Doctoral Degrees (Animal Sciences)

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    The identification of genomic regions associated with tick count, growth traits, and skin thickness in F2 angus x Nguni cattle using genome-wide association analysis
    (Stellenbosch : Stellenbosch University, 2023-12) Mkize, Nelisiwe; Dzama, Kennedy; Mapholi, Ntanganedzeni; Dube, Bekezela; Maiwashe, Azwihangwisi; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.
    ENGLISH ABSTRACT: The aim of the study was to identify genetic determinants associated with tick count, growth traits, and skin thickness in F2 Angus x Nguni crossbred cattle. Two hundred and sixty-six animals were used in the study. Genetic parameters were estimated by fitting a sire model using pedigree records and by fitting an animal model using a kinship matrix in the ASReml software. Hair samples from the animals were genotyped using Illumina BovineSNP150 assay and there were 115 143 SNPs after quality control. A single SNP approach was used for the association tests, using the mixed model function of the mmscore, while adjusting for population stratification and relatedness in GenABEL. A nominal threshold of Pnominal = 5 x 10-5 was applied to the data. Post-GWAS functional annotation, pathway, and cluster analyses were performed using DAVID and ShinyGo bioinformatics resources with the Bos taurus genome used as a background. Fisher's exact test with false discovery rate (FDR) adjustment was used at p (FDR) < 0.05. The heritability estimates from the sire model for tick count, birth, weaning and yearling weights, and skin thickness were 0.21±0.22, 0.36±0.26, 0.32±0.14, 0.32±0.19, and 0.40±0.15, respectively. The respective heritability estimates obtained from an animal model fitting kinship matrix were 0.12±0.15, 0.26±0.16, 0.70±0.18, 0.38±0.18 and 0.58±0.21. These heritability estimates showed the presence of genetic variation for these traits. Thus, improvement of these traits can be expected from selection. Single nucleotide polymorphisms (SNP) for tick count were observed on chromosomes 2 and 4, while those associated with birth weight were on chromosomes 3 and 12. Chromosomes 2 and 18 contained SNPs for weaning weight and chromosome 8 had a SNP for yearling weight. The SNPs for skin thickness were observed on chromosomes 2, 7, 8, 9, and 12. For tick count, functional annotation uncovered enriched gene ontology (GO) terms and pathways related to cellular processes, regulation of biological processes, and response to stimulus. These were relevant for immune system response necessary for understanding host-tick interaction. Candidate genes such as ZNF746, GIMAP8, and RARRES2 could be potential biomarkers for tick control in cattle. The enriched GO terms and pathways for growth traits were related to ubiquinol- cytochrome-c reductase activity, plasma membrane raft, DNA ligase, ATP dependent among others. These categories were relatable to cell differentiation, skeletal muscle development, and metabolism regulation. The uncovered potential candidate genes for growth traits were TRPM8, SPP2, UQCRFS1, MB, TMEFF1, CAVIN4, and MSANTD3. For skin thickness, the enriched GO terms and pathways were related to immune response, cell differentiation, and transmembrane receptor tyrosine-protein kinase among others. The categories were enriched through FER and NTRK2 genes, which could be regarded as potential candidate genes for skin thickness in this population. The study uncovered some novel and previously identified genes as well as biological mechanisms related to tick count, growth traits, and skin thickness in the F2 Angus x Nguni population. These genes could be used to facilitate genetic improvement of tick count, growth traits, and skin thickness in this population.
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    The potential of nutrifen® in broiler chicken production
    (Stellenbosch : Stellenbosch University, 2023-03) Nyeleka, Sipokazi; Pieterse, Elsje; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.
    ENGLISH ABSTRACT: Plant-derived feed additives are currently the preferred alternatives in the search to replace antibiotic growth promoters (AGPs) in broiler chicken production. The emergence of plant-derived feed additives over the past decade is propelled by the European Union’s ban on AGPs (Regulation 1831/2003/EC) from all animal production. Owing to their secondary bioactive compounds that promote the survival of beneficial bacteria in the gastrointestinal system of broiler chickens, plant derived feed additives are being explored for use in the broiler meat industry. Although the broiler meat industry suffered tremendous losses since the outbreak of COVID-19, broiler meat still outcompetes the retail of beef, pork, and mutton. The broiler meat industry is still the fastest growing meat industry worldwide and is currently the biggest consumer of AGPs. Since their introduction to the broiler meat industry, AGPs enabled this industry to rear large volumes of flocks through minimising the effects of increased stocking density on farms. However, AGPs are increasingly receiving scrutiny as research findings associate their use in broiler meat production with the development and spread of multi-drug resistant pathogenic bacteria. These bacteria are considered a serious threat to human health and the environment. Consequently, international food and health bodies such as the Food and Agriculture Organisation (FAO), the World Health Organisation (WHO) together with consumers are calling for the adoption of feed additives that will not pollute the environment and will not compromise the health of the animal. Feed additives derived from plants meet these requirements. Although research on plant-derived feed additives is ongoing, it is mainly focused on production parameters such as weight gain and portion sizes where broilers are reared in ideal or optimum environmental conditions. For this reason, there is little emphasis on the functional use of plant-derived feed additives when broilers are challenged with common environmental stressors such as stocking density. Consequently, little is known about the efficacy of some plant-derived feed additives to minimize the production effect of stressful environmental conditions. Nutrifen® is a feed additive developed from the seeds of fenugreek (Trigonella foenum-graecum L.). The present study investigated the potential of Nutrifen® to minimise the production effects when broiler chickens are challenged through stocking density. The first objective of the study characterized Nutrifen® in terms of chemical composition, antioxidant potential, and overall presence of phenolic compounds. Nutrifen® was shown to be characterized by a high crude fibre and crude protein content. The presence of polyphenols in Nutrifen® was confirmed by the total phenolics (TPC) test, while the antioxidant potential was confirmed by the ferric reducing ability of plasma (FRAP) and the 2,2-diphenyl- 1-picrylhydrazylradical (DPPH) DPPH results. The second objective of this study involved determining the effect of different levels of Nutrifen® in broiler diets on feed intake (FI) and visceral organ development in a trial that was repeated six times. Nutrifen® was included at five inclusion levels (i.e. 0g/ton; 0.44g/ton; 0.88g/ton; 0.132g/ton; and 0.176g/ton) in broiler diets, which were fed to 300 day-old chicks. It was concluded that under well ventilated, clean housing conditions, the birds did not reject any of the treatment diets. In the absence of a significant treatment effect, the lowest level of Nutrifen® inclusion (i.e. 0.44g/ton) which was assumed to be the most cost-efficient to include in broiler diets, was used to investigate the third and fourth objectives. In objective three, stocking density was used as a stressor, where 204 day-old Cobb500TM unsexed broiler chicks were used. The chicks were reared to final stocking densities of 20kg/m2 (low stocking density; 10 birds per pen) and 28kg/m2 (high stocking density; 14 birds per pen). The experiment was a 2X2 factorial completely randomized design, with each diet- stocking density combination replicated six times. The results of this study show that that 0.44g/ton Nutrifen® did not improve the live weight (LW), body weight gain (BWG), and average daily gain (ADG) of broilers kept at a high stocking density. The fourth objective of the study determined the influence of Nutrifen® (i.e. included at 0.44g/ton) on organ health, carcass, and shelf-life display quality of broilers reared at the abovementioned stocking densities. The same birds used in objective three were used for this study. From the results obtained, it is apparent that supplementing the diets of stressed broilers with 0.44g/ton Nutrifen® decreased carcass and portion weights. In addition, the pH of the breast muscle was significantly lower for the stressed broilers on the day of slaughter and water retention of the breast muscle was poor for these broilers. However, the weight of the Bursa of Fabricius of the stressed broilers was significantly higher compared, when compared to the birds maintained at the lower stocking density. In conclusion, Nutrifen® can be supplemented as a feed additive in broiler diets at 0.44g/ton without compromising growth or resulting in intestinal damage in broilers, maintained under optimum environmental conditions and a low stocking density.
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    Sensory analysis, consumer preference and meat quality of wild versus farmed tilapia on the Malawian market
    (Stellenbosch : Stellenbosch University, 2023-03) Mlotha, Vincent; Salie, Khalid; Marais, Jeannine; Molotsi, Annelin H. ; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.
    ENGLISH ABSTRACT: Fish is a healthy food and contribute significantly to global food security, nutrition, and trade. Tilapia from both wild and farmed sources is a popular fish and contributes to global fish supply. There is lack of published information on tilapia supply, quality, consumption patterns and consumer preference for tilapia in Southern Africa. The aim of this study was to review tilapia consumption trends, assess consumer preference, analyse sensory profile, identify tilapia species, and determine the proximate composition, fatty acid profile and heavy metal concentration of wild versus farmed tilapia on the Malawian market. The objectives of this study were 1)to review literature on tilapia consumption in Southern Africa focusing on supply, quality, and consumer preference for wild versus farmed tilapia for a 20-year period (2000 to 2019); 2)to assess consumer preference for wild versus farmed tilapia found on the Malawian market; 3) to identify wild and farmed tilapia species on the Malawian market using deoxyribonucleic acid (DNA) analysis; 4) to assess the sensory profile of tilapia by descriptive sensory analysis; 5) to analyse the chemical composition, fatty acid profile and heavy metal concentrations in wild versus farmed tilapia. The tilapia were from five sources namely: 1) wild tilapia from Malawi; 2) farmed tilapia from Malawi; and farmed tilapia imported from 3) China; 4)Zambia and; 5) Zimbabwe. The review covered 10 countries, namely, Angola, Botswana, Eswatini, Lesotho, Malawi, Mozambique, Namibia, South Africa, Zambia, and Zimbabwe. The 10 countries were selected because of the significant contribution of tilapia towards economics and food security in the respective countries. FAO time series data on tilapia production and annual per capita fish supply were used for the review and covered a 20-year period from 2000 to 2019. In the consumer preference study, tilapia consumers (n=200) in Lilongwe Malawi were interviewed in a quantitative survey. Four qualitative focus group discussions (FGDs), with eight participants per group, were conducted to gain a deeper understanding of consumer preference for wild versus farmed tilapia. In the tilapia species identification study, deoxyribonucleic acid (DNA) analysis was used to identify the tilapia species while descriptive sensory analysis (by a trained panel of eight members) was used to assess the descriptive sensory quality of the tilapia. Proximate composition (moisture, crude protein, total crude fat and ash) of the tilapia was determined following standard official methods, fatty acids were analysed by gas chromatography and flame-ionization detector (GC-FID) method while inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the concentrations of heavy metals in the tilapia samples. The review of tilapia consumption data showed that wild tilapia declined while farmed tilapia and tilapia imports, particularly from China, contributed to fish supply in Southern Africa. Tilapia capture data for Malawi showed a declining trend from the year 2007 to 2019, although a few peaks were observed in some years (2005 to 2010). Among the 10 countries, Zambia was the leading producer of farmed tilapia. In 2000, Zambia produced 4020 tonnes of farmed tilapia, and this grew to 38390 tonnes in 2019. In 2019, Zambia produced over half of the total farmed tilapia in Southern Africa. The increases in farmed tilapia imports demonstrated the potential acceptability of farmed tilapia. The consumer preference study showed that consumers (98%, n=197) were aware of the various types and sources of tilapia sold on the Malawian market (wild versus farmed and locally produced versus imported tilapia). Sixty five percent (n = 130) of the consumers preferred wild tilapia from Malawi due to its quality (appearance, aroma, taste, and texture) even though they perceived the price of the wild tilapia to be higher than that of farmed tilapia. Forty two percent (n = 84) of the consumers often purchased wild tilapia while 34% (n = 67) purchased farmed tilapia. Correspondence analysis (CA) revealed that consumers from high tilapia consumption frequency (1-2 times tilapia consumption per week) were more likely to purchase frozen farmed tilapia than consumers from medium (1-2 times tilapia consumption per month) and low tilapia consumption frequency (5-6 times tilapia consumption per year). DNA analysis revealed that all the wild and farmed tilapia analysed showed over 98% similarity with Oreochromis niloticus in a search in GenBank and they were identified as Oreochromis niloticus. The sensory analysis experiment showed that there were statistical differences in only three sensory attributes of the fish evaluated in this study (musty mouldy aroma, earthy flavour, and musty mouldy flavour). The chemical analyses showed that farmed tilapia from Malawi had the highest total fatty acid concentration (115.62 mg/g) and all specific fatty acids except C22:0 and C20:5n3 only while wild tilapia from Malawi had the lowest total fatty acid concentration (23.06 mg/g). All the tilapia analysed in this study contained relatively high amounts of essential minerals particularly potassium (K), phosphorus (P), sodium (Na), magnesium (Mg), and calcium (Ca). Potassium was higher than Na in all the tilapia analysed. All non-essential heavy metals in all the tilapia were below the maximum recommended limits according to Food and Agriculture Organisation (FAO) and World Health Organisation (WHO) standards. The study provides valuable insights for policy analysis and development of strategies to upscale sustainable aquaculture and fisheries and facilitate fish trade by demonstrating demand and supply gaps, elucidating consumer preference, and purchasing behaviour, and providing updated information on the chemical composition of tilapia on the Malawian market.
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    Determination of variance components for skin traits of ostriches in South Africa
    (Stellenbosch : Stellenbosch University, 2023-03) Nemutandani, Khetho Ratshilumela; Engelbrecht, Anel ; Cloete, Schalk W. P. ; Dzama, Kennedy; Tada, Obert; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.
    ENGLISH ABSTRACT: In the South African ostrich industry, production of high quality leather is a necessity for sustainability and competitiveness on the world market. However, most skins are downgraded due to poor quality, constraining enterprise revenue. The aim of this study was to identify factors contributing to skin value, to determine genetic and environmental parameters for ostrich skin traits, as well as to evaluate the performance of pure and crossbred ostriches for skin traits. Skin size (SSZ), skin grade (SG) and quill value (QV) were assessed as predictors of skin value, using multiple regression techniques. Pearson’s correlations among independent variables confirmed that SG was the dominant driver of skin value, as indicated by a high negative correlation (r=-0.88) with skin income. Skin traits such as nodule size score (NSZ), nodule shape score (NS), hair follicle score (HF) and pitting score (PIT) mostly failed to reflect the variation in skin value accounted for by QV and SG, respectively. Single-trait heritability estimates, derived on South African Black (SAB) birds, for skin traits such as SSZ, skin weight (SW) and skin thickness (ST) were 0.37±0.06, 0.27±0.06 and 0.20±0.05, respectively. Overall, direct heritability ranged from low (0.08) for pitting scores to high (0.42) for hair follicle scores. Genetic correlations of slaughter weight (SLW) with SSZ, SW and ST were 0.92, 0.48, and 0.15. A positive genetic correlation of 0.33 was found between SLW and NSZ. A high genetic correlation of 0.71 existed between scores for NS and NSZ. For threshold traits, heritability estimates ranged from 0.17 for nodule direction (NDIR) to 0.47 for nodule outliers (OUTL) in the 5- trait threshold model analysis for non-linear and binomial traits. In the 6-trait linear- threshold analysis including SSZ as a linear trait, heritability estimates ranged from 0.20 for NDISTR to 0.39 for OUTL. For both sets of analyses, significant genetic correlations were found between OUTL and PIT (respectively 0.49 and 0.71). Evaluation of purebreds showed that Zimbabwean Blue (ZB) and Kenyan Red (KR) birds outperformed their SAB contemporaries for most size-related traits (P<0.05). Heterosis were found for SLW, SSZ, and NSZ, for SAB and ZB as well as for SAB and KR combinations. The effect of the taller KR dam line was significant for SLW, neckline total length, neckline crown length and neckline width in the middle. However, most of the size dependent genetic group effects were reduced or removed when farm weight was modelled as a covariate across analyses. High scores for HF were observed for all the crosses though. It was concluded that: 1. Skin grading was the dominant force in determining skin value; 2. Genetic variation existed and exploitable levels of variation were found in most quantitative skin characteristics; therefore genetic progress appear feasible through selection; 3. Genetic progress can also be achieved for traits not conforming to the assumptions of normality; 4. ZB and KR birds performed better for size-related traits than their SAB contemporaries, indicating that commercial crossbreeding could improve slaughter weight and size-related traits in hybrids. Overall, this study provides information to the ostrich industry regarding options for the exploitation of additive genetic gains, the choice of breeds, as well as crossbreeding options. This information will provide a sound foundation for genetic improvement of skin traits that is based on scientific principles.
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    Studies on genetic responses and genomic characterisation in South African and Australian sheep
    (Stellenbosch : Stellenbosch University, 2022-04) Nel, Cornelius Loftus; Cloete, Schalk W. P.; Dzama, Kennedy; Swan, A. A.; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: The current scope of small stock breeding in South African (SA) Merinos is constrained. In contrast to Australia (AUS) and New Zealand, no traits indicative of animal resilience or fitness are currently being recorded. Furthermore, the use of genomic selection (GS) could be a valuable tool to widen the scope of breeding objectives, but has not been formally explored on local populations. SA hosts multiple Merino resource flocks that are well recorded for a series of difficult to measure fitness traits, which can be exploited to the benefit of evaluating similar traits in commercial Merinos. The Elsenburg Merino flock is a resource flock that has been divergently selected for reproductive success on number of lambs weaned (NLW) that separates the H-Line (positive selection) from the L-Line (negative selection). The first aim of this study was to elaborate genetic parameters and realized genetic trends obtained in the Elsenburg flock as a demonstration of responses to genetic selection on a lowly heritable, sex-limited trait recorded late in an animal’s lifetime. Apart from a focus on production and reproduction traits, the genetics and factors influencing lamb survival received special attention. A second aim of this study was to use marker data to better define the population genetic architecture of important SA and AUS sheep breeds, with a focus on the across country compatibility of SA and AUS ovine genetic resources. A third aim of this study was to assess the benefits of genomic information in genetic prediction of SA Merinos. Genetic trends in the Elsenburg lines showed that long term divergent selection for NLW did not have severely detrimental effects on the genetic change in other production traits, with a possible exception of clean fleece weight and staple strength. Despite the low heritability, favorable genetic trends (~1% of the overall mean) per year were reported for NLW in the H-Line. Genetic change was more moderate, but also worthwhile for component traits, namely conception rate and litter size. Survival to weaning, as a trait of the lamb, also showed a rate of gain close to 1% in the early years of the experiment, which contradicted the premise that lamb survival is not amenable to genetic selection. As measured by rectal temperature, H-Line lambs also performed better during cold stress conditions, and the fitness of H-Line lambs was strongly linked to increased cold stress adaption. Population genetic parameters such as linkage disequilibrium and effective population size reiterated the fact that the genetic diversity of sheep can be high both across and within breeds, especially for Merinos. According to across country imputation, there is opportunity to combine SA and AUS Merino databases. This was supported by parameters of divergence (FST), principal component analysis and relatedness, but a narrow spectrum approach of specific populations is most likely to deliver the best results. The outcomes of GS were promising when a single-step GBLUP was used to predict genetic merit in unvalidated candidates for a series of production and reproduction traits. However, results varied across flocks and traits, and more research is needed to optimize these results. The study provided a foundation for further research on these and related topics.