Theses and Dissertations (Animal and Wildlife Sciences)

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An environmental, economic and nutrient index for milk and plant-based beverages in South Africa
(Academy of Science of South Africa, 2025-08) Maree, Enrike; Blignaut, James Nelson; Du Toit, Cornelius Jacobus Lindeque; Meissner, Heinz H.
Sustainable decision-making in the food sector is critical in addressing global challenges, such as climate change, resource scarcity, and malnutrition. Particularly, the milk and plant-based beverage sectors lack a comprehensive sustainability index tailored to assess economic, nutritional, and environmental impacts. We developed a specialised sustainability model for milk and plant-based beverages, adaptable to different countries. The Dairy Index for Environment, Economics, and Nutrition (DiEET) revealed that bovine milk scored 3.67 (nutritional), 0.161 (environmental), and 1.543 (economic); almond beverages scored 1.55, 0.172, and 1.103; soy beverages scored 2.21, 0.193, and 1.277; and oat beverages scored 1.204, 0.165, and 1. 083. These findings highlight the need to balance nutrition, economic viability, and environmental sustainability in food choices. The model, based on scientific data and requiring minimal user input, provides a practical tool for stakeholders to assess and compare sustainability across products. By enabling informed decision-making, this study promotes a more sustainable future, advocating for practices that consider all dimensions of sustainability in the food sector. Continuous refinement and validation of the model are essential to maintain its relevance amidst evolving data and industry practices, ensuring its effectiveness in guiding stakeholders towards sustainable dietary choices. SIGNIFICANCE : This study provides a comprehensive sustainability index for milk and plant-based beverages, addressing critical gaps in current assessments. By integrating environmental, economic, and nutritional indicators, the DiEET offers a holistic approach to evaluating food products. The findings highlight the trade-offs between nutritional quality, economic viability, and environmental impact, emphasising the need for balanced decision-making in agricultural production. This model serves as a practical tool for stakeholders, promoting consumer education and guiding industry practices towards sustainability. Its application can enhance sustainability evaluations and contribute to global efforts in monitoring sustainable development goals.
Effect of graded nutrient density and exogenous enzymes on the profitability of laying hen production in South African conditions
(University of Pretoria, 2024-06) Nkukwana, Thobela T.; Plumstead, Peter; u17151229@tuks.co.za; Grahame, Mackayla Mary
High energy feed ingredients are expensive and increase feed cost, thus lower energy diets may present an economic benefit. Precision nutrition and feed intake (FI) estimation can ensure nutritional requirements are met within the hen’s characteristic caloric intake and physical intake capacity. As dietary energy increases, the FI linearly decreases. However, diets should be nutritionally balanced as hens overconsume a high energy diet which results in a decrease in nutrient intake, poor feed efficiency, and high risk of prolapse due to excessive fat deposition. The aim of this study was to evaluate the relationship between graded energy levels and FI and the cost benefit in egg production of Hy-line Silver Brown laying hens at 40-weeks of age for a period of 70 days. The experimental design consisted of 8 treatments (TRT) with 16 replicate pens per TRT and 8 birds per replicate pen. Dietary TRT contained graded energy levels in ME (MJ/kg) as follows: TRT1, positive control (PC, 11.60), TRT2, negative control 1 (NC1, 11.46), TRT3, negative control 2 (NC2 = 50% NC1:50% NC3, 11.33), TRT4, negative control 3 (NC3, 11.20), TRT5 to TRT8 (TRT4 plus supplementation of various carbohydrate exogenous enzymes). The hens and feed allocation per pen were weighed at placement, and then on a weekly basis and mortality was recorded. Performance parameters included egg production, egg weight, feed conversion ratio (FCR) and FI. Results showed no differences in egg production and weight across TRTs. The FI for TRT1 was the lowest (P<0.05) compared to other TRT, while TRT4 had the lowest ME value and highest FI (P<0.05). A trend was seen in FI; as energy decreased FI linearly increased for TRTs 2 to 4. Treatment 5 had the highest FCR, while TRT2 had the lowest (P<0.05), and TRT1 was intermediate (P<0.05) to TRTs 2, 3 and 4. Treatments 3,4,5,7 and 8 all demonstrated a similar FI. The FCR for TRT3 and TRT4 were higher (P<0.05) than that of TRT1 and TRT2. Treatment 1 had the highest cost per ton, while TRT4 had the lowest. The feed cost per egg (FCE) decreased linearly as energy decreased, showing that cost per egg is directly related to energy density of feed. Treatment 1 had the highest (P<0.05) cost per egg, while TRT4 which had the lowest (P<0.05) ME/kg had the lowest (P<0.05) FCE compared to other TRTs. Treatment 2,3,5,6,7, and 8 had similar FCE. The feed cost per hen (FCH), income hen (IH), income minus feed cost (IF), and income from egg (IE) did not show significant differences across the experimental period. In conclusion, laying hens fed a diet with lower energy levels had improved FCR with no compromise in egg production and egg weight, implying that low energy levels can improve the profitability of hen production as long as feed is optimally balanced in nutrients. Additionally, no effects were seen on supplementation of exogenous enzymes on laying hen performance and economics.
Analyses of the variation in feed efficiency measures of MOET-produced Droughtmaster SA cattle in intensive and extensive feeding systems
(University of Pretoria, 2024) Webb, Edward Cottington; elandie888@gmail.com; Du Preez, Elandie
Feed is one of the major expenses in the beef industry, so it is beneficial to select animals that consume less feed for the same level of production. This study aimed to compare the feed efficiency and residual feed intake of Droughtmaster SA weaners of different double muscling genotypes (F94L and NT821) produced by multiple ovulation embryo transfer (MOET) between the GrowSafe system and veld. In this study, several feed efficiency measures were recorded from 150 Droughtmaster SA bulls and heifers over two years. Primary data obtained for evaluation showed that there was a positive association between the double muscling mutations and low residual feed intake (efficient animal). Sex (male and female), residual feed intake rank, double muscling mutation (F94L, NT821, None), and other efficiency variables were analysed using the General Linear Model using the SPSS Software (Version 29). The results confirmed that variations in residual feed intake do exist. The research also suggested that the ranking of efficient animals in the GrowSafe system and on veld remained the same. The results of the study validated that the GrowSafe system can identify the same bulls and heifers with low RFI as on veld, which indicated that the performance testing period can be significantly reduced and cattle can be marketed at an increased price in a shorter time frame. There was no significant difference in efficiency parameter ranking of weaners in the intensive feeding system (GrowSafe System) versus on veld, as well as no significant difference between efficiency parameter measures of different double muscling genotypes when the entire population of cattle were accounted for. Significant differences did exist between efficiency parameter measures of different double muscling genotypes within gender groups. Subsequently, this may lead to decreased reproductive efficiency, since Droughtmaster SA cattle are an early maturing breed. The results of this study may have a practical implication on breeding goals, since selecting more feed-efficient animals may result in less efficient animals in terms of reproduction.
