Browsing by Author "Marima, Jacqueline Keena"

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    The application of genomics and transcriptomics for the characterization of the genetic diversity of tick-resistance in Angus, Brahman, Nguni, and Santa Gertrudis cattle artificially infested with Rhipicephalus microplus and Rhipicephalus decoloratus
    (Stellenbosch : Stellenbosch University, 2022-04) Marima, Jacqueline Keena; Dzama, Kennedy; Jonsson, Nicholas N.; Dube, Bekezela; Marufu, Munyaradzi Christopher; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: Tick resistance is a complex polygenic trait that is governed by immuno-genetic mechanisms that are currently not fully understood. It is, however, currently accepted that the Bos indicus, Zebu and Sanga breeds, which are better adapted to the harsh environmental conditions of the tropical and subtropical regions, often exhibit superior tick resistance as opposed to their Bos taurus counterparts. Breeding for natural host resistance presents a transformational alternative for tick control that will see cattle production industries move away from the excessive and often incorrect usage of chemical acaricides for tick control. However, selective breeding for this trait using tick count data, which varies according to the environment, is unreliable and often produces variable results. Marker-assisted selected breeding and the development of accurate prediction tests with practical feasibility in the field will enhance the accuracy of selection and increase genetic gains. Omics technologies, including transcriptomics, genomic and proteomics are tools that have been instrumental in uncovering putative genes, pathways, and potential biomarkers in cattle. Despite the progress made, there is still a lot that remains misunderstood about the tick resistance trait. Further studies are required. While previous studies have investigated tick resistance in the different breeds and tick species in isolation of each other, in this study a comparison between two tick species (Rhipicephalus microplus and R. decoloratus) and three cattle breeds of different lineages was presented; the Bos indicus Brahman breed, the Bos taurus Angus breed and the indigenous Bos taurus africanus Nguni breed. The differentially expressed genes and their single nucleotide polymorphisms (SNPs) genotypes were of particular interest when studying the different host tick associations presented in this study. The study also included the transcriptome analysis of samples from the Santa Gertrudis, a composite breed recognised for its superior tick resistance while simultaneously boasting good reproductive and production efficiency and meat quality. Using a 150K Bovine SNP chip to genotypes samples from the Angus, Brahman and Nguni breeds, the SNP genotypes, allele frequencies and dosages of SNPs of 37 candidate genes were determined. A total of 257 SNPs were discovered but the SABT2 gene produced a SNP (ARS-BFGL- NGS-94983) that showed a significant correlation with tick count and significantly different allele frequencies between breeds. No functional information regarding the role of the SATB2 gene in host resistance to tick, their further investigations are warranted. The microarray analysis of blood samples from Santa Gertrudis cattle artificially infested with the invasive R. microplus tick species revealed variable levels of tick resistance accompanied by variable gene expression profiles across the tick-resistant and tick-susceptible phenotypes. It was evident that upon long term exposure to the R. microplus the tick-resistant Santa Gertrudis cattle displayed an increased ability to develop and mount more robust adaptive responses against the tick infestations than the tick-susceptible animals Lastly, the RNA sequencing study allowed the identification of several putative genes that have featured in previous studies of tick resistance in cattle. Using inter-breed and inter-tick species contrast across the Angus, Brahman, and Nguni cattle breeds as well as between the R. microplus and R. decoloratus tick species, variable gene expression profiles were observed. The CCL26 and MZB1 appeared as two of the factors to note in the inter-tick species comparisons, while the MMP12 gene was identified in the inter-breed comparison. The Nguni breed produces significantly different gene expression patterns than both the Angus and the Brahman breeds. The differential expression of the highlighted gene led to the conclusion that tick resistance is not only characterised by innate and adaptive immune responses but there are other crucial role players, presented in this study as components of the extracellular matrix. The three studies included here inform further investigations into the roles of the highlighted genes and SNPs to further elucidate the complex phenotype of host resistance to ticks.
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    Gene expression profiles associated with beef cattle resistance to Rhipicephalus ticks
    (Stellenbosch : Stellenbosch University, 2017-03) Marima, Jacqueline Keena; Dzama, Kennedy; Dube, Bekezela; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: Tick resistance is a complex trait influenced by numerous environmental, physiological and genetic factors. The length of the association between cattle breeds and tick species may play a vital role in the potency of the immune responses generated by the host post-infestation. The genetically determined components of host resistance, which may have evolved due to long periods of evolution of breeds in the presence of specific tick species, are regarded the most important factors of host resistance to ticks. The isolation and characterisation of genes associated with natural host resistance may provide a low-cost, environmentally sound and sustainable chemical-free alternative for tick control through gene introgression and improved accuracy of selection in breeding programs. This study examined the tick burdens and associated gene expression profiles in two ancient (Nguni – R. decoloratus and Brahman – R. microplus) and four modern (Nguni – R. microplus, Brahman – R. decoloratus, Angus – R. decoloratus and Angus – R. microplus) host-tick associations following artificial infestation. Approximately 100 unfed tick larvae of a single species were used to infest each animal, thereafter tick counts were enumerated 18-days post-infestation. Skin biopsies, from which RNA was extracted for use in the gene expression analyses, were collected pre-infestation from non-parasitized sites and 12-hours post-infestation at visible tick-bite sites. The panel of genes analysed comprised of cytokines (TLR5, TLR7, TLR9, TRAF6, CD14), chemokines and their receptors (CCR1, CCL2, CCL6), toll-like receptors (IL-1β, CXCL8, IL-10, TNF) and other candidate genes (BDA20, OGN, TBP, LUM, B2M) whose expression was normalized against RN18S1 (or β-actin-like). Custom 96-well RT2 Profiler PCR arrays, fitted with primers designed and optimised by Qiagen, were used for real-time PCR analyses using RT2 SYBR® Green dye and an ABI 7500 Standard real-time PCR cycler. The effects of breed, tick species and breed by tick species interaction on tick count were analysed using XLSTAT (2016) and SAS Enterprise Guide (2016). The fold regulation/change values were generated via the online RT2 Profiler PCR Array Data Analysis Web-portal (SABioscience - Qiagen), using the ΔΔCT method. The effects of breed, tick species and breed by tick species interaction on the differential gene expression of each gene were analysed using XLSTAT and SAS (2016). The expression levels of LUM, B2M, TRAF6 and TPB showed significant breed variations. The Nguni and Angus differed for TBP and TRAF6, while the Brahman and Angus differed for LUM and B2M. LUM and B2M displayed significantly higher expression levels in the Brahman and Nguni cattle. Significant breed, tick species and breed by tick species interaction effects were detected from the tick count data, with the Brahman carrying less ticks than both the Angus and Nguni cattle, while the R. microplus resulted in heavier tick burdens than the R. decoloratus ticks. In both experiments, there was a lack of evidence of any breed by tick species interaction which would implicate the effect of length of association between breeds and tick species in the host response to tick challenge in respect with gene expression and tick burden.