The impact of the herd health interventions in small ruminants in low input production systems in Ethiopia.

Introduction: Diseases have a negative impact on production and profitability of small ruminants. A good herd health program can decrease the number of sick animals and improve herd performance. Methods: In a longitudinal study, small ruminant herd health interventions such as community-based strategic gastrointestinal (GI) parasite control, prevention and control of major respiratory diseases and capacity development activities were implemented. In four districts of Ethiopia, where the Community Based Breeding Program (CBBP) is implemented, morbidity and mortality data were collected from January 2018 to July 2021 in 1047 smallholder farms with the objective of evaluating the impact of herd health interventions. A total of 2,643 sick animals and 516 deaths of small ruminants were recorded during the study period. The disease cases were categorized into eight groups: gastrointestinal, neurological, reproductive, respiratory, skin, systemic, other diseases (eye disease, foot disease etc) and unknown diseases. Chi-square and proportions were used to analyze morbidity and mortality by district, agro-ecological zone and age of the animal. Results: The data showed that the general trend in the occurrence of cases and morbidity rate were decreasing from 2018 to 2021 in intervention villages. Overall, the morbidity rate in young animals (7.36%) was highier than in adults (3.49%) and the mortality rate difference between young and adult animals was also statistically significant (p < 0.001). The morbidity and mortality rates varied significantly (p < 0.001) among districts and among agro-ecologies. According to the data, treating and following up of infected animals reduced the mortality rate significantly. The relative risk of death in treated animals after the case reported was 0.135. Generally, the intervention impact analysis revealed that morbidity rate was significantly decreased (p = 0.009) in intervention years (6.31% in 2018 to 3.02% in 2021) and that herd health interventions provide an added value. Conclusion: Generally, herd health intervention had significant impact in reducing the morbidity rates in years and treatment and follow up of sick animals due to early reporting reduced mortality rate significantly. It is recommended that the herd health management should be the core activity under small ruminant production programs.

First Molecular and Phylogenetic Identification of Toxoplasma Gondii in Sheep Liver Intended for Human Consumption in Northern Tunisia.

The aim of this study was to estimate the molecular infection prevalence of Toxoplasma gondii in sheep liver tissues destined for human consumption. A total number of 224 liver tissues were collected from slaughtered sheep in Sejnane slaughterhouse (Northwest Tunisia). PCR was used to detect T. gondii DNA in liver tissues followed by phylogenetic analysis of amplicons. The phylogenetic tree was then constructed to compare the partial sequences of the ITS1 gene with GenBank sequences.The overall molecular prevalence of T. gondii in sheep livers was 25% (56/224). The highest molecular prevalence of T. gondii was recorded in sheep aged of less than one year old (27.3%; 52/190). Infection prevalence was significantly higher in Noire de Thibar breed (33%; 17/51) compared to other breeds (p = 0.023). There were no differences depicted according to sheep's gender. The T. gondii sequences obtained in the present study (GenBank accession numbers: OR509829 and OR509830) were 98.40-100% homologous to T. gondii sequences published in the GenBank. These results highlight a high level of T. gondii contamination of tissues destined for human consumption. Further studies are needed to improve our knowledge on different genotypes of T. gondii that infect Tunisian sheep population.

Prevalence of Fasciola hepatica infection in slaughtered sheep from Northwest Tunisia and its risk factors: Association with gastrointestinal helminths infection and anaemia.

