Thesis (PhDAgric)--Stellenbosch University, 2017.ENGLISH ABSTRACT: Genome wide association studies (GWAS) have evolved into powerful tools for investigating the genetic association of complex traits, such as gastrointestinal parasite (GIN) resistance. Knowledge on genes associated with GIN resistance can provide information for use in breeding programs. The objective of the study was to identify markers associated with resistance in goats, through the following specific objectives: i) assessing the level of knowledge on GIN, management and control of GIN, ii) determining the prevalence and risk factors of GIN, iii) determining genetic diversity and population structure of goats in Zimbabwe and iv) investigating genomic loci associated with GIN resistance traits using a genome-wide association analyses (GWAS). Surveys were conducted in 135 households, using a pre-tested questionnaires in Chipinge (natural region (NR) I and II), Shurugwi (NR III), Binga and Tsholotsho (NR IV) and Matobo (NR V).
GIN were ranked highest as the most common disease, with 57% of farmers not controlling or treating animals and 63% of farmers not having knowledge on the spread of GIN. A total of 580 blood and faecal samples were collected from goats from the same households, with additional sampling being conducted in the Research station flock. Highest prevalence was determined for Eimeria oocysts (43%) and Strongyles (31%). Area, season, sex and age significantly influenced patterns of GIN infections (P < 0.05). Prevalence was highest in goats from Chipinge and Binga, greater in wet than dry season and in males than females. High prevalences were observed for goats aged 1 and 6 years and the least for goats aged 3. Associated risk factors were also evaluated per area. A subset of the sampled animals (253) was genotyped using the Illumina Goat 50 K SNP beadchip. Population structure analyses were performed using ADMITXURE and PLINK. Five clusters were identified, with distinct populations of Binga and high levels of shared ancestry in goats from Tsholotsho and Matobo districts. Genetic parameters indicated high levels of genetic diversity based on observed (HE) and expected (HO), low linkage disequilibrium (r 2 = 0.03 - 0.18) and low FST (0.01 – 0.04). For genome-wide analyses, two approaches were used: i) single-SNP association using logarithm transformed faecal egg counts, ii) within-population association using case/control data. After quality control, 49 984 SNPs and 44 918 SNPs were available for genome-wide association analyses in GenAbel and PLINK respectively. The study confirmed that GIN resistance traits were heritable (0.27 - 0.56 i.e low - moderate). The analyses revealed significant multiple SNPs that were associated with Eimeria and Strongyles at the genome-wide level. Regions on chromosomes (chr) 4 (P = 2.66 x10-6 and P = 1.45 x10-5) for Eimeira and chr 29 (P = 9.93 x10-6) were found to be associated with GIN resistance, for the Eimeria and Strongyles traits. Genes annotated to the SNP positions were ORC5, DGKB and HRASLS5, respectively. The role of the genes have not been reported in previous studies or implicated in the involvement of biological pathways that have roles in eliciting responses towards GIN infections. Overally, the study demonstrates the utility of the Illumina Goat 50 K SNP, despite that the animals used in the study were not represented in the SNP discovery breeds. Knowledge of these genes and understanding the underlying mechanisms to GIN resistance can be used in the development of breeding programs and hence improve productivity.AFRIKAANSE OPSOMMING: Genoom wye assosiasie studies (GWAS) het ontwikkel in ‘n kragtige instrument vir die ondersoek van genetiese verwantskappe van komplekse eienskappe, soos