ORCID Profile
0000-0002-2877-4767
Current Organisation
University of Nottingham
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Publisher: Cambridge University Press (CUP)
Date: 26-09-2014
DOI: 10.1017/S0031182014001498
Abstract: Parasite burden varies widely between in iduals within a population, and can covary with multiple aspects of in idual phenotype. Here we investigate the sources of variation in faecal strongyle eggs counts, and its association with body weight and a suite of haematological measures, in a cohort of indigenous zebu calves in Western Kenya, using relatedness matrices reconstructed from single nucleotide polymorphism (SNP) genotypes. Strongyle egg count was heritable ( h 2 = 23·9%, s.e. = 11·8%) and we also found heritability of white blood cell counts (WBC) ( h 2 = 27·6%, s.e. = 10·6%). All the traits investigated showed negative phenotypic covariances with strongyle egg count throughout the first year: high worm counts were associated with low values of WBC, red blood cell count, total serum protein and absolute eosinophil count. Furthermore, calf body weight at 1 week old was a significant predictor of strongyle EPG at 16–51 weeks, with smaller calves having a higher strongyle egg count later in life. Our results indicate a genetic basis to strongyle EPG in this population, and also reveal consistently strong negative associations between strongyle infection and other important aspects of the multivariate phenotype.
Publisher: Public Library of Science (PLoS)
Date: 03-03-2009
Publisher: Elsevier BV
Date: 11-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 02-12-2008
Publisher: Wiley
Date: 20-11-2007
DOI: 10.1111/J.1365-2052.2007.01663.X
Abstract: Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) s les from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies in addition to pure taurine, indicine and hybrid X-chromosome in iduals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.
Publisher: Wiley
Date: 10-2006
DOI: 10.1111/J.1365-2052.2006.01496.X
Abstract: To date, investigations of genetic ersity and the origins of domestication in sheep have utilised autosomal microsatellites and variation in the mitochondrial genome. We present the first analysis of both domestic and wild sheep using genetic markers residing on the ovine Y chromosome. Analysis of a single nucleotide polymorphism (oY1) in the SRY promoter region revealed that allele A-oY1 was present in all wild bighorn sheep (Ovis canadensis), two subspecies of thinhorn sheep (Ovis dalli), European Mouflon (Ovis musimon) and the Barbary (Ammontragis lervia). A-oY1 also had the highest frequency (71.4%) within 458 domestic sheep drawn from 65 breeds s led from Africa, Asia, Australia, the Caribbean, Europe, the Middle East and Central Asia. Sequence analysis of a second locus, microsatellite SRYM18, revealed a compound repeat array displaying fixed differences, which identified bighorn and thinhorn sheep as distinct from the European Mouflon and domestic animals. Combined genotypic data identified 11 male-specific haplotypes that represented at least two separate lineages. Investigation of the geographical distribution of each haplotype revealed that one (H6) was both very common and widespread in the global s le of domestic breeds. The remaining haplotypes each displayed more restricted and informative distributions. For ex le, H5 was likely founded following the domestication of European breeds and was used to trace the recent transportation of animals to both the Caribbean and Australia. A high rate of Y chromosomal dispersal appears to have taken place during the development of domestic sheep as only 12.9% of the total observed variation was partitioned between major geographical regions.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-04-2009
Abstract: A survey of genetic ersity of cattle suggests two domestication events in Asia and selection by husbandry.
Publisher: Public Library of Science (PLoS)
Date: 29-08-2013
DOI: 10.1371/ANNOTATION/2727DE85-899F-4104-955D-1C5F3C0D3319
Publisher: Springer Science and Business Media LLC
Date: 27-02-2009
DOI: 10.1007/S00251-009-0359-X
Abstract: There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-gamma and interleukin 1-beta) were selected for sequencing in erse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup s les (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-gamma had lower ersity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-beta had higher ersity and showed signals of balancing selection moderated by recombination, yielding high numbers of erse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.
Publisher: Elsevier BV
Date: 12-2003
Publisher: Wiley
Date: 29-04-2011
DOI: 10.1111/J.1365-2052.2011.02202.X
Abstract: A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F(1) rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL.
