Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds.

BACKGROUND: The genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis of whole-genome sequence data, we considered over 8 million variants from 144 animals, which allows for fine-mapping of potential genomic incompatibilities at high resolution across the genome. RESULTS: We identified several thousand variants that had significantly steep clines ('SCV') across the whole genome, indicating restricted introgression. Some of the SCV were clustered into extended regions, with the longest on chromosome 7, spanning 725 kb and including 27 genes. We found that variants with a high phenotypic impact (e.g. indels, intra-genic and missense variants) likely represent greater genetic barriers to gene flow. Furthermore, our findings provide evidence that a large proportion of breed differentiation in African cattle could be linked to genomic incompatibilities and reproductive isolation. Functional evaluation of genes with SCV suggest that mitonuclear incompatibilities and genes associated with fitness (e.g. resistance to paratuberculosis) could account for restricted gene flow in indigenous African cattle. CONCLUSIONS: To our knowledge, this is the first time genomic cline analysis has been applied to identify restricted introgression in the genomes of indigenous African cattle and the results provide extended insights into mechanisms (e.g. genomic incompatibilities) contributing to hybrid differentiation. These results have important implications for our understanding of genetic incompatibilities and reproductive isolation and provide important insights into the impact of cross-breeding cattle with the aim of producing offspring that are both hardy and productive.

Low doses and short duration of prednisolone administration in guinea pigs experimentally infected with Schistosoma haematobium: Histopathology of liver and lungs.

In our previous study, administration of 5 mg prednisolone for five days pre-Schistosoma haematobium infection in guinea pigs increased susceptibility and produced pathological reactions in the liver and bladder. Since corticosteroids can suppress granuloma formation, maturation, and size, this study sought to investigate if prednisolone given at low doses and short duration can produce granulomatous lesions in the tissues of guinea pigs experimentally infected with S. haematobium. Guinea pigs were shared into six groups: group I and II were the immunosuppressed-infected guinea pigs (I0.5 and I1.5- 20 animals each), group III was the unimmunosuppressed-infected guinea pigs (UI- 20 animals), and group IV, V and VI were the immunosuppressed-uninfected and normal guinea pigs (D0.5, D1.5, and normal- 10 animals each). Prednisolone was given in doses of 0.5 mg/kg and 1.5 mg/kg to the different groups, a day before infection and on day 5 post-infection. The infected groups were subcutaneously injected with 250-300 S. haematobium cercariae. Screening for S. haematobium eggs in urine and fecal samples of animals, and quantitative analysis for leukocyte and red blood cell (RBC) counts in urine samples of guinea pigs began nine weeks post-infection (WPI). Guinea pigs were killed, perfused, worms recovered and sections of the liver, lungs, and bladder excised for histopathological examination at 6, 8, 11, 14 and 16 WPI. S. haematobium eggs were only seen in urine samples of I1.5 at 15 and 16WPI. Although the parasite eggs were seen in fecal samples of all infected guinea pigs from 9WPI, those of UI were sparse and took longer time to hatch. High leukocyte counts were seen in all immunosuppressed groups at 6WPI, which returned to normal levels in D1.5 and D0.5 at 16WPI. At 16WPI, significant numbers of leukocyte and RBC counts were seen in urine samples of I1.5. The immunosuppressed-infected groups had significant numbers of mature and total worm loads than UI group (p > 0.05). However, the worm burden of I1.5 was higher than I0.5 at 14WPI and 16WPI. Non-granulomatous lesions were only recorded in the liver sections of the immunosuppressed-infected animals and in lung sections of UI and I1.5 guinea pigs. Liver lesions seen were hepatocyte degeneration; necrosis; Kupffer cell involvements as hyperplasia, phagocytosis, proliferation; hyperaemia and haemorrhage, and mononuclear leukocyte infiltration. Lung lesions seen in I1.5 at 11-16WPI were hemosiderin depositions and hyperaemia, emphysema and atelectasis, and mononuclear leukocyte infiltrations while in UI, emphysema and mononuclear leukocyte infiltration were seen only at 16WPI. In the immunosuppressed-infected groups, composite liver lesion scores showed that peak lesion severity was at 8WPI and 11WPI in I1.5 and I0.5, respectively. However, there was no significant difference (p = 0.105) in composite liver lesion scores of I1.5 and I0.5. Lung lesion score of UI at 16WPI was significantly higher (p > 0.05) than that of I1.5. Findings from this study show that even at low doses and short duration of administration, corticosteroids can only increase susceptibility of guinea pigs but cannot improve its suitability as experimental models of S. haematobium infection.

Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

BACKGROUND: In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS: We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS: Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

Intranasal Peste des petits ruminants virus vaccination of goats using Irvingia gabonensis gum as delivery system: hematological and humoral immune responses.

Peste des petits ruminants (PPR) in Africa continues to defy conventional vaccinational approaches aimed at its control. There is need for route modification and immunopotentiation of the current vaccination methods, using easily affordable materials. This study evaluates the immunomodulatory potential of Irvingia gabonensis (IG) seed gum extract for intranasal PPR vaccination in goats using attenuated Nigeria 75/1 PPR vaccine. Twenty West African dwarf goats were divided into four groups (n=5). Group 1 was vaccinated intranasally using IG gum as vehicle; Group 2 was vaccinated intranasally without the gum; Group 3 via subcutaneous injection while Group 4 was not vaccinated. Hematology and Serum IgG levels were assessed weekly for 28 days post vaccination (dpv). H-PPR bELISA detected antibodies against PPR by 7th dpv, peaking by 21st dpv with mean percentage inhibitions of 78.2%; 69.6%; 87.0% and 0% in Groups 1, 2, 3 and 4, respectively. Also, significantly lower neutrophil to lymphocyte ratio (P<0.05) were observed by 14th dpv to 28th dpv in the vaccinated groups. The findings of this study show that the use of I. gabonensis seed gum extract for mucoadhesive intranasal PPR vaccine delivery has an immunomodulatory effect on the systemic immune response following PPR intranasal vaccine administration.

The influence of intranasal peste des petits ruminants (PPR) vaccine administration alone or with phytogenic mucoadhesive delivery system on PPR outbreak outcomes in goats.

This study reports the influence of peste des petits ruminants (PPR) vaccination on the clinico-pathological outcomes of PPR in the face of an outbreak. Twenty-two West African dwarf goats procured for a different study started showing early signs of PPR during acclimatization. In response, PPR vaccine was administered either intranasally with phytogenic mucoadhesive gum (Group A; n = 6) or without gum (Group B; n = 6); subcutaneously (Group C; n = 6) or not vaccinated (Group D; n = 4) and studied for 21 days. The clinical scores, hematology, serology and pathology scores were evaluated. Clinical signs of PPR were present in all groups, presenting a percentage mortality of 33%; 33%; 64% and 100% for Groups A, B, C, and D, respectively. Polycythemia and mild leukopenia were observed in all groups, and all animals were seropositive by day 7 post-vaccination. The lung consolidation scores were low in Groups A and B, compared to Group C. Histopathological lesions consistent with PPR was observed in the lymphoid organs, gastrointestinal tract, and lungs with the presence of PPR antigen as detected by immunohistochemistry. The findings suggest that intranasal vaccination with or without mucoadhesive gum may influence the outcome of PPR infection more than the subcutaneous route in the face of an outbreak.

Evaluation of the mucoadhesive strengths of Abelmoschus esculentus and Irvingia gabonensis gums for possible application in veterinary vaccine delivery: the effect of extraction methods.

This study evaluates the effects of different gum extraction methods on the mucoadhesive strengths of Abelmoschus esculentus (AE) and Irvingia gabonensis (IG) gums and the release of vaccine antigen in vaccine-gum formulations. AE and IG gums were extracted employing previously documented methods with acetone or sodium chloride (NaCl) and either oven-dried or freeze-dried. Gum extracts were analyzed for mucoadhesive strengths using a modified rotational cylinder method on animal mucosa. The time taken to detach from the mucosa was taken as the Peak Adhesion Time (PAT). The gum extracts were charged with Peste des petits ruminant vaccine and the antigen release was evaluated using agar gel immunodiffusion technique. The means of the PATS were analyzed using Mann-whitney t-test at p < .05. The NaCl extracted and freeze-dried IG gum showed sustained mean PATs of 1766 ± 73 s; 2116 ± 101 s; 7044 ± 117 s, while the oven-dried IG gum and both AE gums showed short-lived average PATs. Vaccine-gum formulations of IG at ratios 2:1, 1:1 & 1:2 had strong positive reactions while only that of AE at 2:1 showed a strong positive reaction. This study shows that NaCl extracted and freeze-dried IG gum has immunomodulatory potential for mucoadhesive vaccine delivery in ruminants.