We investigated herein the prevalence of Fasciola hepatica infection in sheep at Sejnane slaughterhouse, governorate of Bizerte, Northwest of Tunisia, using three different diagnostic techniques (liver dissection, bile examination, and coprology). Faeces, liver, gall bladder as well as blood samples were collected from 603 slaughtered sheep in two seasons: winter and summer. Faecal egg counts of F. hepatica were estimated using sedimentation technique. Livers were examined for the presence of flukes, and bile collected from gall bladder was examined by sedimentation technique for the presence of F. hepatica eggs. Faecal egg counts of gastrointestinal helminths were estimated using flotation followed by the McMaster technique. Blood samples were used to estimate blood cell count (RBC) (×106/mL), haemoglobin (Hb) (g/dL), and haematocrit (Ht) (%) levels. A total of 1714 F. hepatica flukes were collected from 68 infected livers, the number of flukes per sheep ranged between naught and 195. Bile examination (16.78% ± 1.83; 51/310) showed the higher infection prevalence, followed by liver dissection (11.28% ± 1.17; 68/603) and coprology (9.12% ± 1.08; 55/603) (p = 0.015). Infection prevalences were significantly higher in young sheep aged of less than 1 year (8.13% ± 1.22; 49/498), in cross-bred sheep (10.61% ± 1.39%; 64/478), and in summer (7.13% ± 1.82; 43/293) (p < 0.05). There was no significant difference in infection prevalence by gastrointestinal helminths in F. hepatica-infected and F. hepatica-non-infected animals (p > 0.05). The overall prevalence of F. hepatica-infected anaemic sheep was higher (22.73% ± 4.47; 20/88) than F. hepatica-non-infected anaemic sheep (p < 0.05). Fasciola hepatica infection is frequent in sheep from Sejnane representing hence an important constraint for the development of the sheep industry in this region. Therefore, it is necessary to establish and implement a specific control programme to reduce fasciolosis infection risks including animal owners' education.

Repeated Cross-Sectional Survey of Ectoparasites in Sheep from Central Tunisia: Does Low Prevalence Indicate Good Hygiene or Resistance to Ectoparasites?

Sheep ectoparasites such as chewing lice, fleas and ticks are serious constraints to sheep productivity and are the cause of skin lesions in animals that decrease their market value. This study aims at investigating the ectoparasite fauna infesting small ruminants in the district of Sidi Bouzid (central Tunisia). A total of 1243 Barbarine and Queue Fine de l'Ouest (QFO) sheep were examined every two months for one year. Of the total animals examined, 74 were infested by at least 1 parasite group (5.95%). Three ectoparasite groups were identified as Psoroptes ovis (0.48%; 6/1243), ticks (5.3%; n = 66/1243) and one specimen of Ctenocephalides canis (0.08%; n = 1/1243). The most abundant tick among the 358 specimens was Rhipicephalus sanguineus sensu lato (n = 337; 94.1%), followed by Hyalomma impeltatum (n = 7/358; 1.9%), H. dromedarii (n = 7/358; 1.9%), H. excavatum (n = 5/358; 1.4%) and only two specimens of H. scupense (n = 2/358; 0.55%). The sheep herds showed low infestation prevalence by ectoparasite over the year, with a significant difference according to the seasons (p < 0.05). A higher infestation prevalence was recorded in March (14.36%). Barbarine sheep breed showed significantly higher infestation prevalence (16.8%) compared to QFO (0.8%) (p < 0.01). There were no differences in infestation prevalence according to sex of the animal or age groups. Knowledge of the ectoparasite population harboured by sheep, its activity dynamics and risk factors is required to develop effective ectoparasite control options. The low prevalence of ectoparasite infestation in sheep reported here may be due to possible genetic resistance or simply to successful hygiene measures implemented by farmers.

Genetic diversity of Hyalomma marginatum in Tunisia is not influenced by the bio-climate.

Ticks are important ectoparasites responsible for the transmission of several pathogens with significant medical, veterinary, and economic impacts. Climate and social changes have generated substantial changes in ticks' distribution, abundance, and activity patterns, including ticks belonging to the Hyalomma marginatum species. Knowledge on the genetic structure and dynamics of H. marginatum populations might contribute to a better understanding of their current and future evolution under the effects of anthropogenic factors and eco-climatic changes. In the present study, we investigated the genetic structure and phylogenetic distribution of H. marginatum across three bioclimatic regions in Tunisia using two mitochondrial markers (16S and 12S rRNA). The molecular investigations were based on 47 adult H. marginatum ticks collected from humid, upper semi-arid, and sub-humid regions of Tunisia. Our results revealed a genetic diversity of 0.278% and 0.809% using the 16S and 12S markers, respectively. The low genetic diversity that we observed raises the hypothesis of a bottleneck event occasioned by a reduction in the size of the tick population under the effects of environmental factors and/or human activities. This hypothesis is supported by the population's demographic history analysis, which revealed a clear deviation from neutrality and supports the occurrence of a bottleneck event followed by a demographic expansion. The fact that most 16S and 12S variability was present in the ticks from the humid bioclimatic zone may suggest that those ticks represent the ancestral population. Overall, the analysis has shown that the phylogenetic clusters do not correspond to the bioclimatic zones.

