Detection of Crimean-Congo hemorrhagic fever virus antibodies in cattle in Kenedougou and Mouhoun provinces in Burkina Faso.

Background: Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic disease caused by an Orthonairovirus of the Nairoviridae family transmitted by tick bites and also contact with infected blood, tissues, or body fluids. Until now, fewer studies have been conducted on animals in Burkina Faso. Aim: This study was conducted to investigate the seroprevalence and risk factors of CCHF in two provinces of Burkina Faso. Methods: Serum samples were collected from 371 bovine animals. In addition, questionnaire surveys were performed with cattle breeders. The double-antigen sandwich enzyme-linked immunosorbent assay test was used to determine the presence of antibodies against the CCHF virus in serum samples. Results: The results showed an overall prevalence of 72.2% [95% confidence interval (CI): 67.6%-76.7%)]. Within the 74 herds included in the study, a herd prevalence of 96% (95% CI: 91.4%-100%) was obtained. The prevalence was significantly higher in Mouhoun province (80%, 95% CI: 74%-86%) compared to Kénédougou province (65.6%, 95% CI: 59.1%-72.2%). Multivariable regression analysis showed that females were more likely to be infected (OR = 1.99, 95% CI: 1.1-3.6, p = 0.023) than males. In addition, cross-breed animals (OR = 6.42, 95% CI: 1.71-24.14, p = 0.006) were more likely to be infected compared to local-bred animals. This study revealed the presence of antibodies of the CCHF virus in cattle in the study area, indicating the need to implement control measures in the veterinary sector. Conclusion: Despite the importance of CCHF in public health, no study has been implemented regarding this condition in animals in Burkina Faso. This study described evidence of cattle exposure to the virus in Burkina Faso.

Optimizing type, date, and dose of compost fertilization of organic cotton under climate change in Mali: A modeling study.

Adapting organic farming to climate change is a major issue. Cotton yields in Mali are declining due to deteriorating climatic conditions, soil fertility, and poor management. This study aimed to improve organic cotton yield in Mali in the future climate with the optimal choice of compost type, date, and dose of application. Experimental data collected in 2021 from the Sotuba research station in Mali was used for calibration and evaluation of the crop model DSSAT CSM-CROPGRO-Cotton model using phenology, leaf area index, and seed cotton yield. Climate data from the RCP4.5 and RCP8.5 scenarios of the GFDL-ESM2M model were used for future weather datasets for 2020-2039, 2040-2059, and 2060-2079. The model was able to simulate anthesis and maturity with excellent results, with nRMSE < 4%, and seed cotton yields moderately well, an nRMSE of 26% during calibration and 20.3% in evaluation. The scenario RCP8.5 from 2060 to 2079 gave the best seed cotton yields. Seed cotton yields with RCP4.5 and RCP8.5 were all better with the mid-May application period of small ruminant silo compost at 7.5 t/ha. In such conditions, more than 75% of the cases would produce more than 2000 kg/ha of seed cotton.

Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants.

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

Anal disorders in pregnant and postpartum women: epidemiological, diagnostic and therapeutic aspects in 10 maternities of Bamako in Mali.

Bowel transit disturbances favored by pregnancy and injuries during childbirth would be triggering or aggravating factors for anal pathologies. The objective of this work was to study the epidemiology, diagnosis, and treatment of anal pathologies during pregnancy and 6 weeks after delivery. We carried out a prospective, multi-centric, and analytical study in 10 obstetric units in Bamako from June 1st, 2019, to May 31st, 2020. After informed consent, we enrolled all first-trimester pregnant women admitted to the hospitals and who were followed up through the postpartum. We conducted a rectal examination in each participant and an anoscope in those with an anal symptom. Hemorrhoidal diseases were diagnosed in the case of external hemorrhoids (thrombosis or prolapse) or internal hemorrhoids. During the study period, we followed up 1,422 pregnant women and we found 38.4% (546) with anal pathologies (hemorrhoidal diseases in 13% (192), anal fissure in 10.5% (150) and anal incontinence in 8.6% (123). Risk factors for the hemorrhoidal disease were age of patient ≥30 years old aRR=5.77, 95% CI 4.57-7.34; p=0.000; a existence of chronic constipation aRR=2.61, 95% CI 1.98-3.44; p=0.000; newborn weight >3500 g aRR= 1.61, 95% CI 1.25-2.07; p=0.000 and fetal expulsion time >20 minutes aRR= 6.04, 95% CI 5.07-7.27; p=0.000. The clinical signs observed were constipation, anal pain, bleeding, and pruritus. The treatment was based on counseling on hygiene and diet, the use of laxatives, local topicals, and analgesics along perineal rehabilitation. Anal pathologies were common during pregnancy and 6 weeks after delivery. Pregnant women must be screened systematically for such pathologies. Early diagnostic and appropriate treatment would reduce serious complications.