A phenotypic and genetic analysis of claw lesions in total mixed ration Holstein cattle herds in South Africa
(University of Pretoria, 2024-11) Van Marle-Koster, Este; Mostert, Bernice; robynscheepers@yahoo.com; Joubert, Robyn Clair
Lameness due to claw lesions is a major hurdle for sustainable dairy production worldwide. Hoof trimming is used as a preventative measure, and key to future improvement strategies, providing phenotypic records for genetic interventions. This study aimed to evaluate hoof-trimming data in South African Holstein herds in total mixed ration (TMR) systems to determine the prevalence of claw lesions, investigate phenotypic and genetic parameters thereof, and explore the use of genomic information to provide insight into the underlying genetic architecture of claw lesion traits. Routine hoof-trimming appointments to five dairy herds in the central region of South Africa over a 10-year period, together with genotypes generated during the South African Dairy Genomic Programme provided the data for this study. More than 50% of cows presented with a lesion on any one foot, with digital dermatitis (DD) as the most commonly recorded lesion, followed by the non-infectious lesions sole ulcers (SU), sole haemorrhage (SH), and white line (WL) lesions, most of which occurred in the rear feet. The relationships between housing systems, individual feet, and the different lesions was analysed using chi-square tests as well as correspondence analysis (CA); SU and SH were strongly associated with each other, as were DD and interdigital phlegmon (IP), and SH and WL. These associations between lesions could be used to inform a more simplified approach to lesion recording systems, and contribute to practical prevention strategies on-farm. Phenotypic correlations between individual lesions and groups (infectious, non-infectious, and total lesions) were investigated using Spearman correlation tests. Moderate to strong relationships were observed among non-infectious lesions SH, SU, and WL (0.425–0.576), with the occurrence of SU and WL being strongly positively associated with total non-infectious lesions (0.543–0.576). Similarly, the infectious lesion DD was positively correlated with total infectious lesions (0.984). The estimated heritability of lesion categories varied between 0.008 for total lesions to 0.05 for the total non-infectious lesions category. A genome-wide association study for non-infectious lesions was performed using EMMAX, leading to the identification of one genome-wide significant single nucleotide polymorphism (SNP) and 15 genome-wide suggestive SNP. Candidate genes associated with the significant SNP on chromosome 25 related to abnormal skin morphology, immunity, and inflammation. From the literature, and this study, it is clear that claw lesions are highly polygenic. Differences among definitions and descriptions add to the complexity of the analyses. This study represents the first attempt to investigate claw lesions in South Africa using a combination of phenotypic and genetic data. The results confirmed the lack of adequate phenotypic data for genetic and genomic analyses, due to a lack of consistent farmer recording as well as a lack of coherence among data recording systems. Underlying genetic variability was confirmed and holds potential for further research but this requires consistent and complete phenotypic claw data. The prevalence of lameness remains high and a simplified and standardised recording system will be a first step in improving participation in national recording schemes for applicable research to reduce the incidence of this painful and costly disorder.
Genomic characterization of autozygosity in South African Merino sheep
(University of Pretoria, 2024-11) Visser, Carina; Lashmar, Simon Federick ; micah.forsythe@gmail.com; Forsythe, Micah Ellen
The South African (SA) Merino is a medium-framed, white wool breed, and is one of the most prominent breeds in the SA sheep industry. Because of its local importance, the SA Merino is the only SA sheep breed with sufficient single nucleotide polymorphism (SNP) genotypes to implement genomic selection (GS), and this provides comprehensive sample size (i.e. number) and composition (i.e. representation) of genotypic data to study the breed’s diversity and inbreeding. These estimates play a vital role as tools for breeders to maintain genetic progress whilst conserving diversity within flocks. This study aimed to perform a homozygosity-focused SNP investigation of the past and present inbreeding and autozygosity levels in the SA Merino sheep breed. A total of 1 738 animals (1 567 females and 171 males), genotyped using different versions of the Illumina® Ovine 50K SNP panel, were used to estimate various proxy-indicator parameters of genomic variability, runs of homozygosity (ROH) and heterozygosity-rich region (HRR) profiles, and conserved ROH-based selection signatures for the SA Merino breed. The reported observed (HO=0.351± 0.018) and expected (HE=0.365± 0.0001) heterozygosity, and their relationship to one another (i.e. HO
A genome-wide single nucleotide polymorphism-based investigation of coat colour variation in indigenous South African goats
(University of Pretoria, 2024-11) Visser, Carina; Lashmar, Simon Federick ; tinajansenvanrensburg66@gmail.com; Jansen van Rensburg, Tina
Studying the foundation of coat colour diversity and its origins is essential for classifying goats into distinct ecotypes. This study offers insights into coat colour patterns of indigenous South African goats using single nucleotide polymorphism (SNP) data. A group of 192 goats from three recognised and five non-descript ecotypes alongside 96 South African Angora goats underwent genotyping using the Illumina® Goat SNP50 genotyping panel. Quality control (QC) procedures were carried out using PLINK version 1.9 software, while GCTA software was utilised for principal component analysis (PCA) to study population substructure. Distinct populations substructure was observed, with the highly selected Angora goats forming a separate, tight cluster. Indigenous goat types were clustered into two main groupings, one containing the Jozini, Mboza and Osca types, and the other consisting of a mixture of the ecotypes and remaining non-descript goats. Selection signature investigations employing the FST method and the Manhattan plots for the pairwise FST comparison between the Angora and indigenous goats indicated FST values for specific SNP ranging from 0.8 (least differentiated) to 1 (most differentiated). Twenty-six protein-coding genes were identified close to the ten most differentiated SNP. Genome-wide association studies (GWAS) were conducted with PLINK as well as EMMAX. Fourteen SNP markers linked to coat colour were identified in the GWAS study using PLINK, while the EMMAX analysis identified 16 markers associated with coat colour and its variation. Several genes with a well-recognized role in coat colour expression, including the KIT, MC1R, ASIP, and TYRP1 genes, were harboured in the genomic regions surrounding differentiated and/or phenotype-associated SNPs. These genes were in concordance with those previously reported for commercial goat breeds, which supports the idea of conserved coat colour genetics as a result of shared ancestry. This study highlights how the dispersal of goats into different environments with different ecological pressures led to varied coat colour patterns across populations. It enables classification and conservation and lays the groundwork for further studies on both the genetic and ecological adaptation of these animals.