Conservation agriculture has no significant impact on sheep digestive parasitism.

Conservation agriculture (CONS A) is a sustainable agriculture system based on crop rotation with no tillage. It has various environmental advantages compared to conventional agriculture (CONV A): decreased water evaporation, erosion, and CO2 emissions. In this first study of its kind, we aim to evaluate the impact of this type of agriculture on sheep gastrointestinal parasites. Two lamb groups aged between 5 and 10 months were randomly included to graze separately on CONS A and CONV A pastures. Each group was composed of two batches of three lambs, and these were followed up for two rearing months. Liveweight, hematological parameter variation, and digestive parasites were studied. At the end of the study period, lambs were slaughtered the carcass yield was determined, and a helminthological autopsy was performed on the digestive tracts of the animals to estimate different parasitological indicators. There was no difference between lambs reared on CONS A and those reared on CONV A for all parasite indicators (infestation intensity, abundance, and prevalence). The same trend was also obtained for hematological parameters, liveweight evolution, and carcass yield. These results prove that there is no impact of CONS A on the sheep's digestive parasitism. Further studies are needed to support these findings on larger animal samples and to investigate the impact of conservation agriculture on other parasite species. Similar studies could also be conducted on ruminant species.

Epidemiological situation of bovine tropical theileriosis in an arid region in central Tunisia with a phylogenetic analysis of Theileria annulata.

BACKGROUND: Tropical theileriosis, Theileria annulata infection, is the most prevalent summer disease in Tunisia. It is transmitted by Hyalomma scupense, a two-host tick known to be endophilic. OBJECTIVES: The present study aimed to estimate the infection prevalence of cattle by T. annulata in two districts from central Tunisia. METHODS: Blood samples collected from 270 Holstein cattle from the Sidi Bouzid (140 samples) and Kasserine districts (130 samples) were analysed by Giemsa staining and T. annulata-specific PCR. RESULTS: In both regions, PCR revealed a prevalence of 32.6%. This was significantly higher than the 6.3% prevalence obtained by Giemsa staining blood smears (p < 0.001). Giemsa staining also revealed a low parasitaemia of 0.05%. The PCR-based prevalence was not statistically different between the two districts (31.4 ± 0.04 and 33.8 ± 0.04% in Sidi Bouzid and Kasserine districts, respectively, p = 0.6). On the contrary, the results of blood smear examination (2.85 and 10% in Sidi Bouzid and Kasserine, respectively) differed significantly between the two sampling sites (p = 0.01). There was no evidence of a statistically significant difference between the overall molecular infection prevalence when the samples were segregated based on animals' age or gender (p = 0.1 and 0.2, respectively) and a similar trend was observed for Giemsa staining. Ten PCR amplicons of the Tams1 gene (721 bp) were subsequently sequenced from the two regions. The phylogenetic analyses showed 100% similarity between all sequences. The unique conserved Tams1 sequence was deposited in GenBank under the accession number OP428816 and used to infer its phylogenetic relationships with those available in the GenBank repository. CONCLUSIONS: This is the first report of the presence of T. annulata in this region of central Tunisia which has no history of tropical theileriosis. Priority areas for future studies include understanding the origin of these T. annulata-positive animals in a region where the presence of a known natural vector tick, H. scupense, has not been reported. Given that the disease severely constrains cattle productivity, it would also be worthwhile to investigate if other potential vectors for T. annulata, such as Hyalomma dromedarii, are present in the arid regions.

First morphometric and molecular characterization of Fasciola spp. in Northwest Tunisia.