Effect of textile colour on vector mosquito host selection: a simulated field study in Mali, West Africa.

BACKGROUND: The effect of clothing colour on the biting rates of different vector mosquito species is not well understood. Studies under tropical field conditions are lacking. This study aimed to determine the influence of clothing colours on mosquito biting rates in rural and suburban settings in West Africa. METHODS: We performed a simulated field study in a suburban and a rural site in Mali using Mosquito-Magnet traps utilizing CO2 and other attractants, which were covered with black, white, and black/white striped textile sheets covers. These targets operated continuously for 10 consecutive days with bright nights (around full moon) and 10 consecutive days with dark nights (around new moon). Trapped mosquitoes were collected and catch rates counted hourly. Mosquitoes were morphologically identified to the species complex level (Anopheles gambiae s.l. and Culex pipiens s.l.) or species level (Aedes aegypti). A subset of Anopheles specimens were further identified by molecular methods. RESULTS: Under bright-night conditions, An. gambiae s.l. was significantly more attracted to black targets than to white and striped targets; during dark nights, no target preference was noted. During bright nights, Cx. pipiens s.l. was significantly more attracted to black and striped targets than to white targets; a similar trend was noted during dark nights (not significant). For day-active Ae. aegypti, striped targets were more attractive than the other targets and black were more attractive than white targets. CONCLUSIONS: The study firstly demonstrated that under field conditions in Mali, West Africa, mosquito catch rates were influenced by different clothing colours, depending on mosquito species and light conditions. Overall, light colours were least attractive to host-seeking mosquitoes. Using white or other light-coloured clothing can potentially reduce bite exposure and risk of disease transmission in endemic tropical regions.

Modeling clinical malaria episodes in different ecological settings in Mali, 2018-2022.

Objectives: Following the scaling-up of malaria control strategies in Mali, understanding the changes in age-specific prevalence of infection and risk factors associated with remains necessary to determine new priorities to progress toward disease elimination. This study aimed to estimate the risk of clinical malaria using longitudinal data across three different transmission settings in Mali. Methods: Cohort-based longitudinal studies were performed from April 2018 to December 2022. Incidence of malaria was measured through community health center-based passive case detection. Generalized estimation equation model was used to assess risk factors for clinical malaria. Results: A total of 21,453 clinical presentations were reported from 4500 participants, mainly from July to November. Data shows a significant association between malaria episodes, sex, age group, season, and year. Women had lower risk, the risk of clinical episode increased with age up to 14 years then declined, and in both sites, the dry-season risk of clinical episode was significantly lower compared to the rainy season. Conclusion: Determining factors associated with the occurrence of clinical malaria across different ecological settings across the country could help in the development of new strategies aiming to accelerate malaria elimination in an area where malaria transmission remains intense.

Serological evidence and factors associated with Crimean-Congo haemorrhagic fever in sheep in Burkina Faso.

