Genomics as part of an integrated study of smallholder sheep farming systems in the Western Cape, South Africa
| dc.contributor.advisor | Dzama, Kennedy | en_ZA |
| dc.contributor.advisor | Cloete, Schalk W. P. | en_ZA |
| dc.contributor.advisor | Oosting, Simon | en_ZA |
| dc.contributor.author | Molotsi, Annelin Henriehetta | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences. | en_ZA |
| dc.date.accessioned | 2017-11-22T11:59:56Z | |
| dc.date.accessioned | 2017-12-11T10:57:42Z | |
| dc.date.available | 2017-11-22T11:59:56Z | |
| dc.date.available | 2017-12-11T10:57:42Z | |
| dc.date.issued | 2017-12 | |
| dc.description | Thesis (PhD)--Stellenbosch University, 2017. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: The aim of this study was to evaluate the productivity of smallholder sheep farming systems in the Western Cape, South Africa, using an interdisciplinary approach, combining socio-economic factors and genomics. The objectives were firstly to investigate sheep breeding practices followed in smallholder sheep farming systems and to determine socio-economic factors that influence offtake rate of flocks in the Western Cape, South Africa. Secondly, to compare genetic diversity and population structure of smallholder sheep flocks to Western Cape resource flocks. Thirdly, to identify single nucleotide polymorphisms associated with causal variants for the wet-dry phenotype using the ovine 50K SNP bead chip. The final objective was to determine selection signatures within South African sheep populations. To achieve the first objective interviews were conducted with 72 smallholder farmers in three districts of the Western Cape, namely the West Coast, Karoo and Eden. Phenotypic measurements of body weight, body condition score and reproduction (wet and dry phenotype) were obtained from a sample of ewes from the West Coast district from 2011 until 2014. Range condition scores were estimated for two farms in the Karoo and four farms in West Coast district. SURVEYMEANS and SURVEYFREQ in SAS were used to obtain means and frequencies for qualitative data. The production systems were largely small-scale (43-85%) and communal (10-57%). Sheep were mainly kept for consumption purposes. The Dorper was the prominent breed used in all the farming systems and selection emphasis was different for farming systems. Traits selected for by communal farmers included temperament, control of flies, meat taste, growth rate, fertility and foraging ability; whereas small-scale farmers selected for conformation, mothering ability, disease tolerance, heat tolerance and temperament. Lucerne was the predominant source of feed in addition to natural grazing of rangeland. The major constraints mentioned were land availability, drought and water availability. Average range condition scores were low for both districts and grazed vs. rested camps, implicating overgrazing. Carrying capacity was higher than the recommended carrying capacity in the Eden district (both communal and small-scale farmers, 0.26 and 18.5 ha/LSU respectively) and in West Coast for small-scale farmers. The flock structure showed variation between farming systems with mature ewes (39-86%) and young replacement ewes (0.41-46%), young rams (0.41-15%), rams (0-5%) and lambs (0-2%). The wet-dry phenotype was recorded as a measurement of reproductive success over the three year period. The chi-square test indicated significant differences between reproductive performances over the different years with a repeatability of 0.399. Information on the socio-economic status of the farmers, their production system and reason for keeping sheep was obtained. Information on the average numbers of lambs sold and offtake rate was obtained as an economic indicator. A general linear model was fitted on average number of lambs sold and offtake with district, sources of income, participation in government programs and flock size as fixed effects. The majority of smallholder farmers were above 40 years of age and only 32% ranked