Effect of different varieties of rosemary (Rosmarinus officinalisi) plant extracts on in vitro methane production of Eragrostis curvula hay
(University of Pretoria, 2024-11) Hassen, Abubeker; Akanmu, Abiodun; sknthinya@gmail.com; Nthinya, Sebabatso Kamohelo
Methane emissions from livestock contribute substantially to global greenhouse gases, which affects climate change and energy losses in ruminants that negatively impact productivity. To address this issue, the use of natural feed additives rich in plant secondary metabolites has gained interest as a sustainable alternative to synthetic additives. This study evaluates the potential of various rosemary (Rosmarinus officinalis) varieties as natural supplements to reduce methane production during the fermentation of Eragrostis curvula hay. Rosemary varieties, including McConnell’s Blue, Tuscan Blue, Roseus, Mountain Mist, and Silver Fox, were harvested at two physiological stages—eight weeks post-transplanting and at 50% flowering. Metabolomics analysis revealed significant differences in secondary metabolite concentrations across varieties and harvest stages. The different rosemary varieties were evaluated for in vitro gas production and organic matter digestibility and methane inhibition using standard procedures. Three different varieties of rosemary leaves were harvested at 8 weeks after planting (Season 1) and six varieties were harvested at 50% flowering (Season 2). The leaves were freeze-dried and extracted with 85% methanol and 15% water. The plant extracts used as a feed additive in in vitro rumen fermentation experiments at a rate of 75mg/kg feed DM. Wild Rosemary was different to the other varieties in terms of the concentration and presence of most of the metabolites phytochemical profiles, whereas McConnell’s Blue was the only variety that showed seasonal difference. In season 1, McConnell’s Blue variety increased total gas production (TGP) and Tuscan Blue variety decreased methane (CH4) and in vitro organic matter digestibility (IVOMD). In season 2, all the rosemary varieties plant extracts reduced TGP, but no effect was observed for (CH4). The study further identified positive correlations between some metabolites, such as carnosic acid, carnosol, and TGP, (CH4) and IVOMD. These findings underscore the potential of rosemary extracts as sustainable feed additives that support methane reduction.
Co-variance component estimation for South African Hereford, Charolais, and Angus cattle for application in genetic evaluations
(University of Pretoria, 2024-10) Van Marle-Koster, Este; Theron, Helena; hannahkruger1@gmail.com; Kruger, Hannah
This study developed (co)variance components and heritability estimates for growth traits in South African Angus, Charolais, and Hereford cattle, well-established breeds farmed locally for over a century. Genetic parameters are required for genetic evaluations. In this study genetic parameters were estimated for the specific populations by using single- and multi-trait models based on available data over 10-year (2012-2022) and 20-year (2002-2022) periods. Key traits analysed included birth weight, weaning weight, yearling weight, and 18-month weight, Average Daily Gain (ADG), hip height, body length and scrotal circumference. This study developed single and multi-trait models for (co)variance estimations. The single-trait models for Angus birth weight exhibited higher direct heritability estimates (0.41 to 0.49) compared to weaning weight (0.02 to 0.26), yearling weight (0.05 to 0.43), and 18-month weight (0.25 to 0.44) for the Angus breed. The Charolais exhibited similar results, and the Hereford estimates varied across the traits with large variability, birth weight (0.001 – 0.29), weaning weight (0.03 – 0.19), yearling weight (0.07 – 0.25) and 18-month weights (0.01 – 0.56). Single-trait models indicate the role of environmental effects such as inclusion of Sire by Herd (SXH) effects in breed models which raises residual variance, and the Permanent Environment (PE) effect which impacted traits from birth to 18 months, therefore they must be evaluated for inclusion. For Angus, multi-trait heritability estimates were (0.50 ± 0.02, 0.43 ± 0.02) for birth weight, (0.31 ± 0.24, 0.27 ± 0.02) for weaning weight, (0.50 ± 0.04, 0.36 ± 0.03) for yearling weight, and (0.35 ± 0.06, 0.39 ± 0.03) for 18-month weight in the 2012-2022 and 2002-2022 datasets, respectively. Charolais estimates showed birth weight heritability estimates of (0.36 ± 0.04, 0.42 ± 0.03), weaning weight at (0.19 ± 0.03, 0.20 ± 0.03), yearling weight at (0.07 ± 0.02, 0.13 ± 0.03) and 18-month weight at (0.10 ± 0.04, 0.17 ± 0.04) for the same periods. For Hereford (2012-2022 data only), heritability for birth weight was 0.32 ± 0.03, weaning weight 0.20 ± 0.03, yearling weight 0.32 ± 0.06, and 18-month weight 0.46 ± 0.08. Post-wean growth test traits heritability estimates were estimated on the larger data set of 2002-2022. Angus demonstrated moderate to high heritability for ADG (0.19 ± 0.05) and scrotal circumference (0.37 ± 0.07). Charolais exhibited moderate heritability for average daily gain (0.39 ± 0.30) and scrotal circumference (0.57 ± 0.28), and Hereford cattle showed moderate heritability for average daily gain (0.31 ± 0.10) but lower estimates for scrotal circumference (0.21 ± 0.10). The study emphasizes dataset limitations and recommends complete recording and genomic-based parentage testing to improve the accuracy of variance components and estimated breeding values for breeders.