BACKGROUND: Crimean-Congo haemorrhagic fever (CCHF) is caused by an orthonairovirus transmitted by bites from infected ticks or by direct contact with blood or tissues of infected ticks, viraemic patients or viraemic livestock. OBJECTIVE: It was implemented to access the seropositivity and associated factors with CCHF in sheep in two provinces in Burkina Faso. METHODS: Three hundred and sixty-four sheep sera have been taken from 73 herds in four municipalities and two provinces. The double-antigen sandwich ELISA test was used to test for antibodies against CCHF virus (CCHFV). Data have also been collected using questionnaire to assess factors associated with CCHF seropositivity. RESULTS: Fifty-four (54 out to 364 sheep were seropositive given an overall seropositivity of 14.8% (95% confidence interval [CI]: 10.9%-19.8%) with an adjusted seropositivity of 13.1%. The study showed that 15.6% (95% CI: 10.2-21.0) and 14.1% (95% CI: 9.2-19.1) of sheep in the provinces of Mouhoun and Kénédougou, respectively, had antibodies against CCHFV. The highest seropositivity was found in Dédougou municipality (24.4%). The study showed that sheep from the municipalities of Dédougou (AOR = 8.4; 95% CI: 2.2-31.8), N'dorola (AOR = 14.7; 95% CI: 3.8-56.8), Sindou (AOR = 4.9; 95% CI: 1.2-20.7), sheep aged between 27 and 36 months (AOR = 6.4; 95% CI: 2.3-17.3) and sheep with ticks (AOR = 24.8; 95% CI: 7.7-80.1) were more likely to be seropositive to CCHF. CONCLUSIONS: The study revealed that sheep in Burkina Faso experienced contacts with CCHFV and suggests the importance of implementing control action in the country.

In vitro anthelmintic activity of Euphorbia forskalii J. Gay aqueous extracts evaluation on different life stages of Haemonchus contortus.

The use of medicinal plants in the control of gastrointestinal parasitosis is a promising solution for improving the productivity of sheep flocks. In order to evaluate the anthelmintic activity of Euphorbia forskallii, in vitro bioassays were performed on three life stages of Haemonchus contortus. Five aqueous extracts concentrations namely 10 mg/mL; 5 mg/mL; 2.5 mg/mL; 1.25 mg/mL and 0.62 mg/mL were used for adult worm mortality tests. Egg hatch inhibition and L3 larval migration inhibition tests were studied at 5 mg/mL; 2.5 mg/mL; 1.25 mg/mL; 0.62 mg/mL and 0.31 mg/mL. A negative control PBS and a positive control levamisole 2.5 mg/mL were established for each test. A phytochemical screening was performed to determine the presence of some secondary metabolites. The results obtained showed the presence of total polyphenols, total flavonoids and condensed tannins within the aqueous extracts of E. forskalii. A high and significant (P < 0.05) morality rate compared to the negative control with an LC50 of 2.30 mg/mL was obtained. Inhibition of egg hatch and larval migration were high and significant (p < 0.05) compared to the negative control. There was an IC50 of 1.03 mg/mL and 0.92 mg/mL respectively for inhibition of egg hatching and L3 larval migration. The present study revealed the in vitro anthelmintic activity of E. forskalii aqueous extracts and allows us to consider in perspective complementary studies to confirm this activity.

Pigs' management practices and exposure to Trichinella spp. in pigs and warthogs in the northern area of Senegal.

Background and Aim: Trichinellosis is a neglected and emerging foodborne zoonosis in Africa. Trichinella infection occurs through the consumption of raw or undercooked infected meat and meat products. This study aimed to assess pigs' management practices and determine the exposure of pigs and warthogs to Trichinella spp. in the northern area of Senegal. Materials and Methods: Surveys and observations were carried out among 40 pig farmers to assess husbandry practices regarding Trichinella spp. life cycle. In addition, 201 pig meat juices and 83 warthog meat juices were extracted and tested for anti-Trichinella antibodies by indirect enzyme-linked immunosorbent assay. Results: Most (97%) of farms practiced a traditional farming system with free-ranging of pigs in 85% of farms. Farms had local pig breed without housing and supplementary feeding. Some farmers (27.5%) used slaughter waste to feed pigs and farmers were not aware that free-range farming is a source of infection to Trichinella infection. They were also unaware that some pig diseases could be transmitted to humans. The seroprevalence of Trichinella infection was 10.9% (95% confidence interval [CI]: 6.6-15.2%) in pigs and 10.8% (95% CI: 4.16-17.52%) in warthogs with significantly higher seroprevalence in male (22.2%: 95% CI: 6.6-37.8%) compared to female (9.2%; 95% CI: 4.9-13.5%) (p < 0.05). Conclusion: The confirmation of exposure to Trichinella spp. in this area in pigs and warthogs shows a significant risk of transmission of this disease to humans if the farming conditions and the health surveillance system are not respected. However, control measures are needed to reduce any risk of transmission of Trichinella infection to humans.

