Thesis (MScAgric)--Stellenbosch University, 2017.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.AFRIKAANSE OPSOMMING: Die globale impak van bosluise en bosluis-oordraagbare siektes op veebedrywe word as ʼn belangrike kwessie beskou. Die vermoë van 'n dier om weerstand teen hierdie geleedpotiges te bied, wissel tussen rasse maar ook binne ʼn ras. Bosluisweerstand is 'n oorerflike eienskap wat gebruik kan word om vir weerstandbiedende rasse te selekteer, wat op hulle beurt dan in selektiewe teelprogramme ingesluit kan word. Die Suid-Afrikaanse Nguni beesras is bekend vir sy vermoë om weerstand te bied teen bosluise en bosluisoordraagbare siektes. Die Nguni is 'n plaaslik aangepaste beesras wat minimale sintetiese teling en seleksie ondergaan het en is veral goed aangepas by moeilike omgewingstoestande. Kopie getalvariasies (CNVs) wat binne die beesgenoom voorkom, kan toegeskryf word aan die verskille in aanpassings en siekteweerstandseienskappe wat by beeste waargeneem word. Hierdie variasies bestaan uit verwyderde gene, duplikasies en invoegings groter as 1kb. Kopiegetal veranderlike streke (CNVRs) oorvleuel of lê naby aan gene wat verantwoordelik is vir verskeie biologiese en molekulêre funksies en kan moontlik ʼn verklaring bied vir onderliggende weerstandsmeganismes. Hierdie studie het die verwantskap van CNVR's met bosluisweerstand in Suid-Afrikaanse Nguni-beeste ondersoek. In die eerste eksperiment is die aantal bosluise op 347 Nguni beeste, wat in drie verskillende provinsies in Suidd-Afrika voorgekom het, oor 'n tydperk van twee jaar aangeteken. Deur gebruik te maak van SAS (weergawe 7.1) is 'n algemene lineêre model analise op loggetransformeerde bosluisgetalle uitgevoer om die nie-genetiese effekte van bosluisweerstand te bepaal. Die effekte van die plek, seisoen, jaar van bosluistelling, geslag en ouderdom van die dier is in die analise ingesluit. Faktore wat ʼn beduidende invloed op mate van bosluisweerstand gehad het, het plek, seisoen, jaar van bosluistelling en die dier ouderdom, ingesluit. In die tweede eksperiment is opsomming statistieke van bosluistelling per plek gebruik om die 347 Nguni-beeste as vatbaar (0) of weerstandig (1) oor twee vlakke van weerstand (L1 en L2) te klassifiseer. Deoksiribonukleïensuur wat uit hare en bloedmonsters verkry is, is aan genotipe analise met behulp van die Illumina BovineSNP 50-toets onderwerp. Na gehaltebeheer en verwydering van verdagte data met PLINK, het 41 193 SNPs vir verdere ontledings behoue gebly. PennCNV het 1 501 CNVs geïdentifiseer wat in 344 unieke CNVR's saamgevoeg is. 'n Assosiasie-ontleding met behulp van STATISTICA 64 het 17 beduidende CNVRs geïdentifiseer wat met bosluistelling geassosieer kon word. Sewentien gene oorvleuel of lê naby aan hierdie CNVRs en speel 'n belangrike rol in verskeie molekulêre en biologiese prosesse. Hierdie prosesse speel ʼn belangrike in verskeie sel-, immuun-, metaboliese en reproduksie response
