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

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Stellenbosch : Stellenbosch University
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.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
Thesis (PhDAgric)--Stellenbosch University, 2022.
Tick-resistance, Genomics, RNA, Cattle -- Breeding, Ticks -- Insecticide resistance, UCTD