Gastrointestinal parasites of baboons (Papio papio) in Niokolo-Koba National Park, Senegal.

Background: Primates can harbor parasites that could be pathogenic or not for humans and primates themselves. It is necessary to know the parasitological situation of the primates that are under surveillance in the park. Aim: To estimate the prevalence and diversity of gastrointestinal parasites, including zoonotic potential parasites, in baboons in the Niokolo-Koba National Park located in Senegal. Method: Fecal samples (n = 50) from two groups of baboons (A and B) were collected in October 2019. The samples were processed using the flotation technique and the modified Ritchie method. Slides were examined microscopically and the parasite identification was based on morphology, color, and parasite content. Results: A total of seven nematodes (Strongyloides sp., Trichirus sp., Ancylostoma sp., Mammo monogamus, Enterobius sp., Strongyloides stercoralis, Strongyle digestif), one cestode (Bertiella sp.), and one trematode (Fasciolopsis sp.) were identified. The overall prevalence was 78%, while the prevalence of poly-infected samples was 49%. The parasite with zoonotic potential, S. stercoralis, was identified in group B samples. Trichuris sp., which is common and pathogenic to humans and primates, was present with prevalence of 52% and of 32% in groups A and B, respectively. Conclusion: These results suggest that baboons are infested with zoonotic parasites and this situation could expose people working in this park to infection. Contact between humans and these baboons or their feces could expose them to infection with zoonotic parasites.

Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle.

A total of 106 West African taurine cattle belonging to the Lagunaire breed of Benin (33), the N'Dama population of Burkina Faso (48), and N'Dama cattle sampled in Congo (25) were analyzed for Copy Number Variations (CNVs) using the BovineHDBeadChip of Illumina and two different CNV calling programs: PennCNV and QuantiSNP. Furthermore, 89 West African zebu samples (Bororo cattle of Mali and Zebu Peul sampled in Benin and Burkina Faso) were used as an outgroup to ensure that analyses reflect the taurine cattle genomic background. Analyses identified 307 taurine-specific CNV regions (CNVRs), covering about 56 Mb on all bovine autosomes. Gene annotation enrichment analysis identified a total of 840 candidate genes on 168 taurine-specific CNVRs. Three different statistically significant functional term annotation clusters (from ACt1 to ACt3) involved in the immune function were identified: ACt1 includes genes encoding lipocalins, proteins involved in the modulation of immune response and allergy; ACt2 includes genes encoding coding B-box-type zinc finger proteins and butyrophilins, involved in innate immune processes; and Act3 includes genes encoding lectin receptors, involved in the inflammatory responses to pathogens and B- and T-cell differentiation. The overlap between taurine-specific CNVRs and QTL regions associated with trypanotolerant response and tick-resistance was relatively low, suggesting that the mechanisms underlying such traits may not be determined by CNV alterations. However, four taurine-specific CNVRs overlapped with QTL regions associated with both traits on BTA23, therefore suggesting that CNV alterations in major histocompatibility complex (MHC) genes can partially explain the existence of genetic mechanisms shared between trypanotolerance and tick resistance in cattle. This research contributes to the understanding of the genomic features of West African taurine cattle.

Polyphenolic Profile, Anti-Inflammatory and Anti-Nociceptive Activities of Some African Medicinal Plants.