their wealth status as poor. The smallholder sheep farming systems in the Western Cape were male dominated. District significantly influenced average number of lambs sold and offtake rate. The Karoo district sold a higher average number of lambs per year (41 ± 8.8), with West Coast and Eden selling the same average number of lambs per year at 7 ± 2.2 and 7 ± 2.6, respectively. Offtake rate for the respective districts were not significantly different and were 17 ± 17% for Eden, 48 ± 20% for the Karoo and 46 ± 20% for West Coast. To achieve the second objective blood samples were obtained from 295 sheep of which 172 had been identified as smallholder Dorpers, 4 smallholder White Dorpers, 46 purebred Dorpers, 26 purebred South African Mutton Merinos and 47 purebred Namaqua Afrikaners. Genetic diversity was estimated using allelic richness (Ar), observed heterozygosity (Ho), expected heterozygosity (He) and inbreeding coefficient (F). Population structure analysis was performed using fastSTRUCTURE to determine the breed composition of each genotyped individual. The Namaqua Afrikaner had the lowest He of 0.280 ± 0.18 while the He of smallholder Dorper, Dorper and South African Mutton Merino did not differ and were respectively 0.364 ± 0.13, 0.332 ± 0.16 and 0.329 ± 0.17. The inbreeding coefficient was highest for the pure breeds, Namaqua Afrikaner, Dorper and South African Mutton Merino compared to the average inbreeding coefficient for the smallholder Dorper population. There was evidence of introgression with Namaqua Afrikaner, South African Mutton Merino and White Dorpers in the smallholder Dorper population. Similarly, the latter population was more genetically diverse than the purebred Dorper, South African Mutton Merino and Namaqua Afrikaner breeds from the resource flock. To achieve the third objective wet-dry records were obtained from smallholder farmers (n = 176) and the Nortier Research Farm (n = 131) for the 2014 breeding season. A logistic regression model was fitted to adjust the data for the fixed effects of farm, breed, and age of the ewe and mating weight as a covariate. Linkage disequilibrium (LD) and inbreeding coefficient were estimated using PLINK. Association analysis was performed using the genome-wide efficient mixed-model association package (GEMMA) to determine whether any significant SNPs were associated with the wet-dry reproductive trait. The wet-dry phenotype differed significantly between the smallholder (0.63 ± 0.04) and research farm flocks (0.79 ± 0.04). Genome-wide linkage disequilibrium (LD) across all populations amounted to r2 = 0.36. Dorpers from the smallholder flock exhibited rapid LD decay versus the resource ovine populations. Inbreeding levels were also lower for the smallholder flock (4 ± 0.003%) versus the research flock (13 ± 0.008%). No significant SNPs were identified after correction for false discovery rate. The heritability estimate for the wet-dry trait, using SNP information, was 0.24. To achieve the last objective a study was done to obtain selection signatures in the three purebred sheep breeds using HAPFLK and Bayescan methods. Selection signatures obtained from HAPFLK included 26 significant SNP loci which were associated with genes that play a role in the physiological pathways of the immune system, nervous system and pigmentation. Using Bayescan, 92 SNP loci were under selection and some were associated with genes influencing the immune system and polledness. Candidate genes obtained from this study included genes that play a role in the immune system, the nervous system, reproduction (GNRH1), pigmentation (MREG, KITLG), muscle growth (GDF11) and heat shock protein (DNAJC28). Smallholder sheep farming systems on a socio-economic scale were unsustainable. However, on an environmental scale using genetic diversity as an indicator, smallholder sheep were more sustainable. Selection signatures linked to fitness and robustness may to contribute to literature investigating the adaptation of South African ovine genetic resources to variability in ambient temperature. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om die produktiwiteit van klein-skaapboerderystelsels in die Wes-Kaap, Suid-Afrika, te evalueer deur 'n interdissiplinêre benadering te gebruik deur sosio-ekonomie en genomika te kombineer. Die doelwitte was eerstens om skaap teelpraktyke te ondersoek wat gevolg word in klein-skaapboerderystelsels en om sosio-ekonomiese faktore te bepaal wat die produksie van skaapkuddes in die Wes-Kaap, Suid-Afrika beïnvloed. Tweedens, was die genetiese diversiteit en populasie struktuur van klein-skaapkuddes met Wes-Kaapse Department van Landbou se navorsing kuddes vergelyk. Derdens was enkel nukleotied polimorfismes identifiseer wat verband hou met oorsaaklike variante vir die nat-droog fenotipe met behulp van die ‘50K SNP beadchip’. Die finale doel was om seleksie patrone binne Suid-Afrikaanse skaap populasies te bepaal. Om die eerste doelwit te behaal, is onderhoude met 72 kleinboere in drie distrikte van die Wes-Kaap, naamlik die Weskus, Karoo en Eden, uitgevoer. Fenotipiese metings van liggaamsgewig, liggaamskondisie telling en reproduksie (nat en droog fenotipe) is van 2011 tot 2014 verkry uit ooie van die Weskus distrik. Veld kondisie beramings is gedoen vir twee plase in die Karoo en vier plase in die Weskus. ‘SURVEYMEANS’ en ‘SURVEYFREQ’ in SAS is gebruik om gemiddeldes en frekwensies vir kwalitatiewe data te verkry. Die produksiestelsels was grootliks kleinskaals (43-85%) en kommunale (10-57%). Skape is hoofsaaklik vir verbruiksdoeleindes gehou. Die Dorper was die prominente ras wat in al die boerderystelsels gebruik is en die seleksie keuse het verskil vir boerderystelsels. Eienskappe wat deur kommunale boere geselekteer is, sluit in temperament, beheer van vlieë, vleis smaak, groei tempo, vrugbaarheid en weidingsvermoë; terwyl kleinskaalse boere geselekteer het vir konformasie, moederskapvermoë, siekteverdraagsaamheid, hitteverdraagsaamheid en temperament. Lusern was die oorheersende bron van voer, bo en behalwe natuurlike weiding van land. Die belangrikste beperkings was die beskikbaarheid van grond, droogte en water beskikbaarheid. Gemiddelde veld kondisie was laag vir beide distrikte en wat impliseer oorbeweiding. Die dravermoë was hoër as die aanbevole dravermoë in die Eden-distrik (beide kommunale en kleinboere, onderskeidelik 0.26 en 18.5 ha / LSU) en in die Weskus vir kleinskaalse boere. Die kudde-struktuur het variasie getoon vir die verskillende boerderystelsels met volwasse ooie (39-86%) en jong vervangings ooie (0,41-46%), jong ramme (0,41-15%), ramme (0-5%) en lammers (0-2 %). Die nat-droog fenotipe is aangeteken as 'n meting van reproduksiesukses oor drie jaar. Die chi-kwadraat toets dui op beduidende verskille tussen reproduktiewe prestasie oor die verskillende jare met 'n herhaalbaarheid van 0.399. Inligting oor die sosio-ekonomiese status van die boere, hul produksiestelsel en rede om skape te behou, is verkry. Inligting oor die gemiddelde aantal lammers wat verkoop is en die afkoopkoers is as 'n ekonomiese aanwyser verkry. ‘n Algemene lineêre model is toegepas vir gemiddelde aantal lammers verkoop met distrik, inkomstebronne, deelname aan regeringsprogramme en kuddegrootte as vaste effekte in die model. Die meerderheid kleinboere was bo 40 jaar en slegs 32% het hul rykdomstatus as arm beskou. Die klein -skaapboerdery stelsels in die Wes-Kaap was deur die manlike geslag oorheers. Distrik het 'n aansienlike invloed gehad op die gemiddelde aantal lammers wat verkoop is en die afkoopkoers. Die Karoo-distrik het 'n hoër gemiddelde aantal lammers per jaar (41 ± 8.8) verkoop, met Weskus en Eden wat dieselfde gemiddelde aantal lammers per jaar teen onderskeidelik 7 ± 2,2 en 7 ± 2,6 verkoop. Afkoopkoers vir die onderskeie distrikte was nie beduidend anders nie en was 17 ± 17% vir Eden, 48 ± 20% vir die Karoo en 46 ± 20% vir die Weskus. Om die tweede doelwit te bereik, is bloedmonsters verkry van 295 skape waarvan 172 geïdentifiseer is as