Publisher: Springer Science and Business Media LLC
Date: 15-10-2013
Abstract: Coccidiosis, caused by species of the apicomplexan parasite Eimeria , is a major disease of chickens. Eimeria species are present world-wide, and are ubiquitous under intensive farming methods. However, prevalence of Eimeria species is not uniform across production systems. In developing countries such as Ethiopia, a high proportion of chicken production occurs on rural smallholdings (i.e. 'village chicken production’) where infectious diseases constrain productivity and surveillance is low. Coccidiosis is reported to be prevalent in these areas. However, a reliance on oocyst morphology to determine the infecting species may impede accurate diagnosis. Here, we used cross-sectional and longitudinal studies to investigate the prevalence of Eimeria oocyst shedding at two rural sites in the Ethiopian highlands. Faecal s les were collected from 767 randomly selected chickens in May or October 2011. In addition, 110 chickens were s led in both May and October. Eimeria oocysts were detected microscopically in 427 (56%, 95% confidence interval (95% CI) 52-59%) of the 767 faecal s les tested. Moderate clustering of positive birds was detected within households, perhaps suggesting common risk factors or exposure pathways. Seven species of Eimeria were detected by real time PCR in a subset of s les further analysed, with the prevalence of some species varying by region. Co-infections were common 64% (23/36, 95% CI 46-79%) of positive s les contained more than one Eimeria spp. Despite frequent infection and co-infection overt clinical disease was not reported. Eimeria oocysts were detected significantly more frequently in October (248/384, 65%, 95% CI 60-69%), following the main rainy season, compared to May (179/383, 47%, 95% CI 42-52%, p 0.001). Eimeria oocyst positivity in May did not significantly affect the likelihood of detecting Eimeria oocyst five months later perhaps suggesting infection with different species or immunologically distinct strains. Eimeria spp oocysts may be frequently detected in faecal s les from village chickens in Ethiopia. Co-infection with multiple Eimeria spp was common and almost half of Eimeria positive birds had at least one highly pathogenic species detected. Despite this, all s led birds were free of overt disease. Although there was no evidence of a difference in the prevalence of oocysts in faecal s les between study regions, there was evidence of variation in the prevalence of some species, perhaps suggesting regional differences in exposure to risk factors associated with the birds, their management and/or location-specific environmental and ecological factors.
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.RVSC.2016.08.010
Abstract: Most studies of infectious diseases in East African cattle have concentrated on gastro-intestinal parasites and vector-borne diseases. As a result, relatively little is known about viral diseases, except for those that are clinically symptomatic or which affect international trade such as foot and mouth disease, bluetongue and epizootic haemorrhagic disease. Here, we investigate the seroprevalence, distribution and relationship between the viruses involved in respiratory disease, infectious bovine rhinotracheitis virus (IBR), bovine parainfluenza virus Type 3 (PIV3) and bovine viral diarrhoea virus (BVDV) in East African Shorthorn Zebu calves. These viruses contribute to the bovine respiratory disease complex (BRD) which is responsible for major economic losses in cattle from intensive farming systems as a result of pneumonia. We found that calves experience similar risks of infection for IBR, PIV3, and BVDV with a seroprevalence of 20.9%, 20.1% and 19.8% respectively. We confirm that positive associations exist between IBR, PIV3 and BVDV being seropositive for any one of these three viruses means that an in idual is more likely to be seropositive for the other two viruses than expected by chance.
Publisher: Elsevier BV
Date: 05-2005
DOI: 10.1016/J.VETIMM.2005.02.004
Abstract: African bovine trypanosomiasis, caused by the protozoan parasite Trypanosoma congolense, is endemic throughout sub-Saharan Africa and is a major constraint on livestock production. A promising approach to disease control is to understand and exploit naturally evolved trypanotolerance. We describe the first attempt to investigate the transcriptional response of susceptible Boran (Bos indicus) cattle to trypanosome infection via a functional genomics approach using a bovine total leukocyte (BOTL) cDNA microarray platform. Four male Boran cattle were experimentally infected with T. congolense and peripheral blood mononuclear cells (PBMC) were collected before infection and 13, 17, 23 and 30 days post-infection (dpi). A reference experimental design was employed using a universal bovine reference RNA pool. Data were normalised to the median of a set of invariant genes (GAPDH) and BRB-Array tools was used to search for statistically significant differentially expressed genes between each time-point. Using a set of 20 microarray hybridisations, we have made a significant contribution to understand the temporal transcriptional response of bovine PBMC in vivo to a controlled trypanosome infection. The greatest changes were evident 13 dpi after parasites were first detected in the blood. Significant differences were observed in clusters of protein kinase C subunits and MHC class I/II related molecules.
Publisher: Springer Science and Business Media LLC
Date: 15-06-2009
Abstract: The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms. Comparative evolutionary analysis of chicken ( Gallus gallus ) and zebra finch ( Taeniopygia guttata ) genes identified interleukin 4 receptor alpha-chain (IL-4Rα), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in erse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced ersity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites. Haplotype networks indicate that red JF is the primary contributor of ersity at chicken IL-4Rα: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high ersity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.
Publisher: Public Library of Science (PLoS)
Date: 19-08-2013
Publisher: Elsevier BV
Date: 07-2003
Publisher: Proceedings of the National Academy of Sciences
Date: 03-11-2009
Abstract: The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species erged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 in iduals representing 61 Pecoran species. We produced a highly resolved phylogeny for this erse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to lify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of s les within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient s les. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.
Publisher: Routledge
Date: 25-07-2008
Publisher: Springer Science and Business Media LLC
Date: 20-03-2009
Publisher: Wiley
Date: 10-2003
Publisher: Proceedings of the National Academy of Sciences
Date: 18-05-2011
Abstract: African bovine trypanosomiasis caused by Trypanosoma sp., is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection, but the potentially more productive Bos indicus zebu breeds are much more susceptible. Zebu cattle are well adapted for plowing and haulage, and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL), and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection, and the former contained TICAM1, which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African taurine cattle, making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate.
