Browsing by Author "Le Roex, Nikki"

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    The complete genome sequence of the African buffalo (Syncerus caffer)
    (BioMed Central, 2016-12-07) Glanzmann, Brigitte; Moller, Marlo; Le Roex, Nikki; Tromp, Gerard; Hoal, Eileen G.; Van Helden, Paul D.
    Background: The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem. It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. To date, no complete genome sequence for S. caffer had been available for study and the genomes of other species such as the domestic cow (Bos taurus) had been used as a proxy for any genetics analysis conducted on this species. Here, the high coverage genome sequence of the African buffalo (S. caffer) is presented. Results: A total of 19,765 genes were predicted and 19,296 genes could be successfully annotated to S. caffer while 469 genes remained unannotated. Moreover, in order to extend a detailed annotation of S. caffer, gene clusters were constructed using twelve additional mammalian genomes. The S. caffer genome contains 10,988 gene clusters, of which 62 are shared exclusively between B. taurus and S. caffer. Conclusions: This study provides a unique genomic perspective for the S. caffer, allowing for the identification of novel variants that may play a role in the natural history and physiological adaptations.
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    Context‐dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host
    (Wiley Open Access, 2018) Tavalire, Hannah F.; Beechler, Brianna R.; Buss, Peter E.; Gorsich, Erin E.; Hoal, Eileen G.; Le Roex, Nikki; Spaan, Johannie M.; Spaan, Robert S.; Van Helden, Paul D.; Ezenwa, Vanessa O.; Jolles, Anna E.
    Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade‐offs between immune and reproductive investment lead to the evolution of distinct life history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB), an important zoonotic pathogen, in a free‐ranging African buffalo (Syncerus caffer) population. We characterize these phenotypes as “infection resistance,” in which hosts delay or prevent infection, and “proliferation resistance,” in which the host limits the spread of lesions caused by the pathogen after infection has occurred. We found weak evidence that infection resistance to bTB may be heritable in this buffalo population (h2 = 0.10) and comes at the cost of reduced body condition and marginally reduced survival once infected, but also associates with an overall higher reproductive rate. Infection‐resistant animals thus appear to follow a “fast” pace‐of‐life syndrome, in that they reproduce more quickly but die upon infection. In contrast, proliferation resistance had no apparent costs and was associated with measures of positive host health—such as having a higher body condition and reproductive rate. This study quantifies striking phenotypic variation in pathogen resistance and provides evidence for a link between life history variation and a disease resistance trait in a wild mammalian host population.
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    Gene polymorphisms in African buffalo sssociated with susceptibility to Bovine tuberculosis infection
    (Public Library of Science -- PLoS, 2013-05) Le Roex, Nikki; Koets, Ad P.; Van Helden, Paul D.; Hoal, Eileen G.
    Bovine tuberculosis (BTB) is a chronic, highly infectious disease that affects humans, cattle and numerous species of wildlife. In developing countries such as South Africa, the existence of extensive wildlife-human-livestock interfaces poses a significant risk of Mycobacterium bovis transmission between these groups, and has far-reaching ecological, economic and public health impacts. The African buffalo (Syncerus caffer), acts as a maintenance host for Mycobacterium bovis, and maintains and transmits the disease within the buffalo and to other species. In this study we aimed to investigate genetic susceptibility of buffalo for Mycobacterium bovis infection. Samples from 868 African buffalo of the Cape buffalo subspecies were used in this study. SNPs (n = 69), with predicted functional consequences in genes related to the immune system, were genotyped in this buffalo population by competitive allele-specific SNP genotyping. Case-control association testing and statistical analyses identified three SNPs associated with BTB status in buffalo. These SNPs, SNP41, SNP137 and SNP144, are located in the SLC7A13, DMBT1 and IL1a genes, respectively. SNP137 remained significantly associated after permutation testing. The three genetic polymorphisms identified are located in promising candidate genes for further exploration into genetic susceptibility to BTB in buffalo and other bovids, such as the domestic cow. These polymorphisms/genes may also hold potential for marker-assisted breeding programmes, with the aim of breeding more BTB-resistant animals and herds within both the national parks and the private sector.
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    Host genetic factors in susceptibility to mycobacterial disease in the African buffalo, Syncerus caffer
    (Stellenbosch : Stellenbosch University, 2014-04) Le Roex, Nikki; Hoal, Eileen; Van Helden, Paul; Koets, A. D.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences, Molecular Biology and Human Genetics.
    ENGLISH ABSTRACT: Bovine tuberculosis (BTB) is a chronic, infectious disease found in domestic livestock and wildlife, and has serious biodiversity, economic and public health implications. African buffalo act as a wildlife reservoir of BTB, maintaining and transmitting the disease within the environment. The research presented in this thesis addresses the role of host genetic variation in resistance to BTB infection in African buffalo, and reviews the possible practical application of such information. Annual BTB prevalence within the African buffalo population in Hluhluwe iMfolozi Park, South Africa, was evaluated over a seven year period in order to define the extent of M. bovis infection. Prevalence changes over time suggest that the test and cull operation currently in place is performing successfully with respect to the original aims of the programme. A review of genetic studies of BTB in livestock and wildlife collated previous findings in this field and provided a collection of possible candidate genes and variants. It also highlighted a lack of research in wildlife, and the limitations of working with species with insufficient genetic data. To overcome the absence of whole-genome data, next-generation sequencing was performed on nine African buffalo, in order to identify novel genetic variants in this species. Upwards of 76 000 novel SNPs within gene regions were identified, and subsequent fluorescent genotyping of 173 SNPs showed a 57% validation rate. From the validated set, 69 SNPs located in genes related to the immune system were selected for association testing with BTB status in African buffalo, and were fluorescently genotyped in 868 individuals. Three SNPs, in the Solute Carrier family 7, member A13 (SLC7A13), Deleted in Malignant Brain Tumour-1 (DMBT1) and Interleukin 1 alpha (IL1α) genes, were identified as significantly associated with BTB status. Very little sequence information of the NRAMP1 (SLC11A1) gene was obtained from the next-generation sequencing performed, and this gene has been associated with brucellosis, salmonella and paratuberculosis in other animal species, making it an excellent candidate for BTB resistance. To characterise this gene in African buffalo, Sanger sequencing was performed to generate the complete coding region, and partially sequence the 5’UTR, intronic and 3’UTR regions. Fifteen novel polymorphisms and three microsatellites were identified within the gene. Finally, a review was prepared to assess the applicability of genetic information on BTB resistance to selective breeding programmes for African buffalo. Phenotypic, marker-assisted and genomic breeding strategies were discussed, with particular emphasis on their suitability to African buffalo. Identifying genes and variants involved in BTB resistance in African buffalo provides potential targets for drug or vaccine development, as well as information that could be incorporated into selective breeding programmes. This may support new management options for controlling the BTB epidemic in the game parks of South Africa, as an alternative to, or in conjunction with, lethal control
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    Novel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencing
    (PLoS, 2012-11-07) Le Roex, Nikki; Noyes, Harry; Brass, Andrew; Bradley, Daniel G.; Kemp, Steven J.; Kay, Suzanne; Van Helden, Paul D.; Hoal, Eileen G.
    The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.76coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43–54% of the Bowtie SNPs and 57–58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.