The aim of this study was to characterize the Tunisian Fasciola spp. flukes by morphometric and molecular analyses. Flukes were collected from livers of sheep slaughtered in Sejnane slaughterhouses (Bizerte gouvernorate, Northwest Tunisia) between January and March 2021.Five morphometric parameters were determined for all the liver flukes, as follows: (i) total body length (BL), (ii) distance between ventral sucker and the tail (VS-T), (iii) distance between oral sucker and ventral sucker (OS-VS), (iv) abdomen diameter (AD), (v) tail diameter (TD) and the body length to width ratio (BL/BW). Molecular identification of the fluke specimens was carried out by polymerase chain reaction, restriction fragment polymorphism (PCR-RFLP) of a 680 bp sequence of the internal transcribes spacer 1 (ITS1) gene and by amplification, sequencing, and phylogenetic analysis of a 500 bp sequence of the ITS2 gene. Morphometric measurements showed that the mean of the total body length of the adult flukes was 21.1 ± 2.7 mm with minimum and maximum lengths of 13 and 31 mm, respectively. The PCR-RFLP analysis revealed a single profile consisting of three bands of approximately 370, 100, and 60 bp. Fasciola sequences described in the present study (GenBank numbers: OQ457027 and OQ457028) showed 99.58-100% identity to Fasciola hepatica. In conclusion, the results of this study show that molecular and phylogenetic analyses confirm the presence of a single species of F. hepatica in the Sejnane region Northwest of Tunisia. However, further studies are needed to identify the occurrence of Fasciola species in other Tunisian regions.

Substitution of soyabean meal by faba bean improves body weight, sperm production and testosterone concentration in mature Queue Fine de l'Ouest rams.

The current study aimed at investigating the effects of partial or total substitution of soybean meal with faba bean on reproductive parameters of Queue Fine de l'Ouest rams. Eighteen adult rams (49.8 ± 3.7 kg and 2.4 ± 1.5 years old) were divided into three homogenous groups. Rams received oat hay ad libitum and 3 types of concentrate (33 g/BW0.75) where soybean meal was the main protein source (SBM diet, n = 6), partially (50%, SBMFB diet, n = 6) or totally (100% FB diet, n = 6) substituted in nitrogen basis by local faba bean. The volume of ejaculate, sperm concentration and sperm mortality rate were measured weekly by collecting semen using an artificial vagina. Serial blood samples were collected 30 days and 120 days after the beginning of the experiment in order to assess plasma testosterone concentrations. The results showed that hay intake was affected (P < 0.05) by the nature of the nitrogen source incorporated (1032.3 ± 12.2; 1026.8 ± 56.6 and 972.8 ± 39.05 g DM/d for SBM, FB and SBMFB respectively. The average live weight of the rams increased from 49.8 ± 0.4 (week 1) to 57.3 ± 0.9 kg (week 17) without effect of the diet. A positive effect of faba bean incorporation in the concentrate was observed on ejaculate volume, concentration and spermatozoa production. All these parameters were significantly higher in SBMFB and FB groups than in SBM group (P < 0.05). The protein source did not affect the percentage of dead spermatozoa and the total abnormalities which were similar for the three diets (38.7; 35.8 and 38.1% for SBM; SBMFB and FB, respectively). The mean testosterone concentration was higher (P < 0.05) in rams fed with faba bean (1.7 ± 0.7 to 1.9 ± 0.7 ng/ml for the SBMFB and the FB groups respectively) than in rams fed SBM diet (1.06 ± 0.5 ng/ml). It was concluded that the substitution of soybean meal by faba bean improved the reproductive performance and did not affect sperm quality in Queue Fine de l'Ouest rams.

Going to scale-From community-based to population-wide genetic improvement and commercialized sheep meat supply in Ethiopia.