Publisher: Springer Science and Business Media LLC
Date: 2012
Publisher: S. Karger AG
Date: 2022
DOI: 10.1159/000529376
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-03-2015
Abstract: Highly protective effect of co-infections on mortality due to East Coast fever and consequences for disease epidemiology and control.
Publisher: Wiley
Date: 02-2006
DOI: 10.1111/J.1365-2052.2005.01363.X
Abstract: Microsatellite markers are commonly used for population genetic analyses of livestock. However, up to now, combinations of microsatellite data sets or comparison of population genetic parameters from different studies and breeds has proven difficult. Often different genotyping methods have been employed, preventing standardization of microsatellite allele calling. In other cases different sets of markers have been genotyped, providing differing estimates of population genetic parameters. Here, we address these issues and illustrate a general two-step regression approach in cattle using three different sets of microsatellite data, to combine population genetics estimates of ersity and admixture. This regression-based method is independent of the loci genotyped but requires common breeds in the data sets. We show that combining microsatellite data sets can provide new insights on the origin and geographical distribution of genetic ersity and admixture in cattle, which will facilitate global management of this livestock species.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-06-2003
Abstract: Trypanosomosis, or sleeping sickness, is a major disease constraint on livestock productivity in sub-Saharan Africa. To identify quantitative trait loci (QTL) controlling resistance to trypanosomosis in cattle, an experimental cross was made between trypanotolerant African N'Dama ( Bos taurus ) and trypanosusceptible improved Kenya Boran ( Bos indicus ) cattle. Sixteen phenotypic traits were defined describing anemia, body weight, and parasitemia. One hundred seventy-seven F 2 animals and their parents and grandparents were genotyped at 477 molecular marker loci covering all 29 cattle autosomes. Total genome coverage was 82%. Putative QTL were mapped to 18 autosomes at a genomewise false discovery rate of .20. The results are consistent with a single QTL on 17 chromosomes and two QTL on BTA16. In idual QTL effects ranged from ≈6% to 20% of the phenotypic variance of the trait. Excluding chromosomes with ambiguous or nontrypanotolerance effects, the allele for resistance to trypanosomosis originated from the N'Dama parent at nine QTL and from the Kenya Boran at five QTL, and at four QTL there is evidence of an overdominant mode of inheritance. These results suggest that selection for trypanotolerance within an F 2 cross between N'Dama and Boran cattle could produce a synthetic breed with higher trypanotolerance levels than currently exist in the parental breeds.
Publisher: Public Library of Science (PLoS)
Date: 15-08-2014
Publisher: American Physiological Society
Date: 12-2006
DOI: 10.1152/PHYSIOLGENOMICS.00100.2006
Abstract: To examine differences in cytokine profiles that may confer tolerance/susceptibility to bovine African trypanosomiasis, N'Dama (trypanotolerant, n = 8) and Boran (trypanosusceptible, n = 8) cattle were experimentally challenged with Trypanosoma congolense. Blood s les were collected over a 34-day period, and RNA was extracted from peripheral blood mononuclear cells. The expression levels of a panel of 14 cytokines were profiled over the time course of infection and between breeds. Messenger RNA (mRNA) transcript levels for the IL2, IL8, and IL1RN genes were significantly downregulated across the time course of infection in both breeds. There was an early increase in transcripts for genes encoding proinflammatory mediators ( IFNG, IL1A, TNF, and IL12) in N'Dama by 14 days postinfection (dpi) compared with preinfection levels that was not detected in the susceptible Boran breed. By the time of peak parasitemia, a type 2 helper T cells (T H 2)-like cytokine environment was prevalent that was particularly evident in the Boran. Increases in transcripts for the IL6 (29 and 34 dpi) and IL10 (21, 25, and 29 dpi) genes were detected that were higher in the Boran compared with N'Dama. These findings highlight the implications for using murine models to study the bovine immune response to trypanosomiasis, where in some cases cytokine expression patterns differ. Overall, these data suggest that the trypanotolerant N'Dama are more capable of responding very early in infection with proinflammatory and T H 1 type cytokines than the trypanosusceptible Boran and may explain why N'Dama control parasitemia more efficiently than Boran during the early stages of infection.
Publisher: Frontiers Media SA
Date: 20-07-2018
Publisher: Proceedings of the National Academy of Sciences
Date: 17-04-2015
Publisher: Proceedings of the National Academy of Sciences
Date: 29-07-2008
Abstract: European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of ≈1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and China and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.
Publisher: Proceedings of the National Academy of Sciences
Date: 16-09-2008
Publisher: Springer Science and Business Media LLC
Date: 29-09-2016
DOI: 10.1186/S12711-016-0252-7
Abstract: The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are h ered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek's disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses. The large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production. We confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Olivier Hanotte.