Quality of South African soybean meal as a factor affecting the efficacy of exogenous protease in broiler diets
(University of Pretoria, 2025-02) Jansen van Rensburg, Christine; reubenkholmes@gmail.com; Holmes, Reuben Kaare
The poultry feed industry relies heavily upon soybean meal (SBM) as a relatively affordable, high quality source of protein. Soybean meal composition and quality may vary between batches, mainly contributed to variation in production practice, cultivar and processing technique. Dietary supplementation with a mono-component, exogenous protease, has the potential to reduce feed cost, improve the health and welfare of poultry and reduce the already substantial carbon footprint of poultry production. The effects and interaction of exogenous protease in soybean-maize based diets, however, is unpredictable and cost- effective inclusion is not always realised. Matrices have to be adjusted continually to accommodate the differences in nutritional composition. Studies on the effects of exogenous protease on ileal amino acid digestibilities have yielded contradicting results. Given that the South Africa crushing industry is relatively young, having an understanding of the relationship of protease on apparent ileal amino acid digestibility (AIAAD) and SBM quality is important. However, insufficient data is available in order to more fully understand this relationship. To improve our understanding of the nutritional composition and quality of local SBM, two surveys were conducted in which SBM samples were collected from various soybean processors in South Africa. Survey 1 comprised of SBM samples which were collected from seven of the largest processors in South Africa from June to October 2020. Survey 2 comprised of SBM samples from five of the largest processors from September 2019 to March 2020. Both sets of samples were analysed for nutritional composition, including amino acid (AA) concentration and quality parameters. From samples collected for Survey 2, one low quality (LQ), one high quality (HQ) SBM sample and one over-processed sample (OP) were selected. An under processed (UP) sample was also obtained which served as a negative control. These four samples were incorporated into maize-soybean based diets, either with or without an exogenous protease and fed to broilers in a digestibility study aimed at investigating the interaction between SBM quality and protease efficacy. In the two surveys conducted, significant differences were observed among at least one of the seven sources for Survey 1 and one of the five sources for Survey 2 in all nutritional components and quality parameters except for zinc, iron or copper. The findings highlighted substantial variability in South African SBM indicating challenges in achieving consistency in SBM composition due to various factors including cultivar, planting and harvesting techniques and origin. The significant variability observed between processors indicates that ensuring consistency in SBM composition and quality is challenging. The efficacy of protease varied across treatments containing different SBM qualities. Protease supplementation significantly increased the apparent ileal digestibility of crude protein (CP). The impact of protease on AIAAD was most pronounced in the treatment. with UP, followed by HQ, LQ, and then OP. This suggests that protease supplementation may be effective in increasing the AIAAD of some AAs in SBMs that have not undergone sufficient thermal exposure. This may also suggest that it may not always be justified to use a protease to increase the AIAAD of nutritionally important AAs, such as essential AAs, in diets containing SBM that contains insufficiently processed SBM. With protease supplementation it may not be accurate to assume improvement in CP digestibility based on fixed matrix values recommended by the manufacturer. Nutritionists have to regularly adjust matrices according to batch and supplier. Protease supplementation led to higher ileal CP digestibility across all SBM samples, but this did not consistently translate to increased digestibility of all AAs. The varying effects of protease supplementation on AIAAD indicates an interaction between processing level and protease efficacy on AA digestibility. Protease supplementation had a greater effect on SBM with lower CP content. Therefore, it is, incorrect to assume a linear relationship between CP digestibility and AA digestibility. The use of protease in soybean-maize diets could potentially enhance the utilization of dietary protein. However, its effectiveness varies. Further research into how protease functions on SBM would be beneficial, given that its impact on SBM of different qualities is unpredictable and challenging to quantify.
Beta-adrenergic agonists, ractopamine hydrochloride and salbutamol, as performance enhancers in the finisher pig
(University of Pretoria, 2025-02) Jansen van Rensburg, Christine; Steyn, Willem J.; u17000752@Tuks.co.za; De Jager, Jean-Pierre
Ractopamine HCl and salbutamol are beta-adrenergic agonists that enhance the performance indicators of pigs when administered in their diet. The aim of the study was to determine the effect of ractopamine HCl and salbutamol on the performance of the finisher pig. A total of 440 pigs (Topigs TN70) served as the subject. The pigs were divided into 40 pens of 11 each. The pigs were fed 5 different treatments in the finisher phase, the 5 treatments were: 1. Negative control (NC): No additives included (16% crude protein (CP) in finisher diet) 2. Positive control: Ractopamine HCl inclusion (6 mg/kg of feed) and current recommendation of 16% CP in the finisher diet. 3. Ractopamine HCl (6 mg/kg of feed), but only 13% CP in the finisher diet while dietary essential amino acid concentrations were similar to the positive control diet. 4. NC diet + salbutamol 10% at 6 mg/kg 5. NC diet + salbutamol 10% at 4 mg/kg The pigs were fed the same diets in the grower phases 1, 2 and 3, the diets consisted of mainly maize, soya, wheat bran sunflower oil cake and a grower vitamin and mineral premix. Feed intake, live weight gain and feed conversion ratio (FCR) were measured. Cold carcass weight, warm carcass weight, lean percentage, dressing percentage and moisture loss were also measured. There were significant differences (p<0.05) in live weight gain, FCR, feed intake and lean percentage when comparing the group fed salbutamol with the group fed ractopamine HCl and the group without the beta-agonist in their diet. The group of pigs fed salbutamol in their diet had performed significantly (p<0.05) better. However, this group, together with the group of pigs fed ractopamine HCl, exhibited a higher return on investment (ROI) during the study. In conclusion, ractopamine HCL and salbutamol enhanced the performance of finisher pigs during this study, although it is expedient to validate these findings for future studies.
An environmental, economic and nutrient index for milk and plant-based beverages in South Africa
(University of Pretoria, 2025-01) Du Toit, Cornelius Jacobus Lindeque; Blignaut, James Nelson; enrike.maree@goalsciences.org; Maree, Enrike
Amidst growing global concerns over sustainability, the imperative for sustainable agriculture has become increasingly important. This urgency is propelled by heightened awareness among consumers and policymakers, the pressing demands of an increasing global population, and the critical influence of dietary choices on environmental sustainability. Recognising a gap in the literature, this study aimed to contextualise the sustainability of milk and plant-based beverages within the South African milieu, evaluating their nutritional profiles, environmental footprints and economic affordability through a comprehensive literature review. The investigation challenged the prevailing one dimensional approach in climate-aware consumer choices and policymaking, advocating for a new, contextually relevant perspective. Central to this research is the development of a sustainability model, the dairy index for the environment, economics and nutrition (DiEET) designed to provide a holistic assessment of the economic, nutritional and environmental dimensions of milk and plant based beverages. Based on the model results, milk held a superior nutritional and economic profile with scores of 1.932 and 0.848, respectively, in comparison to plant-based beverages with nutritional scores of 0.766-1.629 and economic scores of 0.574-0.713. Soy beverages obtained the highest scores between the plant-based beverages. Environmental scores highlighted bovine milk, with a score of 0.161, as the least environmentally sustainable beverage in comparison to plant-based beverages with scores of 0.165 to 0.193, showing an environmental trade-off of producing an affordable and nutritious product. In contrast to the nutrient rich food index (NRFi), the model results are less impacted by fortified nutrients. Using NRFi, the study showed that almond beverage has the highest nutrient score (32.573-64.808) in comparison to bovine milk with a maximum score of 8.288, which conflicts with nutrient comparisons and the results of the DiEET model. Environmental and economic results obtained from literature followed similar trends to the results obtained by the DiEET model. The study’s findings, both from literature and using the new DiEET model, underscore the complexity of achieving sustainability in the food system and highlights the trade-offs between nutritional value, environmental impact and affordability. This model is an initial step towards integrating multifaceted sustainability indicators into country-specific sustainability policies, thereby informing consumers and promoting a more sustainable, nutritionally adequate and economically viable food system in South Africa and beyond.
The effect of fibre type in a diet containing fine maize to improve the performance and health of pigs during the final finisher phase
(University of Pretoria, 2024-07) Jansen van Rensburg, Christine; mostert.jd@gmail.com; Mostert, Jan David Huygen
The importance of maize grind size in commercial pig rations are oversighted, a substantial amount of nutrients is annually lost due to undigested maize. Pig production could benefit from an increased nutrient availability, without increasing the feed costs. The challenges producers are faced with when feeding a finer feed are firstly; fine feed tend to bridge in the feeding system and secondly; gastric ulcers often develop. In this study, the effects of using a finer maize (741 µm) particle in finisher pig rations in combination with sunflower meal were investigated to alleviate the risk of gastric ulceration. Finisher pigs of Topigs Norsvin genetics were fed in a commercial set-up, with industry standard rations, after which they were slaughtered at a commercial abattoir. A total of 288 pigs were used for the study, divided into six treatment groups with six replicates each. The trial was designed with six treatments in a 2 x 3 factorial arrangement, examining the main effects of fibre source (wheat bran and sunflower meal) and maize grind size (720 μm, 741 μm, and 774 μm). Statistical analysis was conducted by ANOVA using SAS software, while blocking was applied to minimise facility effect. The pigs were fed these treatment rations during the finisher phase, from 19 weeks-of-age until slaughter at 22 weeks-of-age, when pigs are most likely to develop gastric ulcers. Average daily feed intake (ADFI), feed conversion ratio (FCR), average daily gain (ADG), gastric ulceration scores and carcass characteristics were evaluated during this study. Total tract nutrient digestibility was evaluated using chromium dioxide as an indigestible marker. There was no significant difference (P > 0.05) in the performance parameters and carcass characteristics of the pigs during this study. Pigs administered sunflower meal as fibre had a significant difference (P < 0.05) in digestion of amino acids, crude fibre and starch during the trial. There was no increase in gastric ulcerations all through the study. It was concluded that a diet with medium maize particle sizes of 741 µm on average and with the inclusion of fibre from sunflower meal, enhanced digestibility and did not negatively impact the gastrointestinal tract (GIT) of finisher pigs during this study.
The effect of grinding size and amylase enzyme supplementation on potential ruminal and total tract starch digestion of maize in dairy cows
(University of Pretoria, 2023) Erasmus, L.J. (Lourens Jacobus); Du Toit, C.J.L.; colleenengel@mweb.co.za; Engelbrecht, Colleen
Although the market price of maize depends on environmental and political factors, thus deeming it variable, South Africa uses maize as the primary energy concentrate in ruminant diets, providing the energy for high-performance animals. Producers recently experienced the severity of the impact of these environmental factors, with maize prices reaching a record high during 2016 due to droughts from 2014 to 2016, decreasing the milk-to-feed price ratio in South Africa to a critical level. Since international milk prices still have not recovered after the 2014 global price crash, it is critical to formulate diets accurately and purposefully for optimal production. One factor that can significantly affect this goal is finding ways to reduce the wastage of nutrients in the digestive tract. Many factors, including genetics, cultivar, variety, geographical location, year, climatic conditions, and agronomic practices, directly influence the nutrient value and digestibility of grains. In addition to these production parameters, the ratio of amylose to amylopectin, which makes up the type of starch contained in the endosperm of grains, and the particle size of milled grains have a substantial effect on the digestibility of the grain component in feed. The encapsulation of maize starch particles in a bed of hydrophobic proteins called prolamin primarily influences the digestibility of the starch in maize. The type of starch is the second factor that affects starch digestibility since amylose is less digestible than amylopectin because of its molecular structure. It is commonly accepted that finer ground maize leads to less starch in the manure, thus indicating improved starch digestion. The digestibility of grains is directly altered by the amylose-to-amylopectin ratio of grains. In-vitro rumen digestibility increased as the amylose content of grains decreased. Amylose has tighter intermolecular bonding between starch molecules than amylopectin. Commercial feed enzyme development is a radical innovation in dairy cow nutrition. Ronozyme®. Rumistar is an α-amylase enzyme specifically developed to improve starch digestion in the rumen of ruminants. This study aimed to determine the efficiency and the interaction between maize processing and the addition of exogenous enzymes and to provide additional insights into these two most important factors that affect ruminal starch disappearance and the post-ruminal digestibility of starch in ruminants. This trial was conducted in two phases, assessing total tract starch digestion in the first phase and ruminal digestion in the second. The first phase of the trial was conducted on a commercial dairy farm. One diet was fed throughout the trial period, with the maize component ground into three different milling sizes (coarse maize with a mean particle size of >3 mm, fine maize with a mean particle size of <3 mm, and micro-milled maize with a particle size of <1 mm). The cows were randomly allocated to two treatment groups. The feed of one group was supplemented with an additional exogenous amylase enzyme, while the other group served as the control. This study reported the impact of different particle sizes in the maize fraction of the feed and the addition of an amylase enzyme on milk yield, milk composition, and the manure nutrient profile. Phase Two of the trial was conducted as a cross-over design with four rumen cannulated cows at the University of Pretoria’s experimental farm to determine the rate of starch disappearance over time. Each cow served as a repetition of the trial, and the study was executed in two periods, with one sampling day per period. Before the start of the study, two of the cows were adapted to the enzyme treatment by adding the enzyme directly into the rumen via a cannula twice a day for 21 days before the 24-hour in-sacco trial to allow the cows to adjust to the diet and conditions. Ruminal pH and temperature were measured and recorded at every enzyme insertion. The treatments were inverted for the second round. A seven-hour, in-vitro starch digestibility assay was run with an adapted rumen fluid mixture for the different treatments. Ruminal volatile fatty acid production was measured for the different treatment runs. In the first phase, which focused on total tract starch digestibility, no significant differences were found in milk yield when the diets with different maize particle sizes supplemented with amylase enzyme were compared. Milk fat was not affected by either the supplementation of the amylase enzyme or the particle size of the maize component in the feed. However, a significant interaction was found between treatment and particle size (P<0.05). The feeding of coarse maize resulted in higher milk fat production in the control group that received the base diet with no supplemental enzyme, but the effect was suppressed when the amylase enzyme was added. Particle size significantly affected milk protein, with a smaller particle size resulting in an increased milk protein percentage (P<0.05). The particle size of the maize component in the diet significantly affected the faecal starch content, with less starch in the faeces of the cows eating the finer ground particles (P<0.05). Manure neutral detergent fibre was significantly affected by the maize particle size and enzyme interaction. Overprocessing effects seemed to reduce the neutral detergent fibre content of micro-milled maize in conjunction with the supplemental enzyme. Across the particle sizes, the mean protein content of the manure was significantly lower for the enzyme treatment, suggesting reduced hindgut fermentation as a result of improved rumen fermentation. In the second phase, ruminal starch degradability was measured using a seven-hour in-vitro digestibility assay. Analysed digestibility of coarse maize was half that of fine maize, with the digestibility of micro-milled maize being an additional 25% higher than fine maize. As expected, in the in-sacco digestibility assay, digestibility curves showed that the maize particle size had a significant impact on the soluble fraction A, which increased with the degree of processing (P<0.005). The particle size did not affect the insoluble fraction B. The fast digestible fraction was lower with the supplemental enzyme, but total tract digestibility was improved (P<0.05). This corresponded with the volatile fatty acid results, showing increased volatile fatty acid production with the supplemental enzyme across all maize particle sizes. Propionic acid production was raised, and the acetate-to-propionate ratio was reduced. There is no doubt that the use of exogenous enzymes with amylolytic and proteolytic activity in diets with a high starch amylase content for ruminants is already under way although the precise mode of action and the limitations of the metabolic system in grains are not yet well understood. More research is necessary to understand all the factors that are influencing and being influenced by these enzymes in order to utilise them for the benefit of the animal and the producer.
Effects of different stunning methods on carcass characteristics and the conversion of muscle to meat in commercially farmed Nile crocodiles (Crocodylus niloticus)
(University of Pretoria, 2024-07) Webb, E.C. (Edward Cottington); Myburgh, Jan G.; Hugo, Arno; U18004297@tuks.co.za; Van den Bergh, Natasha
From the 1950s to the 1960s crocodilians were hunted for their skins, which led to many wild populations being killed. Subsequently, all crocodilians were added to Appendix I or II of the Convention on International Trade of Endangered Species of Wild Fauna and Flora. Restocking wild populations by crocodilian breeding started in 1974, and African countries began showing an interest in commercial crocodilian production in 1984. In South Africa, Nile crocodiles (Crocodylus niloticus) are the preferred species farmed. The crocodilian farming industry mainly produces skins, while meat is the main by-product. Alternative income methods, like meat production, should be considered to increase the feasibility of the industry. There is little knowledge about the conversion of muscle to meat and meat quality in Nile crocodile carcasses. Furthermore, various stunning methods are accepted and used in the commercial crocodilian industry. However, the effect of these methods on crocodilian welfare and meat quality are unknown. This study was conducted to determine baseline values for the conversion of muscle to meat and some physicochemical parameters (i.e., thaw loss, cooking loss, shear force, and fatty acid composition) of farmed Nile crocodiles. This study also assessed the effects of preferred stunning methods on commercially farmed Nile crocodiles’ meat quality. Lastly, this study investigated the effects of different anatomical locations on the conversion of muscle to meat. This study was conducted in May 2023 on a commercial crocodile farm in the Limpopo Province, South Africa. Twenty female Nile crocodiles were stunned and slaughtered from a single pen using two stunning methods (i.e. free bullets and electrical stunning). Carcass temperature and pH measurements and samples for muscle metabolomic analyses were taken from three anatomical locations (i.e. the transversospinalis capitus, longissimus dorsi, and ilio-ischiocaudalis muscles). Samples for the analysis of physicochemical characteristics were taken from the ilio-ischiocaudalis muscle within the tail. Lastly, live weight, blood loss during bleeding, cold carcass weight, and cut weights (i.e., the forequarter, rib casing, hindquarter, and tail tip) were measured. This study showed significant differences in the carcass pH at each time interval between the stunning methods. Significant differences in carcass pH were seen at 6, 9, and 12 hours post mortem between the anatomical locations. Moreover, significant post mortem differences were seen in the glucose and glucose-6-phosphate concentrations between the stunning methods. The anatomical locations showed significant post mortem differences in the glycogen, glucose, and glucose-6-phosphate concentrations. Furthermore, the stunning methods showed no significant differences in the tail meat’s thaw loss, cooking loss, or shear force. This study further showed that the primary fatty acids in the intermuscular and intramuscular fat of the tail are oleic, palmitic, and linoleic acids and that the content of individual fatty acids differ between these tissues. Lastly, a dressing percentage of 61.25% was found, and the tail cut was the highest yielding cut. The results of this study showed that the free bullets stunning method caused less stress than the electrical stunning method. However, the stunning method did not significantly affect the meat quality parameters. Thus, both stunning methods produced similar and acceptable carcass and meat quality. This study further indicated that the tail had a slower glycolytic rate than the neck and body. Thus, the tail may have more slow-twitch muscle fibres than the neck and body.
Effects of different stunning methods on the welfare and carcass quality of finisher pigs in South African pork abattoirs
(University of Pretoria, 2024-07-24) Webb, E.C. (Edward Cottington); naomilupton7@gmail.com; Lupton, Naomi
The purpose of this research was to study the effects of different stunning systems on the welfare of pigs in South African abattoirs. Four stunning systems were evaluated: 84% CO2, emergency head-only electrical, standard head-to-heart electrical, and an experimental 80% Argon 20% CO2 (Ar-CO2) admixture. pH data, pig behaviour inside the stunner and muscle metabolites were studied in this research. Both the Ar-CO2 and emergency head-only stunning methods were deemed problematic on the basis of animal welfare. The Ar-CO2 method had the sharpest and fastest pH decline. The 84% CO2 and standard electrical head-to-heart stunning methods had similar rates of pH decline, with CO2 having a lower pH than electrical stunning at every point. The behaviour displayed during gas stunning treatments was recorded by way of cameras located inside the stunner. Those stunned by 84% CO2 lost their consciousness significantly faster than those stunned by Ar-CO2. During the Ar-CO2 stunning, four out of five pigs squealed while under the admixture’s influence, indicating that the animals were distressed during this process. Squeals were not heard while the pigs were exposed to the 84% CO2. pH profiles did not differ significantly between head-to-heart electrical stunning and 84% CO2 stunning, implying that the stunning treatment itself did not have a big effect on the post mortem pH and its decline. The author recommends that further research in the South African pork industry be focused on improving and refining current CO2- and electrical stunning systems. Pre-slaughter handling plays a big role in the animal’s psychological- and physiological state during stunning and must be further improved upon.
In vitro maturation of Southern white rhino (Ceratotherium simum simum) oocytes
(University of Pretoria, 2024-09-05) Webb, E.C. (Edward Cottington); De la Rey, Morne; cherbst00@gmail.com; Herbst, Carla
Currently there are only two northern white rhinoceros left in the world, both are females. The decline in numbers, to the point of extinction, can be attributed to poaching, habitat destruction and poor reproductive management. The Southern White Rhinoceros is the closest relative to the northern white rhinoceros and can therefore be used as a model for the research of assisted reproduction technology. For the Southern White Rhinoceros these techniques will also be critical to support breeding programmes in captive animals and to increase genetic diversity in current populations. Assisted reproduction technologies in rhinoceros include semen collection and freezing, artificial insemination, ovum pick-up, in vitro fertilisation and culture and embryo transfer. Since there are only two females left of the northern white rhinoceros, the production of an embryo from collected oocytes and frozen northern white rhinoceros semen is the only way to save the species. The first step would be the successful and repeatable collection of oocytes from cows. In South Africa this step is already achieved by Dr Morne de la Rey. The next step would be the in vitro maturation of the oocytes to reach Metaphase II and produce visible polar bodies. A visible polar body is an indicator of successful maturation and that the oocyte is ready for fertilisation. After fertilisation the presumptive zygotes are cultured until reaching blastocyst stage. Once reaching blastocyst stage, the embryos would be suitable for transfer into a surrogate cow. The surrogate cow would need to be at the correct stage in her cycle to receive an embryo so that it may result in a pregnancy. This study focuses on the in vitro maturation of Southern white rhinoceros oocytes. From collected data an analysis was performed to determine the influence of various factors on the maturation outcome of oocytes. In terms of the environment, factors like season and housing conditions were evaluated. The influence of age on number of follicles aspirated, number of oocytes collected and eventual maturation was considered. Some of the cows were stimulated with GnRH to achieve a higher number of follicles for aspiration and subsequently more oocytes. The influence of this stimulation on oocyte maturation was considered. The main goal of this study was to assess the influence of the media used for maturation on the maturation rate. The first media was formulated by the San Diego Zoo and the second adapted from this formula by Embryo Plus. The biggest difference was the base media. San Diego Zoo media uses TCM199 as a base media where the Embryo Plus media uses DMEM/F12. DMEM/F12 has a higher glucose content than TCM199. Another adaption to the San Diego Zoo media was the substitution of horse follicular fluid with lactic acid and MEM amino acids. Factors such as volume of media, number of oocytes cultured together and CO2 percentage during maturation were also evaluated.
Evaluation of nutritive value, in vitro fermentation, and antimethanogenic potential of native South African macroalgae species
(University of Pretoria, 2024-02-12) Du Toit, Lindique; Rothman, Mark; Schonfeldt, H.C. (Hettie Carina); u14077362@tuks.co.za; Van Tonder, Mariska C.
Macroalgae are, as of yet, an untapped source of nutrients as well as a potential means by which to improve the sustainability of ruminant production. In this study the chemical composition and in vitro digestibility of four South African macroalgae, Gelidium pristoides (Rhodophyta), Porphyra sp. (Rhodophyta), Ulva sp. (Chlorophyta), and Ecklonia maxima (Ochrophyta), which were whole, consisting of both the blade and stipe, were determined. The analyses were repeated for four E. maxima samples which were comprised of the blade, the stipe, the whole macroalgae, and an industry by-product. The effect of including the macroalgae samples in two different rations, a total mixed ration (TMR) and Rhodes grass, at inclusion rates of 5%, 10%, 15%, and 20% on a dry matter (DM) basis on in vitro digestibility was determined. The effect of including the macroalgae spamples to the TMR diet at the same inclusion rates on in vitro total gas and methane production was determined at 3, 6, 9, 12, 24, and 48 hours (hrs) of incubation. The E. maxima samples were also assessed for in vitro microbial protein synthesis. The Rhodophyta and Chlorophyta contained the highest concentrations of crude protein (CP), of which Porphyra sp. had the highest concentration at 191.82g Kg-1 DM. Porphyra sp. also had a significantly (P<0.05) lower concentration of total minerals, 180.49g Kg-1 DM, compared to the other species, 263.74-360.45g Kg-1 DM. The most limiting minerals for including macroalgae into animal feeds in this study were sulphur (S) and potassium (K). The latter was the most limiting for Ulva sp., limiting inclusion to 5.68%, the lowest maximum inclusion rate of all species assessed in this study. Gelidium pristoides had the lowest organic matter (OM) digestibility, 39.95%, significantly (P<0.05) lower by at least 44% compared to any other species. The E. maxima blade and stipe samples had significantly (P<0.05) lower digestibilities compared to the whole and by-product samples by approximately 30%. Only G. pristoides significantly (P<0.05) affected the OM digestibility when included with either the TMR or Rhodes grass compared to either control. Gelidium pristoides reduced the OM digestibility of the TMR diet at inclusion rates of 15% and 20% compared to the TMR. The E. maxima blade showed a trend (0.100.70) between inclusion rate and total gas production of the Rhodophyta and Chlorophyta. Ulva sp. significantly (P<0.05) reduced in vitro methane production at a 20% inclusion rate by 25%. With the exception of G. pristoides, the South African macroalgae assessed in this study could hereby potentially serve as valuable sources of nutrients for ruminants. Of the macroalgae species assessed in this study only Ulva sp. significantly (P<0.05) reduced methane production, however due to the high concentrations at which an effect was observed either extraction of active compounds or ash removal would be required to prevent mineral toxicity. Identification of active compounds in Ulva sp. is necessary for a better understanding of its antimethanogenic effects.
The impact of limestone particle size on the digestibility of dietary calcium and phosphorus and phytase efficacy in broilers
(University of Pretoria, 2024-07-22) Jansen van Rensburg, Christine; Plumstead, Peter; andre99sch@gmail.com; Schoeman, Andre Joseph
The major feed ingredients used in broiler feed formulation are deficient in calcium (Ca), therefore Ca is supplemented, predominantly in the form of limestone, to meet the bird’s requirements. Previous research has highlighted several constraints with limestone supplementation relating to intrinsic and extrinsic characteristics that potentially alter the digestibility of Ca from limestone and indirectly the digestibility of phosphorus (P) from the diet. The particle size of limestone is one characteristic that has not been evaluated extensively, and its effects on Ca and P digestibility are inconclusive. The supplementation of phytase enzymes is a common practice in the broiler industry. While several phytase sources are commercially available, their efficacy may differ significantly. Therefore, the objective of the study was to assess the effects of three limestone samples (LS) sourced from the same mine, each with different particle sizes on Ca and P digestibility and their interaction with two phytase sources. The study comprised two experiments. Experiment one consisted of a 3x2 factorial design with three LS (LS1-125 μm, LS2-174 μm, LS3-733 μm) supplemented in treatment (TRT) diets, with or without the inclusion of phytase (0 or 1 000 FTU/kg feed of phytase A (PhyA) – a Buttiauxella spp. phytase). The second experiment consisted of a similar 3x2 factorial design, with each LS supplemented with either PhyA or phytase B (PhyB – an Escherichia coli phytase) at 1 000 FTU/kg feed. On day (d) 18, 528 birds closest to the average flock weight were moved to a metabolism house (six birds/cage) and randomly assigned to dietary TRTs (eight replicates/TRT). On d 21, ileal digesta was collected and the samples were analysed for Ca, P, and chromium (Cr). Data were analysed in RStudio version 13, using a full factorial for each experiment and means were separated using protected least-square means separation (P < 0.05). The inclusion of LS3 in TRT diets, irrespective of phytase, improved (P < 0.05) the apparent ileal digestibility of Ca (AID) from limestone (AIDLimestone Ca) (LS3: 50.17%; LS2: 42.21%; LS1: 38.05%) and P (AID P) (LS3: 58.26%, LS2: 42.69%, LS1: 37.93%) compared to LS2 and LS1. The supplementation of PhyA at 1 000 FTU/kg feed increased (P < 0.05) AID Ca and AID P compared to unsupplemented diets. Differences in phytase source supplementation were evident (P < 0.05) with the supplementation of PhyA resulting in a 14.18% improvement in AIDLimestone Ca and a 15.92% improvement in AID P compared to the inclusion of PhyB. The results from the study emphasise the significant impact of limestone particle size on Ca and P digestibility, favouring larger particle sizes in broiler diets. Furthermore, the study confirmed the importance of phytase supplementation, while underscoring the varying efficacy between phytase sources.
The genomic characterization of the South African Bonsmara using whole-genome sequencing data
(University of Pretoria, 2024-03-19) Van Marle-Koster, Este; Joubert, Fourie; u18049720@tuks.co.za; Alberts, Daniélle
The South African Bonsmara, a Sanga-derived composite breed, originally developed to be genetically composed of five-eighths Afrikaner (Sanga subspecies) and three-eighths Hereford and Shorthorn, is well-adapted to the diverse South African climate. The breed has an open herd book where females are added based on phenotypic inspection of functional traits, having an unknown base composition of the modern-day Bonsmara. In this study, whole genome sequence (WGS) data of 18 founder animals, and 105 modern-day animals were analysed to assess the within-breed variation, inbreeding and admixture of the Bonsmara and its base breeds. Four Afrikaner (AFR), four Bonsmara (BON), and two Hereford (HFD) animals were sequenced as part of the Beef Genomics Project (BGP), whereas the other eight Hereford founder animals were obtained from the European Nucleotide Archive (ENA) at EMBL-EBI. Furthermore, the whole genome sequence data of the 105 modern-day animals representative of current Bonsmara, Afrikaner and Shorthorn (SHH) herds were added. Following standard quality control, using Plink v2.0, a total of 543 791 and 367 764 autosomal single nucleotide polymorphisms were available for downstream analysis for the founder and modern-day animals, respectively. The average heterozygosity values for the founder animals were highest in the HER (0.580), followed by the BON (0.510) and AFR (0.431), with average inbreeding coefficients (FIS) of -0.572, -0.357 and -0.122 for the HFD, BON and AFR, respectively. The average heterozygosity values for the modern-day animals were highest in the BON (0.379), followed by the AFR (0.329) and the SHH (0.305). Moreover, the inbreeding coefficients for the modern-day animals were 0.154, 0.026 and 0.174 for the AFR, BON and SHH, respectively. Genomic structure analysis indicated that the Bonsmara have the most admixed genome, confirming the development of the breed. The genomic structure analysis also unveiled the ancestry shared between the Bonsmara and certain Afrikaner cattle, confirming infusion used by some breeders. Furthermore, it showed a clear separation between the founder animals and the modern-day animals, despite being from the same breed, with ancestry shared between all of the founders. A comprehensive genomic characterization of the Bonsmara and its base breeds with the use of WGS data will aid in detecting genome-level changes in the historic versus modern genetic composition of the breed over time.
Selection signatures associated with adaptation in South African Drakensberger, Tuli, and Nguni beef breeds.
(University of Pretoria, 2024-02-23) Van Marle-Koster, Este; Visser, Carina; u22608053@tuks.co.za; Gomo, Maxman
Climate change has become a major factor influencing beef production systems. Sanga cattle are a unique genetic resource renowned for their adaptability to diverse climatic conditions. The advent of genomic technologies has allowed opportunities to examine these indigenous cattle at the Deoxyribonucleic acid (DNA) level and may provide insight into genome-level variation associated with adaptive traits. This study aimed to identify signatures of selection within and across the South African Drakensberger (DRB), Nguni (NGI), and Tuli (TUL) populations. A total of 1 706 animals, including 1 117 DRB, 377 NGI, and 214 TUL, were genotyped using GeneSeek® Genomic Profiler™ 150K bovine SNP panel. The R (Biscarini et al., 2018) and PLINK v1.90 (Purcell et al., 2007) analysis tools were used to estimate ROH, ROHet and FST values. A set of 122 632 quality-filtered SNPs were utilized to identify genomic regions under selection based on conserved runs of homozygosity (ROH) and FST-based differentiation of SNPs. The ROH were calculated for various length categories, and a total of 82 871 ROH were identified across all three breeds (mean±standard deviation ROH/animal: DRB=51.82±21.01; NGI=36.09±12.82; TUL=47.94±15.33), with a mean length of 3.90Mb, 2.31Mb and 3.76Mb respectively. The short ROH segments (ROH <4Mb) were most frequent in all breeds. The highest average FROH was observed in DRB (0.081±0.046) followed by TUL (0.074±0.031), while the lowest FROH was found in NGI (0.033±0.024). The estimated mean FST valued between 0.060 (DRB vs NGI & DRB vs TUL), and 0.040 (NGI vs TUL). To identify within-breed selection signatures, genomic regions with the highest frequency for ROH and runs of heterozygosity (ROHet) and observed in more than 20% and 30%, respectively, of the individuals in the population were considered selection signatures. For across-breed selection signatures, regions with FST values falling within the top 0.1% of the empirical FST distribution were considered signatures of positive selection. Annotation of these regions revealed genes which have previously been associated with traits of economic importance such as immunity and adaptation (FKBP4, CTNNA2, MYC, CYSTM1, SRA1, SD14, WDPCP, DTX1, ELMO3, and ADAMTS12), coat colour (MCIR, TUBB3), and reproductive performance (SPARTA33, TCF35, RPS20, CORIN, TXK, NELL2, and TMEM181). Both within-breed (ROH) and across-breed (FST) approaches proved to be useful in identifying genomic regions under selection, and this may contribute to the understanding of the genetic architecture underlying the adaptive traits of local Sanga cattle for sustainable beef production in the future.

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