Community-based breeding programs (CBBPs) have shown, at pilot scale, to be effective and beneficial in achieving genetic progress and in improving livelihoods of smallholder communities. In Ethiopia 134 sheep and goat CBBPs were operational producing their own improved rams and bucks. Based on experience the implementation of further programs is possible with appropriate private and public support. A different challenge is the efficient dissemination of the improved genetics produced in current CBBPs to create population-wide economic impact. We present a framework applied to the Ethiopian Washera sheep breed to meet this challenge. We propose the establishment of a genetic improvement structure that supports a meat commercialization model based on the integration of community-based breeding program cooperatives, client communities and complementary services such as fattening enterprises. We calculated that the recently established 28 community-based breeding programs in the Washera breeding tract can provide genetically improved rams to 22% of the four million head. To reach the whole population 152 additional CBBPs are needed. We simulated the genetic improvements obtainable in the current 28 CBBPs assuming realized genetic progress in CBBPs of a similar breed and calculated the expected additional lamb carcass meat production after 10 years of selection to be 7 tons and the accumulated discounted benefit 327 thousand USD. These benefits could be increased if the CBBPs are linked to client communities by providing them with improved rams: additional meat production would be 138 tons with a value of 3,088 thousand USD. The total meat production of the existing Washera CBBPs was calculated at 152 tons and the joint meat production of CBBPs if integrated with client communities would be 3,495 tons. A full integration model, which includes enterprises purchasing lambs for fattening, can produce up to 4,255 tons of meat. We conclude that Washera CBBPs cooperatives can benefit from a higher level of organization to produce population-wide genetic improvement and economic benefits. Unlike in the dairy and chicken industries, for low input sheep and goat smallholder systems the proposed commercialization model puts breeder cooperatives at the center of the operation. Cooperatives need to be capacitated and supported to become fully functional business ventures.

Marker-assisted introgression of fecundity mutation into Barbarine sheep breed under low input production system.

Fecundity gene introgression has become an economical method to improve sheep prolificacy in developing countries. The FecXBar and FecGH mutations are variants of the BMP15 and GDF9 sheep genes, respectively, identified in Tunisian Barbarine sheep prolific line "W-INRAT," created through a prolificacy-based selection program. The first mutation caused increased prolificacy in heterozygous state and sterility in homozygous ewes. The aim of this work was to increase the number of effective carriers by the introgression of fecundity mutation into non-carrier conventional flocks based on a marker-assisted breeding program. The genotyping was carried out to follow up on the segregation of prolificacy mutation. The conventional ewes, raised in state farms of Tunisia and inseminated by "W-INRAT" rams, yielded 100% carriers females at heterozygous state. These females were selected to be inseminated with conventional rams and produced carriers' lambs with 66.7% males and 33.3% females. The prolific males will be kept in breeding centers to disseminate the fecundity mutation in commercial flocks. This approach facilitates the dissemination of fecundity genes and contributes to livelihood improvement in communities raising Barbarine sheep.

How to succeed in implementing community-based breeding programs: Lessons from the field in Eastern and Southern Africa.

Breeding programs involving either centralized nucleus schemes and/or importation of exotic germplasm for crossbreeding were not successful and sustainable in most Africa countries. Community-based breeding programs (CBBPs) are now suggested as alternatives that aim to improve local breeds and concurrently conserve them. Community-based breeding program is unique in that it involves the different actors from the initial phase of design up until implementation of the programs, gives farmers the knowledge, skills and support they need to continue making improvements long into the future and is suitable for low input systems. In Ethiopia, we piloted CBBPs in sheep and goats, and the results show that they are technically feasible to implement, generate genetic gains in breeding goal traits and result in socio-economic impact. In Malawi, CBBPs were piloted in local goats, and results showed substantial gain in production traits of growth and carcass yields. CBBPs are currently being integrated into goat pass-on programs in few NGOs and is out-scaled to local pig production. Impressive results have also been generated from pilot CBBPs in Tanzania. From experiential monitoring and learning, their success depends on the following: 1) identification of the right beneficiaries; 2) clear framework for dissemination of improved genetics and an up/out scaling strategy; 3) institutional arrangements including establishment of breeders' cooperatives to support functionality and sustainability; 4) capacity development of the different actors on animal husbandry, breeding practices, breeding value estimation and sound financial management; 5) easy to use mobile applications for data collection and management; 6) long-term technical support mainly in data management, analysis and feedback of estimated breeding values from committed and accessible technical staff; 7) complementary services including disease prevention and control, proper feeding, and market linkages for improved genotypes and non-selected counterparts; 8) a system for certification of breeding rams/bucks to ensure quality control; 9) periodic program evaluation and impact assessment; and 10) flexibility in the implementation of the programs. Lessons relating to technical, institutional, community dynamics and the innovative approaches followed are discussed.

Preliminary study on the seasonal questing of Ixodes ricinus group ticks in Ain Draham forest (north-western Tunisia) with analyses of their phylogenetic diversity.