kleinboere Dorpers, 4 kleinboere Witdorpers, 46 suiwer Dorpers, 26 suiwer Suid-Afrikaanse Vleis Merinos en 47 suiwer Namakwa-Afrikaners. Genetiese diversiteit is beraam deur gebruik te maak van alleliese rykdom (Ar), waargenome heterosigotisiteit (Ho), verwagte heterosigotisiteit (He) en intelings koëffisiënt (F). Populasie struktuuranalise is uitgevoer met behulp van fastSTRUCTURE om die rassamestelling van elke genotipeerde individu te bepaal. Die Namakwa-Afrikaner het die laagste He van 0.280 ± 0.18 gehad terwyl die He van kleinboer Dorper, Dorper en Suid-Afrikaanse Vleis Merino nie verskil het nie en was onderskeidelik 0.364 ± 0.13, 0.332 ± 0.16 en 0.329 ± 0.17. Die intelingskoëffisiënt was die hoogste vir die suiwer rasse, Namakwa-Afrikaner, Dorper en Suid-Afrikaanse Vleis Merino in vergelyking met die gemiddelde intelingskoëffisiënt vir die kleinboer Dorper-bevolking. Daar was bewyse van introgressie met Namakwa-Afrikaner, Suid-Afrikaanse Vleis Merino en Witdorpers in die kleinboer Dorper-populasie. Net so, was die laasgenoemde populasie meer geneties diverse as die suiwer Dorper, Suid-Afrikaanse Vleis Merino en Namakwa-Afrikaner rasse van die hulpbron-kudde. Om die derde doelwit te bereik, is nat-droog rekords van kleinboere (n = 176) en die Nortier-navorsingsplaas (n = 131) vir die 2014-teelseisoen verkry. ‘n Logistieke regressiemodel is toegepas om die data vir die vaste effekte van plaas, ras en ouderdom van die ooi en paringsgewig as 'n kovariaat aan te pas. Koppeling onewewigtigheid (LD) en intelingskoëffisiënt is beraam deur gebruik te maak van PLINK. Assosiasie analise is uitgevoer met behulp van die genoom-wye doeltreffende gemengde-model assosiasie pakket om te bepaal of enige beduidende SNP's geassosieer word met die nat droog reproduksie eienskap. Die nat-droog fenotipe het beduidend verskil tussen die kleinboer (0.63 ± 0.04) en die navorsingsplaaskudde (0.79 ± 0.04). Genoom-wye koppeling-onewewigtigheid oor alle populasies beloop r2 = 0.36. Dorpers van die kleinboer kudde het vinnige LD-verval teenoor die navorsings kudde getoon. Intelings vlakke was laer vir die kleinboer kudde (4 ± 0,003%) teenoor die navorsings kudde (13 ± 0,008%). Geen beduidende SNP's is geïdentifiseer na regstelling vir vals ontdekkingskoers nie. Die oorerflikheidsberaming vir die nat-droog eienskap, met behulp van SNP-inligting, was 0,24. Om die laaste doelwit te bereik, is 'n studie gedoen om seleksie patrone in die drie suiwer skaaprasse te verkry met behulp van HAPFLK- en Bayescan-metodes. Seleksie patrone wat van HAPFLK verkry is, het 26 belangrike SNP lokusse ingesluit wat geassosieer was met gene wat 'n rol speel in die fisiologiese weë van die reproduksie, teenwoordigheid van horing en pigmentasie. Met behulp van Bayescan was 92 SNP loci onder seleksie en sommige is geassosieer met gene wat die immuunstelsel beïnvloed en die teenwoordigheid van horings. Kandidaatgene wat uit hierdie studie verkry is, sluit in gene wat 'n rol speel in die reproduksie (GNRH1), pigmentasie (MREG, KITGL), spiergroei (GDF11) en hitte skok proteïene (DNAJC28). Klein-skaapboerdery stelsels was op ‘n sosio-ekonomiese skaal onvolhoubaar. Op 'n omgewingsskaal wat genetiese diversiteit as 'n aanwyser gebruik, was kleinboere egter volhoubaar. Seleksie patrone wat gekoppel is aan fiksheid en robuustheid, mag bydra tot literatuur wat die aanpassing van Suid-Afrikaanse skape genetiese bronne aan veranderlikes in omgewings temperatuur ondersoek. | af_ZA |
| dc.format.extent | 210 pages : illustrations, map | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/102815 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Sheep -- Breeding -- Genomics | en_ZA |
| dc.subject | Smallholder sheep farming systems -- Western Cape | en_ZA |
| dc.subject | Sheep -- Breeding -- Western Cape -- South Africa | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Genomics as part of an integrated study of smallholder sheep farming systems in the Western Cape, South Africa | en_ZA |
| dc.type | Thesis | en_ZA |