gastro-parasiet weerstand. Kennis oor gene wat verband hou met gastro-parasiet weerstand kan inligting verskaf wat gebruik kan word in teeltprogramme. Die doel van hierdie studie was om merkers geassosieer met weerstand in bokke te identifiseer, deur die volgende spesifieke doelwitte: (i) die bepaling van die vlak van kennis oor gastro-parasiete onder kleinboere, hul bestuur en beheer van gastro-parasiete (ii) die bepaling van die voorkoms en risikofaktore van gastro-parasiete (iii) bepaling van genetiese diversiteit en populasisestruktuur van bokke in Zimbabwe (iv) die ondersoek van genomiese lokusse wat verwant is aan gastro-parasiet weerstand eienskappe met behulp van ‘n genoom wye assosiasie studie (GWAS). Opnames is in 135 huishoudings, met behulp van ‘n pre-toetse vraelyste in Chipinge (natuurlike gebied (NG) I en II), Shurugwi (NG III), Binga enTsholotsho (NG IV), en Matobo (NG V) distrikte, wat vyf landbou-ekologiese streke in Zimbabwe verteenwoordig. Gastro-parasiete was die hoogste geklas as die mees algemeenste siekte, met meerderheid van die boere (57%) wat nie beheer toepas of siek diere behandel nie en 63% van die boere wat geen kennis het oor die verspreiding van gastro-parasiet siektes nie. ‘n Totaal van 580 bloed en fekale monsters was versamel van bokke vanuit dieselfde huishoudings, met bykomede monsterversameling gedoen in die Navorsingstasie kudde. Hoogste voorkoms was Eimeria oösiste (43%) en Strongyles (31%). Gebied, seisoen, geslag en ouderdom het die patroon van gastro-parasiete infeksies beduidend beïnvloed (P < 0.05). Voorkoms was die hoogste in bokke vanaf Chipinge en Binga, asook hoër in die nat teenoor droë seisoen en hoër in bokramme teenoor bokooie. Hoë voorkoms is ook waargeneem vir bokke 1 en 6 jaar oud en die minste vir bokke 3 jaar oud. Geassosieerde risikofaktore is ook geëvalueer per area. ‘n Subset van die gemonsterde diere (253) was genotipeerd met behulp van die Illumina Bok 50 K SNP beadchip. Populasiestruktuur analise is uitgevoer met behulp van ADMITXURE en PLINK. Vyf klusters is geïdentifiseerd, elk met sy eie bevolkings van Binga en hoë vlakke van gedeelde afkoms in die bokke vanaf Tsholotsho en Matobo. Genetiese parameters is aanduided van hoë vlakke van genetiese diversiteit gebaseerd op die waargeneemde (HE) en verwagte (HO), lae koppeling onewewigtigheid (r 2 = 0.03 - 0.18) en lae FST (0.01 – 0.04). Vir genoomwye ontledings is twee benaderings gebruik: i) enkel-SNP assosiasie met behulp van logaritme veranderde fekale eiertellings ii) binne-populasie assosiasie met behulp van gevalle/kontrole data. Na gehalte beheer, 49 984 SNPs en 44918 SNPs was beskikbaar vir die genoomwye assosiasie analise in GenAbel en PLINK onderskeidelik. Die studie het bevestig dat gastro-parasiete weerstand eienskappe is oorerflik (0.27 - 0.56 d.w.s lae tot gemiddeld). Die analise het beduidende verskeie SNP’s openbaar wat verband hou met Eimeria en Strongyles by die genoomwye vlak. Streke op chromosome (chr) 4 (P = 2.66 x10-6 and P = 1.45 x10-5) vir Eimeira en chr 29 (P = 9.93 x10-6) is gevind wat verband hou met die gastro-parasiete weerstand, vir die Eimeria en Strongyles eienskappe. Gene geannoteerd naby hierdie SNP posisies was ORC5, DGKB en HRASLS5 onderskeidelik. Die rol van die gene is nog nie aangemeld in vorige studies of hul betrokkenheid by biologiese weë wat reaksie lok teenoor gastro-parasiete infeksie nie. In geheel, toon die studie die nut van Illumina Bok 50 K SNP, ten spyte daarvan dat die diere gebruik in die studie nie die diere verteenwoordig wat gebruik was in die SNP ontdekking rasse nie. Kennis van hierdie gene en die begrip van die onderliggende meganismes van gastro-parasiete weerstand kan gebruik word in die ontwikkeling van teelprogramme en sodoende produktiwiteit verbeter