The aim of the present study was to investigate the polyphenolic profile and the anti-inflammatory and anti-nociceptive activities of four traditionally used medicinal plants from Burkina Faso: Parkia biglobosa, Detarium microcarpum, Vitellaria paradoxa and Sclerocarya birrea. The analysis of the main phenolic compounds was performed by the HPLC-UV-MS method. The anti-inflammatory effect of the aqueous bark extracts was investigated by the λ-carrageenan-induced rat paw edema test. The anti-nociceptive activity was evaluated by the Randall−Selitto test under inflammatory conditions. Seven phenolic acids (gallic, protocatechuic, gentisic, vanillic, p-coumaric, ferulic, and syringic acids), and three flavonoids (catechin, epicatechin, and quercitrin) were identified in the plant samples. High contents of gallic acid were determined in the D. microcarpum, P. biglobosa and S. birrea extracts (190−300 mg/100 g), and V. paradoxa extract was the richest in epicatechin (173.86 mg/100 g). The λ-carrageenan-induced inflammation was significantly reduced (p < 0.001) by the P. biglobosa and D. microcarpum extracts (400 mg/kg p.o.). Under the inflammatory conditions, a significant anti-nociceptive activity (p < 0.001) was obtained after 2−3 h from the induction of inflammation. The effects of the tested extracts could be related to the presence of polyphenols and could be useful in the management of certain inflammatory diseases.

Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso.

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for F ST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.

Dog ownership, demographics, owners' knowledge of rabies, and factors associated with canine rabies vaccination in urban and rural areas of Dedougou, Burkina Faso.

Rabies is a prioritized zoonotic disease in Burkina Faso and is known as a major zoonotic disease with high public health importance. This investigation was conducted to assess community knowledge, dog ecology and demographics, and factors associated with dog vaccination against rabies in the urban and rural areas of Dedougou. Three hundred and sixteen (316) dog-owning households were surveyed in the rural and urban areas of Dedougou using a semi-structured questionnaire. Among participants, 55.7% lived in rural area, and 59.8% were farmers. Only 34.5% of participants had satisfactory knowledge of rabies. About 22% were aware of the required age of dogs' primo vaccination against rabies while 55.7% knew the frequency of booster vaccination. Participants living in households with less than five persons were significantly more likely to be aware of rabies than those living in households with the higher number of persons (P<0.05). Participants who were aware of rabies were more likely to vaccinate their dogs compared to those who were not aware of rabies (P<0.05). In total, 2930 persons were recorded in visited households with 60.6% from rural area, and an average household size of 9.27 persons. Three hundred and thirty seven dogs were found in surveyed households' and 54.9% were from rural area. In overall, a dog per human ratio of 1:8.7 was determinated. Regarding dog ownership practices, the majority of respondents reported that they provided their dogs with water (84.5%) and food (84.8%). This research reported supplementary data on dog ecology and rabies, which could be useful for rabies control planning in Burkina Faso.

Effects of insemination and blood-feeding on locomotor activity of wild-derived females of the malaria mosquito Anopheles coluzzii.

BACKGROUND: Behavioural shifts in the canonical location and timing of biting have been reported in natural populations of anopheline malaria vectors following the implementation of insecticide-based indoor vector control interventions. These modifications increase the likelihood of human-vector contact and allow mosquitoes to avoid insecticides, both conditions being favourable to residual transmission of the malarial parasites. The biting behaviour of mosquitoes follows rhythms that are under the control of biological clocks and environmental conditions, modulated by physiological states. In this work we explore modifications of spontaneous locomotor activity expressed by mosquitoes in different physiological states to highlight phenotypic variability associated to circadian control that may contribute to explain residual transmission in the field. METHODS: The F10 generation progeny of field-collected Anopheles coluzzii from southwestern Burkina Faso was tested using an automated recording apparatus (Locomotor Activity Monitor, TriKinetics Inc.) under LD 12:12 or DD light regimens in laboratory-controlled conditions. Activity recordings of each test were carried out for a week with 6-day-old females belonging to four experimental treatments, representing factorial combinations of two physiological variables: insemination status (virgin vs inseminated) and gonotrophic status (glucose fed vs blood fed). Chronobiological features of rhythmicity in locomotor activity were explored using periodograms, diversity indices, and generalized linear mixed modelling. RESULTS: The average strength of activity, onset of activity, and acrophase were modulated by both nutritional and insemination status as well as by the light regimen. Inseminated females showed a significant excess of arrhythmic activity under DD. When rhythmicity was observed in DD, females displayed sustained activity also during the subjective day. CONCLUSIONS: Insemination and gonotrophic status influence the underlying light and circadian control of chronobiological features of locomotor activity. Overrepresentation of arrhythmic chronotypes as well as the sustained activity of inseminated females during the subjective day under DD conditions suggests potential activity of natural populations of A. coluzzii during daytime under dim conditions, with implications for residual transmission of malarial parasites.

Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso.

In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.

Ancient autozygous segments subject to positive selection suggest adaptive immune responses in West African cattle.

Small-sized and trypanotolerant West African taurine (Bos taurus) cattle are a unique case of human-mediated process of adaptation to a challenging environment. Extensive gene flow with Sahelian zebu (B. indicus), bigger and with some resistance to tick attack, occurred for centuries and allowed the apparition of stable crossbred populations (sanga) having intermediate characteristics. Up to 237 individuals belonging to 10 different taurine, zebu and sanga cattle populations sampled in Benin, Burkina Faso and Niger were typed using the BovineHD BeadChip of Illumina to identify signatures of selection, assessed using three different Extended-Haplotype-Homozygosity-based statistics, overlapping with ancient, originated 1024 or 2048 generations ago, Homozygosity-By-Descent segments in the cattle genome. Candidate genomic regions were defined ensuring their importance within cattle type and using zebu as reference. Functional annotation analysis identified four statistically significant Annotation Clusters in taurine cattle (from ACt1 to ACt4), one (ACs1) in sanga, and another (ACz1) in zebu cattle, fitting well with expectations. ACt1 included genes primarily associated with innate immunity; ACt2 involved bitter taste receptor genes of importance to adaptation to changing environments; ACt3 included 68 genes coding ATP-binding proteins, some of them located on trypanotolerance-related QTL regions, that can partially underlie immune response and the additive mechanism of trypanotolerance; ACt4 was associated with growth and small size (NPPC gene); ACs1 included genes involved in immune response; and ACz1 is related with ectoparasite resistance. Our results provide a new set of genomic areas and candidate genes giving new insights on the genomic impact of adaptation in West African cattle.

Functional characterization of Copy Number Variations regions in Djallonké sheep.

A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50 K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5 Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor > 1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.

Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso.

High-throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well-structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on-farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community-based breeding programs in the South-West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent-offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community-based breeding program will make use of genomic information about admixture levels.

Population Structure Assessed Using Microsatellite and SNP Data: An Empirical Comparison in West African Cattle.

A sample of 185 West African cattle belonging to nine different taurine, sanga, and zebu populations was typed using a set of 33 microsatellites and the BovineHD BeadChip of Illumina. The information provided by each type of marker was summarized via clustering methods and principal component analyses (PCA). The aim was to assess differences in performance between both marker types for the identification of population structure and the projection of genetic variability on geographical maps. In general, both microsatellites and Single Nucleotide Polymorphism (SNP) allowed us to differentiate taurine cattle from zebu and sanga cattle, which, in turn, would form a single population. Pearson and Spearman correlation coefficients computed among the admixture coefficients (fitting K = 2) and the eigenvectors corresponding to the first two factors identified using PCA on both microsatellite and SNP data were statistically significant (most of them having p < 0.0001) and high. However, SNP data allowed for a better fine-scale identification of population structure within taurine cattle: Lagunaire cattle from Benin were separated from two different N'Dama cattle samples. Furthermore, when clustering analyses assumed the existence of two parental populations only (K = 2), the SNPs could differentiate a different genetic background in Lagunaire and N'Dama cattle. Although the two N'Dama cattle populations had very different breeding histories, the microsatellite set could not separate the two N'Dama cattle populations. Classic bidimensional dispersion plots constructed using factors identified via PCA gave different shapes for microsatellites and SNPs: plots constructed using microsatellite polymorphism would suggest the existence of weakly differentiated, highly intermingled, subpopulations. However, the projection of the factors identified on synthetic maps gave comparable images. This would suggest that results on population structuring must be interpreted with caution. The geographic projection of genetic variation on synthetic maps avoids interpretations that go beyond the results obtained, particularly when previous information on the analyzed populations is scant. Factors influencing the performance of the projection of genetic parameters on geographic maps, together with restrictions that may affect the election of a given type of markers, are discussed.