faible et/ou haute altitude). Ainsi, ce travail pose les bases de la compréhension de certains mécanismes d'adaptation locale. / Recent technological developments allow an unprecedented access to the whole genome variation and would increase our knowledge on genome diversification using population and landscape genomics. This work is based on the analysis of Whole Genome Sequence data (WGS) with the purpose of characterising genetic diversity in small ruminants (sheep and goats) and exploring genetic bases of local adaptation.First, we addressed a methodological aspect by investigating the accuracy and possible bias in the widely used genotyping approaches to characterize genetic variation in comparison with WGS data. We highlighted strong bias in conventional approaches (SNP chips and exome capture) and also in low-coverage whole genome re-sequencing (1X and 2X), and we suggested effective solutions based on sampling panels of random markers over the genome depending the purpose of the study (assessing neutral diversity, linkage disequilibrium, selection signatures). The various datasets produced allowed assessing genetic resources in various domestic (Moroccan and Iranian indigenous breeds and industrials) and wild populations (bezoars and Asiatic mouflons). We identified a very high diversity in indigenous and wild populations. They constitute a reservoir of alleles allowing them to play a possible key role in the preservation of these species in the context of global changes. The deep study of Moroccan goats showed a high diversity that is weakly structured in geography and populations, and highlighted numerous genomic regions showing signatures of selection. These regions identified different putative adaptive mechanisms according to the population (e.g. panting/sweating to adapt to warm/desert environment).Then, we explored genetic bases of local adaptation to the environment in sheep and goats using a landscape genomics framework. We scanned genomes of 160 sheep and 161 goats representing the eco-climatic Moroccan-wide diversity. We identified numerous candidate variants and genes, which allowed for identifying physiological pathways possibly underlying local adaptation. Especially, it seems that respiration and cardiac process have key roles in the adaptation to altitude. Our results suggest dissimilar adaptive mechanisms for the same environment in sheep and goats. However, we highlighted several cases of common metabolic pathways in different species. Moreover, we characterized some patterns for the variation of genetic differentiation in some candidate genomic regions over environmental gradients. This allowed us to visualise different adaptive reaction depending genes. This work points the way towards a better understanding of some mechanisms underlying local adaptation.

Fire is generally used as a management tool for different vegetation types such as savannas and grasslands in southern Africa. In the False Thornveld of the Eastern Cape, fire is commonly used to control bush encroachment and to increase grass production, as grasses are important source of forage for domestic livestock. At the University of Fort Hare farm in the Eastern Cape, a trial was set up in 1980 to investigate the effect of burning frequency on vegetation. There are six treatments replicated twice in a completely randomized design on a 100 m x 50 m plots. The treatments comprise no burn, annual, biennial, triennial, quadrennial and sexennial burns. From this trial a study was conducted to investigate long term effect of burning frequency on species and soil seed bank diversity. Two 100 m line transects located 25 m apart were laid within each plot, and the herbaceous and woody species were identified and recorded along the line transects. Relative abundances (%) for each species were calculated for each treatment. Soil samples were collected at an interval of 13.3 m along the line transects. The samples were placed in paper bags and kept for use in a germination experiment. The seedling emergence germination method was used in the glasshouse to determine emerging seedlings, pots were filled with Hygromix growth medium and the soils from the fire trials 12 X 6 = 72 were spread on top. Soil from the control plots were also pre-treated with heat, smoke and the combination of heat and smoke. The experiment started in January 2010 and was terminated in April 2010. The Shannon-Weaver Diversity Index was used to determine species diversity for standing vegetation and germinated seedlings. Data were tested for normality and species abundances were transformed. Analysis of Variance (ANOVA) was applied to test treatment effects on geminated seedlings, species abundance and diversity at α = 0.05 significance level. Significant differences between treatment means were determined by post v hoc tests using Fischer‟s Least Significant Difference test at α = 0.05. The Pearson Moment Correlation test was used to test the relationship between vegetation and soil seed banks. Treatments had significant effects on herbaceous, woody species abundance and diversity (P < 0.05), but there was no significant treatment effect on soil seed bank diversity and on pre-germination treatments (P > 0.05). The annual, biennial and triennial burns were dominated by Themeda triandra while the quadrennial, sexennial and the control treatments were dominated by Sporobolus fimbriatus and Melica decumbens. A. karroo dominated the woody component across all treatments, but it did not change in abundance. S. fimbriatus was the most abundant in the soil seed bank across all the treatments and also in all pre-germination treatments. Species diversity was high in standing vegetation in the quadrennial, sexennial and the control treatments. There was no significant correlation between the standing vegetation and soil seed bank diversities (P > 0.05). Based on these findings it is apparent that fire can change vegetation in an area to be dominated by fire tolerant or fire intolerant species. Fire frequency, heat and smoke affects soil seed banks to a lesser extent in the False Thornveld. For the management of the False Thornveld of the Eastern Cape, less frequent burning is recommended as it increases aboveground species diversity.

Selon les nouvelles orientations agroécologiques qui s’imposent largement, il convient d’élaborer des systèmes d’élevage adaptés aux contraintes environnementales, efficients et pourvoyeurs de services écosystémiques bénéfiques pour l’environnement et la société. La question se pose singulièrement dans nos territoires antillais et ceci dans le cadre d’une demande pressante en produits carnés de qualité et à forte valeur patrimoniale comme l’est la viande caprine en Guadeloupe. Les petits ruminants, principalement élevés au pâturage, sont exposés aux infestations par les nématodes gastro-intestinaux (NGI) qui constituent une cause majeure de morbidité et de mortalité. Le déploiement de techniques adaptées et applicables sur le terrain s’avère nécessaire. Aussi des méthodes de gestion intégrée du parasitisme sont préconisées parmi lesquelles sont étudiées les stratégies d’alimentation des animaux. Il convient d’améliorer la capacité de l’animal hôte à tolérer les effets négatifs (résilience) ou à contrôler les infestations par les NGI (résistance) par la complémentation alimentaire. L’objectif de cette thèse était de définir des stratégies de complémentations des chevreaux en croissance, stade physiologique le plus touché par les NGI et dont les performances zootechniques conditionnent directement le revenu des producteurs (la production de viande).L’apport de la complémentation a été combinée à une série de recommandations de la gestion intégrée du parasitisme (voie génétique, méthode Famacha ®) et singulièrement à une stratégie de gestion du pâturage mixte avec des génisses. Ont été obtenus, un accroissement des résultats zootechniques (croissance et carcasse), de la note d’état corporel ainsi qu’une amélioration de la réponse physiologique (taux d’hématocrite). Une diminution du nombre de traitements anthelmintiques est observée aussi. Cet essai a abordé l’opérationnalité de la complémentation pour un éleveur. D’une façon générale, ce travail a ouvert aussi des questionnements scientifiques sur l’interaction nutrition*parasitisme avec un focus sur la nutrition azotée à déconnecter de l’alimentation énergétique. / New agroecological guidelines are needed around the world to develop livestock systems that are adapted to the environmental, efficient and environmentally and socially beneficial ecosystem services requirements. The question arises singularly in our Caribbean territories and this in the context of an urgent demand in meat products of quality and ofhigh patrimonial value as is the goat meat in Guadeloupe. Small ruminants, mainly grazed, are exposed to gastrointestinal nematode (NGI) infestations, which are a major cause of morbidity and mortality. The deployment of adapted and applicable techniques in the field is necessary. Therefore, methods of integrated management of parasitism are recommended among which are studied the strategies of feeding of the animals. The ability of the host animal to tolerate adverse effects (resilience) or to control infestations by NGI (resistance) should be enhanced by food supplementation. The objective of this thesis was to define supplementation strategies for growing kidneys, the physiological stage most affected by NGI and whose zootechnical performances directly affect the incarne of producers (meat production).Discussions focus on the development of targeted complementing strategies and attempt to answer questions: how to complement? (ln energy, nitrogen or both); When to complement? (Delay effects or effects during an established infestation). lt was also a question oftesting the life-size recommendations and on several variables (physio­pathological responses and zootechnical responses including carcass characteristics). In this sense this work has presented a certain originality. There was no statistically significant effect on carcass quality, however, in carcass­infected animals the carcasses were more degraded, especially with a low-protein diet. The complementation contribution was combined with a series of recommendations of integrated management of parasitism (genetic pathway, famacha method) and particularly a management strategy of mixed grazing with heifers. An increase in the zootechnical results (growth and carcass), body condition score and an improvement in physiological response, hematocrit) were obtained. A decrease in the number of anthelmintic treatments is also observed. This trial addressed the operationality of complementation for a breeder. In general, this work also opened up scientific questions about the interaction nutrition * parasitism with a focus on nitrogen nutrition to disconnect from the energy suooly

Les légumineuses permettent de réduire les intrants en élevage (engrais, concentrés) en raison notamment de leurs niveaux élevés en protéines. Cependant, à la fois pendant le processus d'ensilage et celui de fermentation dans le rumen, les protéines peuvent subir une importante dégradation, ce qui affecte la valeur nutritive des fourrages et induit des rejets d'azote (N) importants, notamment dans l'urine. Certaines légumineuses peuvent alors être d'un intérêt particulier car elles produisent des composés secondaires qui peuvent modifier positivement les processus fermentaires et digestifs. Ainsi, les tannins condensés (CT) présents dans le sainfoin (SF, Onobrychis viciifolia) sont capables de se lier aux protéines, réduisant leur dégradation dans le silo et le rumen et se traduisant par un transfert de l'excrétion d'azote de l'urine vers les fèces. Le trèfle violet (RC, Trifolium pratense) contient la polyphénoloxydase (PPO), une enzyme qui catalyse l'oxydation de différents composés phénoliques en quinones. Comme les CTs, les quinones sont capables de former des complexes avec les protéines permettant de réduire leur dégradation dans le silo et le rumen. L'objectif de cette thèse était alors d'étudier et de quantifier les bénéfices potentiels de l'utilisation de ces deux espèces de légumineuses bioactives sur i) la qualité et la conservation des ensilages, ii) la fermentation ruminale, l'efficacité digestive et les performances des ovins, et iii) l'empreinte environnementale (excrétion d'N et de CH4). Nous avons effectué deux essais in vitro et deux essais in vivo, basés sur des ensilages composés de ces deux légumineuses, seules ou en mélange avec une graminée (la fléole- T, Phleum pratense L.) qui nous a servie de contrôle. Les essais in vitro nous ont permis de nous focaliser sur la qualité et la conservation des ensilages ainsi que sur la fermentation ruminale, tandis que les essais in vivo se sont concentrés sur la performance et l'efficacité digestive des agneaux, ainsi que sur leur bilan azoté et leurs émissions de CH4. L'inclusion de légumineuses bioactives dans les ensilages d'herbe a amélioré la qualité du fourrage, la fermentation pendant le processus d'ensilage ainsi que la protection des protéines contre une dégradation au sein du silo et du rumen. Globalement, l'alimentation des agneaux avec des mélanges comportant ces légumineuses s'est traduite par une augmentation de l'ingestion de matière sèche, en comparaison des agneaux alimentés avec la graminée pure. Néanmoins, en raison de la digestibilité nettement plus faible de T-SF, probablement due à une composition et une nature des fibres différentes ainsi qu'à la présence de CT, les agneaux ayant reçu T-SF ont montré une ingestion et des performances plus faibles que ceux ayant reçu les ensilages contenant RC. Dans le rumen, il semble que les protéines de RC aient été plus protégées de la dégradation que celles de SF, tandis que dans la suite du tractus digestif, les complexes formés entre protéines et CT (avec SF) se seraient moins dissociés que ceux formés entre protéines et quinones (avec RC), ce qui pourrait en partie expliquer le transfert d'excrétion de l'N de l'urine vers les fèces, observé chez les agneaux alimentés avec T-SF et bénéfique pour l'environnement. SF a également permis de réduire légèrement les émissions de CH4. Ainsi, utiliser des légumineuses bioactives dans les pratiques d'alimentation des ruminants apparaît une stratégie prometteuse pour fournir des produits animaux de façon plus durable. Nos résultats montrent que chaque espèce apporte des avantages différents, plutôt orientés vers la qualité de l'aliment et les performances animales pour RC mais plutôt orientés vers la réduction des rejets pour SF. Des recherches complémentaires sont donc nécessaires pour mieux caractériser ces avantages et élargir les investigations à d'autres espèces, d'autres mélanges et d'autres bénéfices potentiels. (...) / Fodder legume species allow to reduce inputs in livestock breeding systems (fertilizer, concentrates) notably because they contain high levels of crude proteins which are of primary importance in ruminant nutrition. However, during both silage and rumen fermentation processes, proteins are submitted to degradation which affects forage nutritive value and leads to nitrogen (N) losses notably via urine. Some specific legumes can then be of particular interest as they produce plant secondary compounds that can positively affect silage and digestive processes. Condensed tannins (CTs) present in sainfoin (SF, Onobrychis viciifolia) are able to bind with proteins thereby reducing their degradation in the silo and the rumen, resulting in a shift in N excretion from urine to faeces. Red clover (RC, Trifolium pratense) contains polyphenol oxidase (PPO), an enzyme that catalyses the oxidation of different phenolics into quinones. As CTs, quinones are able to form complexes with proteins that will similarly reduce their degradation in the silo and the rumen. The aim of this thesis was to investigate and quantify the potential benefits of using these two bioactive legume species on i) quality and conservation of silages, ii) rumen fermentation, digestive efficiency and sheep performance, and iii) environmental footprint (N excretion and CH4 emissions). We conducted two in vitro and two in vivo trials which were based on silages of pure legumes or of different mixtures with the grass species (timothy T, Phleum pratense L.), which served as control. In the in vitro trials, we focussed on silage quality, silage conservation and rumen fermentation, while in the in vivo trials, we focussed on lambs' performance, digestion efficiency, N balance and CH4 emissions. Including bioactive legumes in mixtures with grass improved, compared to pure grass, forage quality and fermentation during the silage making process, as well as proteins' protection from degradation within both the silos and the rumen. Lambs fed with the mixtures involving legumes responded with an increase in DM intake compared to their counterparts fed with T. Nevertheless, due to a possibly different fibre composition and to the presence of CT which impaired SF digestibility, lambs that consumed T-SF showed lower intake and performance than those that received RC-containing silages. In the rumen, RC proteins appeared more protected from degradation than SF ones, while in the subsequent parts of the digestive tract, the proteins-CT complexes (from SF) might less dissociate than the proteins-quinones ones (from RC). This could partly explain the environment-friendly shift in N excretion from urine to faeces when animals are fed with T-SF. SF also allowed to slightly reduce CH4 emissions. Thus, utilizing bioactive legumes in livestock feeding practices is a promising strategy to produce animal products more sustainably. Our results show different benefits relative to the bioactive legume species involved, directed towards boosted forage quality and animals' performance for RC but towards lowered wastes for SF. Further research is thus needed to better characterize these benefits and enlarging investigations to other plant species, mixtures and potential benefits (e.g. health). This will help to determine the appropriate choice of plant species according to the objectives.

Les membres du genre Morbillivirus, famille Paramyxoviridae sont responsables de graves maladies chez l'homme et les animaux, comme la rougeole, la peste bovine (RP) et la peste des petits ruminants (PPR). Malgré l'existence de vaccins efficaces contre ces maladies, des traitements spécifiques sont souhaitables. L'inhibition de la réplication de ces virus peut-être acquise par interférence ARN (ARNi), un mécanisme d'inhibition post-transcriptionnel déclenché par des séquences courtes d'ARN double-brin (siARN). Le CIRAD a précédemment identifié 3 siARNs ciblant des régions conservées du gène de la nucléoprotéine virale capables d'inhiber au moins 80% de la réplication in vitro des virus de la rougeole, de la RP et de la PPR. Cependant, un problème majeur dans la stratégie d'ARNi est le risque d'apparition de virus résistants. Dans cette étude, nous avons évalué le risque d'apparition de mutants d'échappement du virus de la PPR sous pression de sélection de 3 siARNs appliqués seul ou en association après plusieurs transfections successives in vitro. Excepté pour la combinaison des 3 siARNs, le virus a échappé à l'ARNi après 3 à 20 passages consécutifs, avec des mutations simples ou multiples (synonymes ou pas) ou une délétion de 6 nucléotides dans la zone cible des siARN. Ces résultats mettent en évidence une plasticité génomique inattendue des morbillivirus surtout illustrée par cette délétion non-délétère d'une partie significative d'un gène viral essentiel, qui devrait être considérée comme un obstacle à l'utilisation de l'ARNi comme thérapie antivirale. Cependant, l'utilisation combinée de 3 siARNs peut être proposée pour diminuer le risque d'échappement aux siARNs. / Viruses in the genus Morbillivirus, within the family Paramyxoviridae are responsible for severe humans and animal diseases, including measles, rinderpest (RP) and peste des petits ruminants (PPR). In spite of the existence of efficient vaccines against these diseases, specific treatments to be applied when the infection is already present are desirable. Inhibition of morbillivirus replication can be achieved by RNA interference (RNAi), a mechanism of post-transcriptional gene silencing triggered by small double-stranded RNA (siRNA). The CIRAD previously identified three siRNAs that target conserved regions of the essential gene encoding the viral nucleoprotein and are able to prevent in vitro at least 80% of the replication of measles, RP and PPR viruses . However, a major problem in RNAi is the important risk of emergence of escape mutants. In this study, we investigated the ability of PPR virus to escape the inhibition conferred by single or multiple siRNAs after several consecutive transfections in vitro. Except with the combination of the three different siRNAs, the virus systematically escaped RNAi after 3 to 20 consecutive passages. The mutations were characterized by either single or multiple punctual nucleotide mutations (synonymous or not) or a deletion of a stretch of 6 nucleotides into the siRNA target. These results demonstrate that the genomic plasticity of morbilliviruses, illustrated maily by this significant and no-deleterious deletion in an essential viral gene, should be considered as an obstacle to the use of RNAi in antiviral therapy. However, the combined use of three siRNAs can be proposed to prevent treatment failure with siRNAs.

Les nématodes parasites du tube digestif demeurent une contrainte majeure pesant sur la santé, le bien être et les productions des petits ruminants élevés à l’herbe. Le mode usuel de maîtrise de ce parasitisme repose sur l’emploi répété de molécules chimiques anthelminthiques. Toutefois, le développement et la diffusion généralisée de résistances à ces molécules dans les populations de vers imposent désormais d’utiliser ces traitements avec discernement et de trouver des solutions complémentaires ou alternatives. L’incorporation dans la conduite d’élevage (ration des moutons ou des chèvres) de légumineuses fourragères riches en tannins condensés dotées de propriétés anthelminthiques s’est avérée une option prometteuse pour réduire le recours aux molécules chimiques. Toutefois, une des difficultés d’application de ces plantes tient à la variabilité des résultats observés. En prenant le sainfoin comme modèle de légumineuse contenant des tannins et en s’appuyant essentiellement sur des méthodes in vitro basées sur les larves 3 infestantes, l’objectif général de cette thèse est d’analyser le rôle respectif de facteurs liés à l’environnement, aux variétés génétiques ou aux modes de préservation technologiques sur les propriétés anthelminthiques. Quelque soit le critère envisagé, une forte variabilité a été observée. Les principales variations liées à l’environnement dépendaient de l’année et du cycle de coupe, ainsi que du site d’exploitation. Parmi les 38 variétés testées, 9 se sont avérées à forte activité AH, alors que 22 étaient à très faible activité. Enfin, les résultats ont aussi surtout souligné une plus forte activité antiparasitaire dans des formes séchées ou ensilées par comparaison à des échantillons frais. La comparaison des profils biochimiques liés à cette variabilité a permis une exploration des composés phénoliques expliquant l’activité anthelminthique. L’existence d’une relation dose-réponse a été précisée. Le rôle des tannins condensés a été confirmé, notamment ceux à faible degré de polymérisation et à faible poids moléculaire. L’importance des prodelphinidines qui seraient plus actives que les procyanidines reste à confirmer. De plus, il a été montré que d’autres flavonoides peuvent jouer un rôle, notamment les flavan-3-ols et les flavonols. La différence d’activité entre les échantillons de sainfoin ensilés ou fanés par comparaison aux échantillons frais s‟expliquerait en partie par la présence de formes non glycosidés de flavonols. Ces résultats devraient conduire à développer des méthodes de dosage pour identifier les échantillons de sainfoin, et plus généralement de légumineuses riches en tannins, dotés de propriétés anthelminthiques significatives. / Gastrointestinal nematodes remain a major constraint on the health, welfare and production of small ruminants. Over the past decades, the usual mode of control of this parasitism has mainly relied on the repeated use of chemical anthelmintics. However these treatments are nowadaysfacing some limits among which the most important is the development and widespread diffusion of resistance to these chemical molecules within worm populations. Consequently, the need to find complementary or alternative solutions is becoming urgent. The possible exploitation of forage legumes, rich in condensed tannins, with anthelmintic properties, by incorporation in the diet of sheep or goats, seems a promising option to reduce the reliance on chemical molecules. However, one of the main difficulties to use these plants as nutraceuticals relates to the variations in results. By using sainfoin (Onobrychis viciifoliae) as a model of tannin-containing legume and based on in vitro methods on the infective third stage larvae, the main objectives of this PhD were i) to examine the influence of environmental, genetic (40 different varieties) and technological (mode of preservation) factors on the anthelmintic properties of sainfoin and ii) to analyse whether differences in phenolic compounds might explain the variations. Whatever the factor considered, a high variability in results was observed. The main variations due to the environmental factors depended on the year and the cycle of cutting, as well as on the site of cultivation. Among the 38 varieties tested, only 9 have shown AH activity over 50 %. Last, a higher antiparasitic activity was found in the dried or ensiled forms compared to the fresh samples. A comparison of the biochemical profiles associated with these variations indicated a role of proanthocyanidins plus other phenolic compounds in the anthelmintic properties. The dose-response relationship between the AH activity and the ability to form complex with proteins was defined. The role of condensed tannins was confirmed, particularly those with a low degree of polymerization. The respective importance of prodelphinidins vs procyanidins remains to be further investigated. Moreover, the possible role of other flavonoids, in particular of flavan-3-ols and flavonols was also confirmed. The difference in activity between dried or ensiled forms compared to fresh sainfoin samples was partly explained by the presence of flavonol aglycosides. These results should favour the development of measurements in order to identify sainfoin samples with higher anthelmintic properties.