The present study aimed to investigate the activity dynamics of Ixodes ricinus group ticks in a forest located in north-western Tunisia (Aïn Draham, Jendouba District) and assess the variation of abiotic factors (temperature, Normalized Difference Vegetation Index and relative humidity) during one year survey from September 2016 to August 2017 using the dragging sampling method. A total of 116 questing ticks was collected from the vegetation consisting of 47 adults (19 females and 28 males, sex ratio M:F = 1.47), 45 nymphs and 24 larvae representing 40.5, 38.8 and 20.7% of the total collected specimens, respectively. Adult I. ricinus were collected during October-May, nymphs during May-August and larvae during July-September. There were statistically significant correlations between adult tick numbers and mean daily relative humidity (Pearson r = 0.77; p = 0.003) and mean daily temperature (r = -0.74; p = 0.006). The comparison of 16S rDNA sequences from 20 adult ticks of approximately 444 bp length showed variability among 11 sequences. There was a low genetic variability (<1%) among the I. ricinus isolates collected from the forest. The amplicons showed >99% identity with I. ricinus and Ixodes inopinatus sequences from different countries and published in GenBank. These results should be complemented by further surveys in other Tunisian regions to better understand the influence of environmental factors on the biology of I. ricinus and the occurrence of sympatric I. inopinatus ticks. Different molecular markers should be used for better understanding of their taxonomic status.

Detection and molecular identification of Anaplasma phagocytophilum and Babesia spp. infections in Hyalomma aegyptium ticks in Tunisia.

Tortoises of the genus Testudo are the main hosts of Hyalomma aegyptium ticks. This species serves as a vector of several zoonotic pathogens. Therefore, the present study aimed to investigate the presence of four pathogens associated with H. aegyptium ticks obtained from tortoises from Tunisia. Conventional, multiplex and nested PCRs were used for Aanaplasma phagocytophilum, Ehrlichia canis, Coxiella burnetii and Babesia spp. screening. The molecular analyses revealed the presence of A. phagocytophilum and Babesia spp. None of the ticks, were infected by E. canis or C. burnetii species. Co-infection was detected in four ticks. As a conclusion, this is the first detection of A. phagocytophilum and Babesia spp. in H. aegyptium ticks collected from tortoises, in Tunisia. Thus, considering these results, the spur-thighed tortoise constitute a potential host of H. aegyptium which plays an important role in the transmission of pathogenic agents affecting both human and animals. In term of public health, a strict control and surveillance should be carried to reduce the circulation of such pathogens between different hosts.

First insights into the microbiome of Tunisian Hyalomma ticks gained through next-generation sequencing with a special focus on H. scupense.

Ticks are one of the most important vectors of several pathogens affecting humans and animals. In addition to pathogens, ticks carry diverse microbiota of symbiotic and commensal microorganisms. In this study, we have investigated the first Tunisian insight into the microbial composition of the most dominant Hyalomma species infesting Tunisian cattle and explored the relative contribution of tick sex, life stage, and species to the diversity, richness and bacterial species of tick microbiome. In this regard, next generation sequencing for the 16S rRNA (V3-V4 region) of tick bacterial microbiota and metagenomic analysis were established. The analysis of the bacterial diversity reveals that H. marginatum and H. excavatum have greater diversity than H. scupense. Furthermore, microbial diversity and composition vary according to the tick's life stage and sex in the specific case of H. scupense. The endosymbionts Francisella, Midichloria mitochondrii, and Rickettsia were shown to be the most prevalent in Hyalomma spp. Rickettsia, Francisella, Ehrlichia, and Erwinia are the most common zoonotic bacteria found in Hyalomma ticks. Accordingly, Hyalomma ticks could represent potential vectors for these zoonotic bacterial agents.

A climate-based model for tick life cycle: positive semigroup theory on Cauchy problem approach.

The distribution of ticks is essentially determined by the presence of climatic conditions and ecological contexts suitable for their survival and development. We build a model that explicitly takes into account each physiological state through a system of infinite differential equations where tick population density are structured on an infinite discrete set. We suppose that intrastage development process is temperature dependent (Arrhenius temperatures function) and that larvae hatching and adult mortality are temperature and water vapor deficit dependent. We analysed mathematically the model and have explicit the [Formula: see text] of the tick population.

Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep.

BACKGROUND: Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in indigenous sheep, but its genetic control remains unknown. RESULTS: Here, we report 397 genome-wide signatures of selection overlapping 991 genes from the analysis, using ROH, LR-GWAS, XP-EHH, and FST, of 600 K SNP genotype data from 165 Tunisian sheep showing high and low levels of tick infestations and piroplasm infections. We consider 45 signatures that are detected by consensus results of at least two methods as high-confidence selection regions. These spanned 104 genes which included immune system function genes, solute carriers and chemokine receptor. One region spanned STX5, that has been associated with tick resistance in cattle, implicating it as a prime candidate in sheep. We also observed RAB6B and TF in a high confidence candidate region that has been associated with growth traits suggesting natural selection is enhancing growth and developmental stability under tick challenge. The analysis also revealed fine-scale genome structure indicative of cryptic divergence in Tunisian sheep. CONCLUSIONS: Our findings provide a genomic reference that can enhance the understanding of the genetic architecture of tick resistance and cryptic divergence in indigenous African sheep.

High Toxoplasma gondii frequency of infection in the genital tract of ewes previously positive for the parasite DNA in meat, in Sidi Bouzid, Tunisia.

The aim of the present study was to estimate the molecular prevalence of T. gondii along various segments of the genital tract of confirmed chronically infected ewes. Genital tracts were collected from 42 ewes; meat samples from the same ewes were previously confirmed positive for T. gondii DNA. The whole DNA was extracted from 4 parts of the genital tract (ovary, horns, body of the uterus and vagina). PCR was used to amplify a 114 base-pairs of T. gondii B1 gene. For all studied samples, 95.2 % had at least one infected genital part. Toxoplasma gondii infection was confirmed by sequencing 20 amplicons randomly chosen. The majority of infected animals has 4 T. gondii-infected genital anatomical parts. Principal component analysis (PCA) revealed a cluster of adult animals (>24 months) with positive PCR in the ovaries and the vagina and another cluster of Barbarine animals having positive PCR in the horns and body of the uterus. General linear model confirmed PCA results and showed a significant higher prevalence of T. gondii in the ovaries and vagina of older animals (p = 0.001 and p = 0.02, respectively) and a higher prevalence of T. gondii in the horns of the uterus of Barbarine animals (p = 0.03). Toxoplasma gondii seems to highly persist along the various segments of the ewe's genital tract but further investigations are necessary to link such prevalence with the pathological implications.

Three easy fixes for sire use can enhance genetic progress in community-based breeding programmes.

We analysed options to optimize the use of sires in sheep and goat community-based breeding programmes (CBBP) for three scenarios occurring under field conditions: premature sale of selection candidates, fixed service periods of selected sires and incomplete sire pedigrees. The first scenario was studied by looking at the outcome of combinations of selection pressures in successive selection stages. A compromise of early sale of sire candidates and genetic progress can be obtained by selecting in two stages, such that selection pressure in the first stage is chosen in terms of achieving an acceptable selection potential after the second stage. Simulations showed the dependency of this compromise on selection accuracies and correlation between selection criteria. For a typical sheep CBBP, only 20% of the top three months weighting male lambs need to be retained to achieve 80% of the potential selection differential on six months weight. For the second scenario, two alternatives to fixed service periods were analysed. When across-age BLUP EBVs are not available, individual sires can be programmed to stay in service according to their initial ranking. In typical sheep, CBBPs genetic progress can be increased by about 9% over response to selection with optimum fixed sire service periods. When BLUP EBVs are available, a simulated retrospective analyses of across-age selection of sires in two current sheep CBBPs increased more than twofold the average breeding values actually observed. Thirdly, we studied the benefit of considering possible sires and their mating probabilities when estimating BLUP breeding values instead of setting such sires as unknown. In a current goat CBBP with up to three possible sires included in the pedigree, the accuracy of breeding values nears the accuracy when sires are known and are higher than accuracies when sires are unknown or when possible sires are ignored.

Genome Divergence and Dynamics in the Thin-Tailed Desert Sheep From Sudan.

With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies.