Browsing by Author "Pickering, Leanne Hayley"

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    The relationship between copy number variations and tick resistance in South African Nguni cattle
    (Stellenbosch : Stellenbosch University, 2017-12) Pickering, Leanne Hayley; Dzama, Kennedy; Wang, Magretha Diane; Muchadeyi, Farai Catherine; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: The impact of ticks and tick-borne diseases on global livestock industries is an area of major concern. The ability of an animal to resist these arthropods varies within and between breeds. Tick resistance is a heritable trait, which can be exploited by using resilient breeds and incorporating them into selective breeding programmes. One such breed, known for its resilience to ticks and tick-borne diseases, is the South African Nguni. The Nguni is a locally adapted cattle breed, which has undergone minimal synthetic breeding, and is well adapted to harsh environmental conditions. Copy number variations (CNVs), present within the bovine genome, are attributable to the differences observed in adaptive and disease resistance traits in cattle. These variations comprise of deletions, duplications and insertions greater than 1kb in size. Copy number variable regions (CNVRs) overlap or lie within close proximity of genes responsible for multiple biological and molecular functions and could explain the underlying mechanisms of resistance. This study investigated the non-genetic effects of tick count and the association of CNVRs with tick resistance in South African Nguni cattle. In the first experiment, tick counts were recorded over a two-year period on 347 Nguni cattle across three different provinces in South Africa. Using SAS (Version 7.1) a general linear model was run on log transformed tick counts to determine the non-genetic effects of tick resistance. The effects of location, season, year of tick count, sex and age of the animal on tick count were tested. Factors which significantly affected tick resistance included location, season, year of tick count and the animal’s age. In the second experiment, summary statistics of tick count per location were used to classify 347 Nguni cattle as susceptible (0) or resistant (1) across two levels of resistance (L1 and L2). Deoxyribonucleic acid extracted from hair and blood samples was genotyped using the Illumina BovineSNP 50 assay. After quality control and sample pruning using PLINK, 41 193 SNPs remained for further analyses. PennCNV identified 1 501 CNVs which were merged into 344 unique CNVRs. An association analyses using STATISTICA 64 was run which identified CNVRs associated with tick count. Seventeen CNVRs located on chromosomes 1, 2, 6, 7, 8, 9, 12, 15, 17, 20, 21, 22, 24 and 29 demonstrated a significant (p<0.05) association with tick resistance. Seventeen genes overlapped or lay in close proximity to these CNVRs and played a vital role in various molecular and biological processes. These processes all play an integral role in determining various cellular, immune, metabolic and reproductive responses.