Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo

The present study was financially supported by the German Academic Exchange Service Deutscher Akademischer Austauschdienst (DAAD) through the In-Country/In-Region scholarship program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.Deutscher Akademischer Austausch Dienst (DAAD

Dynamique des Troupeaux de Petits Ruminants Saheliens dans Les Exploitations Rurales au Senegal

Les races locales de petits ruminants (PR) sahéliens du Sénégal sont très adaptées à l’élevage extensif malgré les contraintes alimentaires et sanitaires surtout dans le contexte actuel de changement climatique. Importante source de protéines pour les populations, les PR leur génèrent aussi des revenus substantiels. En dépit de cette importance socio- économique, peu d’études ont porté sur les performances et la gestion des animaux dans leur environnement d’élevage. L’objectif de ce travail est d’étudier la dynamique des troupeaux de PR dans la zone semi-aride du Ferlo. Ainsi, des enquêtes rétrospectives transversales par la méthode des 12 derniers mois ont étéréalisées dans 52 troupeaux ruraux durant le mois d‘avril 2017. Sur l’ensemble des troupeaux enquêtés 604 ovins et 450 caprins ont été enregistrés avec des tailles moyennes de 19,48±9,63 et 21,43±11,35 têtes par troupeau respectivement pour les ovins et les caprins. Le taux de mises-bas annuel est de 84,1 ± 5,4% pour les chèvres et 85,5 ± 5,3% pour les brebis. La mortalité a particulièrement touché les jeunes animaux avec des fréquences respectives de 16,8 ± 3,0 et 13,2 ± 3,0% pour les ovins et les caprins. L’achat a été le principal motif d’entrée d’animaux dans les exploitations tandis que la mortalité et la vente ont constitué les principaux motifs de sortie respectivement pour les ovins et les caprins. Le taux d’exploitation de 23,8 ± 2,1% pour les ovins contre 26,8 ± 2,5% pour les caprins et les mâles adultes sont principalement les plus exploités. Les contraintes et constats identifiés dans cette étude doivent être pris en compte pour le développement des filières ovine et caprine dans la zone semi-aride du Sénégal. Local breeds of Sahelian small-ruminant (SR) in Senegal are highly adapted to extensive farming systems despite feeding and health constraints, especially in a climate change context. As an important source of protein for populations, SR also generate substantial income. Despite this importance, their productivity in rural farming systems is rarely studied. The main objective of this study is to analyze demographic dynamics of SR’s flocks in the Ferlo zone using last twelve months retrospective surveys. The surveys were carried out on 52 flocks belonging to 32 rural households. With a predominance of adult females, a total number of 604 sheep and 450 goats are counted with an average size of 19.48 ± 9.63 and 21.43 ± 11.35 heads per flockrespectively for sheep and goat. The annual birth rate was 84.1 ± 5.4 for goats and 85.5 ± 5.3% for sheep. Young animals were particularly affected by mortalitywith a frequency of 16.8 ± 3.0 and 13.2 ± 3.0% respectively for sheep and goats. Purchase was the main reason for entrance of animals into the flocks. For animal exits, mortalities were the main reason for sheep whereas for goats, sales were the main reasons. The global offtake rate was 23.8 ± 2.1% for sheep and 26.8 ± 2.5% for goats and adult males were mostly concerned. Despite low productivity, SR breeding remains an important economic activity for the rural populations

Reproductive Performance of Glossina palpalis gambiensis (Diptera: Glossinidae) when fed frozen or fresh bovine blood meals

The tsetse and trypanosomoses control by sterile insect technique (SIT), requires mass production of quality tsetse pupae and consequently high-quality blood meal for the fly feeding. The reproductive performances of Glossina palpalis gambiensis (Diptera : Glossinidae), fed frozen or fresh blood meals has been studied. Three diets of slaughtered bovine blood stored at -18 °C for six months (R6), three months (R3) and one month (R1) were used in the present investigation. Fresh blood samples stored at 4°C and renewed every four days were used as control (R0). The defibrinated blood was packaged in batches of 30 x 20 ml vials. For each blood meal, 30-day feeding tests were conducted at the beginning and end of freezing. All blood meal was irradiated using 137 caesium irradiation before being used. The parameters monitored daily were: the number of dead flies (fed and unfed), the number and weight of pupae and the emergence rate. No difference in survival rates was observed for the three regimes (df: 15; Chi-square: 7.53; p > 0.05), on average 32.1% (R0), 32.4% (R6), 37.5% (R3) and 38.2% (R1). However, flies fed with the six-month-old frozen blood were less efficient in pupa production (df: 3; F: 6. p < 0.001) and pupae weight (df: 3, F: 3.24, p < 0.05) compared to the control. The mortality rate was affected by the duration of freezing: 26.7% for R6 and 8% for the other diets (p <0.05). The implications of our results in terms of blood meal management for efficient production of insectary pupae were discussed

Multivariate Analysis for Morphological Characteristics of N’Dama Cattle Breed in Two Agro-ecological Zones of Côte d’Ivoire

Information on morphological characteristics is a prerequisite to sustainable breed improvement, utilization, and conservation. In this study, 108 N’Dama cattle cows from 11 farms of central and northwestern regions of Côte d’Ivoire were described using visual appreciation criteria and linear body measurements. The variables were studied using principal component analysis (PCA) and discriminant analysis. Results indicated that the most common N’Dama is fauve (83.33%) and it has straight back profile (69.44%) and lyre horn (74.07%). Agroecological zone has a significant (p˂0.01) effect on linear body measurements of N’Dama. The central region animals had higher head width (18.94 ± 2.18 cm), skull length (22.51 ± 2.18 cm), skull width (16.51 ± 1.72 cm), muzzle circumference (40.83 ± 2.58 cm), distance between horns (15 ± 1.90 cm), ear length (17.46 ± 2.57 cm), chest length (160.11 ± 15.8 cm), chest depth (71.55 ± 7.41 cm), and body length (125.13 ± 12.22cm) than those of northwestern region N’Dama. Thus, their respective values were: 15.41 ± 2.85 cm, 18.62 ± 2.6 cm, 12.44 ± 3.94 cm, 38.8 ± 2.61 cm, 13.72 ± 1.52 cm, 16.41 ± 1.61 cm, 143.84 ± 8.35 cm, 65.25 ± 4.1 cm, and 119.18 ± 12.38 cm. PCA revealed that N’Dama morphometric variability performed from the 9 variables (Lt, lt, Lc, lc, pt, hg, Pth, Lcp and Lf) were more associated with the first two factors. In regards to the discriminant analysis, these 9 variables distinguished the N’Dama significantly (p˂0.05) into two populations that corresponds with the two agroecological zones

Morphological and microsatellite DNA diversity of Djallonké sheep in Guinea Bissau

BACKGROUND: The present study aimed at characterizing the Djallonké Sheep (DS), the only local sheep breed raised in Guinea-Bissau. A total of 200 animals were sampled from four regions (Bafatá, Gabú, Oio and Cacheu) and described using 7 visual criteria and 8 measurements. These parameters have been studied by principal components analysis. The genetic diversity and population structure of 92 unrelated animals were studied using 12 microsatellite markers. RESULTS: The values of quantitative characters in the Bafatá region were significantly higher than those obtained in the other three regions. A phenotypic diversity of the DS population was observed and three genetic types distinguished: animals with “large traits” in the region of Bafatá, animals with “intermediate traits” in the regions of Gabú and Oio and animals with “small traits” in the Cacheu region. The hair coat colors are dominated by the white color, the shape of the facial head profile is mainly convex and the ears “erected horizontally”. Most of the morphobiometric characteristics were significantly influenced by the “region” and “sex of animals”. The average Polymorphism Information Content (PIC) of 0.65 ± 0.11 supports the use of markers in genetic characterization. Gabú subpopulation had the highest genetic diversity measures (He = 0.716 ± 0.089) while Cacheu DS subpopulation presented the smallest (He = 0.651 ± 0.157). Only Gabú and Bafatá subpopulations presented significant heterozygote deficiency across all loci indicating possible significant inbreeding. Mean values for F(IT,) F(ST), F(IS) and G(ST) statistics across all loci were 0.09, 0.029, 0.063 and 0.043 respectively. The overall genetic differentiation observed between the four DS subpopulations studied was low. Bafatá and Gabú are the most closely related subpopulations (D(S) = 0.04, genetic identity = 0.96) while Bafatá and Cacheu were the most genetically distant subpopulations (D(S) = 0.14, genetic identity = 0.87). Using Bayesian approach, the number of K groups that best fit the data is detected between 2 and 3, which is consistent with the morphological analysis and the factorial analysis of correspondence. CONCLUSIONS: The molecular results on DS population of Guinea-Bissau confirmed the ones obtained with morphological analysis. The three genetic types observed phenotypically might be due to a combination of the agro-ecological differences and the management of breeding rather than genetic factors. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-021-01009-7

Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense

Animal African trypanosomosis, caused by blood protozoan parasites transmitted mainly by tsetse flies, represents a major constraint for millions of cattle in sub-Saharan Africa. Exposed cattle include trypanosusceptible indicine breeds, severely affected by the disease, and West African taurine breeds called trypanotolerant owing to their ability to control parasite development, survive and grow in enzootic areas. Until now the genetic basis of trypanotolerance remains unclear. Here, to improve knowledge of the biological processes involved in trypanotolerance versus trypanosusceptibility, we identified bovine genes differentially expressed in five West African cattle breeds during an experimental infection by Trypanosoma congolense and their biological functions. To this end, whole blood genome-wide transcriptome of three trypanotolerant taurine breeds (N’Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou) were profiled by RNA sequencing at four time points, one before and three during infection. As expected, infection had a major impact on cattle blood transcriptome regardless of the breed. The functional analysis of differentially expressed genes over time in each breed confirmed an early activation of the innate immune response, followed by an activation of the humoral response and an inhibition of T cell functions at the chronic stage of infection. More importantly, we highlighted overlooked features, such as a strong disturbance in host metabolism and cellular energy production that differentiates trypanotolerant and trypanosusceptible breeds. N’Dama breed showed the earliest regulation of immune response, associated with a strong activation of cellular energy production, also observed in Lagune, and to a lesser extent in Baoulé. Susceptible Zebu Fulani breed differed from other breeds by the strongest modification in lipid metabolism regulation. Overall, this study provides a better understanding of the biological mechanisms at work during infection, especially concerning the interplay between immunity and metabolism that seems differentially regulated depending on the cattle breeds

A Spatio-temporal Model of African Animal Trypanosomosis Risk

[b]Background[/b]African animal trypanosomosis (AAT) is a major constraint to sustainable development of cattle farming in sub-Saharan Africa. The habitat of the tsetse fly vector is increasingly fragmented owing to demographic pressure and shifts in climate, which leads to heterogeneous risk of cyclical transmission both in space and time. In Burkina Faso and Ghana, the most important vectors are riverine species, namely Glossina palpalis gambiensis and G. tachinoides, which are more resilient to human-induced changes than the savannah and forest species. Although many authors studied the distribution of AAT risk both in space and time, spatio-temporal models allowing predictions of it are lacking.[b]Methodology/Principal Findings[/b]We used datasets generated by various projects, including two baseline surveys conducted in Burkina Faso and Ghana within PATTEC (Pan African Tsetse and Trypanosomosis Eradication Campaign) national initiatives. We computed the entomological inoculation rate (EIR) or tsetse challenge using a range of environmental data. The tsetse apparent density and their infection rate were separately estimated and subsequently combined to derive the EIR using a "one layer-one model" approach. The estimated EIR was then projected into suitable habitat. This risk index was finally validated against data on bovine trypanosomosis. It allowed a good prediction of the parasitological status (r(2) = 67%), showed a positive correlation but less predictive power with serological status (r(2) = 22%) aggregated at the village level but was not related to the illness status (r(2) = 2%).[b]Conclusions/Significance[/b]The presented spatio-temporal model provides a fine-scale picture of the dynamics of AAT risk in sub-humid areas of West Africa. The estimated EIR was high in the proximity of rivers during the dry season and more widespread during the rainy season. The present analysis is a first step in a broader framework for an efficient risk management of climate-sensitive vector-borne diseases

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in Galliformes

The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub-Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first-generation whole-genome sequence draft assembly used as a reference for a study by a Pool-seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB2, possibly explaining losses in plumage coloration phenotypes in domesticated populations

The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen, Coxiella burnetii

International audienceQ fever is a highly infectious disease with a worldwide distribution. Its causative agent, the intracellular bacterium Coxiella burnetii, infects a variety of vertebrate species, including humans. Its evolutionary origin remains almost entirely unknown and uncertainty persists regarding the identity and lifestyle of its ancestors. A few tick species were recently found to harbor maternally-inherited Coxiella-like organisms engaged in symbiotic interactions, but their relationships to the Q fever pathogen remain unclear. Here, we extensively sampled ticks, identifying new and atypical Coxiella strains from 40 of 58 examined species, and used this data to infer the evolutionary processes leading to the emergence of C. burnetii. Phylogenetic analyses of multi-locus typing and whole-genome sequencing data revealed that Coxiella-like organisms represent an ancient and monophyletic group allied to ticks. Remarkably, all known C. burnetii strains originate within this group and are the descendants of a Coxiella-like progenitor hosted by ticks. Using both colony-reared and field-collected gravid females, we further establish the presence of highly efficient maternal transmission of these Coxiella-like organisms in four examined tick species, a pattern coherent with an endosymbiotic lifestyle. Our laboratory culture assays also showed that these Coxiella-like organisms were not amenable to culture in the vertebrate cell environment, suggesting different metabolic requirements compared to C. burnetii. Altogether, this corpus of data demonstrates that C. burnetii recently evolved from an inherited symbiont of ticks which succeeded in infecting vertebrate cells, likely by the acquisition of novel virulence factors