Theses and Dissertations (Animal and Wildlife Sciences)

Permanent URI for this collectionhttp://hdl.handle.net/2263/9669

Browse

Now showing 1 - 20 of 399

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.
Effects of dietary supplementation of condensed tannin and calcium nitrate in total mixed rations on long-chain fatty acid metabolism and carcass characteristics of dohne merino lambs
(University of Pretoria, 2023-10-08) Webb, E.C. (Edward Cottington); Hassen, Abubeker; andyhasewinkel@gmail.com; Hasewinkel, Andrea Joyce
For a methane mitigation strategy to be sustainable it must either have no affect on product quality or have an added cobenefit in terms of improving the quality of meat. This study evaluated the effect of Acacia mearnsii (as a source of condensed tannin) and calcium nitrate used as anti-methanogenic additives on carcass characteristics and meat quality. This study evaluated the effect of 1% urea or 3.2% calcium nitrate (CaN) as a non-protein-nitrogen (NPN) source in a total mixed ration (TMR) with or without the supplementation of 4.2% Acacia mearnsii tannin on carcass characteristics, fatty acid metabolism and hematological parameters of Dhoné Merino lambs. Forty lambs averaging 34.7±4kg were blocked according to weight and sex. Within each block lambs were randomly assigned into one of four treatment groups: Urea-based TMR, Urea-based total mixed ration with tannin, CaN-based TMR and CaN-based total mixed ration with tannin. Two lambs were assigned per pen and each pen was replicated five times. Lambs were adapted to the ration over 21 days. Four ewe lambs from each treatment and four ram lambs from each treatment were randomly assigned to this study and fed beyond 60 days in the trial. On day 61 hematological and serum samples were taken from the jugular vein of those 32 lambs. Lambs were slaughtered between 61 days and 103 days on trial. Four sheep (two ewes and two rams from each treatment group) were slaughtered at a lighter weight (45kg<2n<48kg and 50kg<2n<55kg, respectively) and four sheep (two ewes and two rams from each treatment group) were slaughtered at a heavier weight (48.1kg<2n<51kg and 55.1kg<2n<60kg, respectively). Acacia Mearnsii, a condended tannin supplement (also referred to throught out the dissertation as ‘tannin”) increased the days on trial and decreased the cold carcass weight (CCW) and dressing percent (D%; P<0.005) of lambs. The tannin supplement had no effect on body composition, liveweight (LW), subcutaneous fat depth (SCF; over the 8th and 10th ribs), eye muscle area (EMA), carcass pH or temperature (P>0.05). Although tannin treatment had no effect on the percent of moisture and ash in the longissimus dorsi, there was an increase in the percent of ether extract (EE%; P<0.01). Calcium nitrate did not affect any of these parameters (P<0.05), except for a decrease in D% (P=0.05). The sex of the lambs affected all parameters except for carcass pH and temperature (P>0.05). Ewes took longer to reach their light and heavy slaughter weights than rams (P<0.05). In terms of body composition, ewes increased fatness and decreased muscle and bone percent (P<0.001). In accordance with this, ewes increased SCF depth over the 8th and 11th ribs (P<0.010 and P=0.001). As a result, moisture was higher in rams (P<0.01) and EE% was higher in ewes (P<0.001). Cold carcass weight (CCW) and EMA were greater in rams and D% was higher in ewes (P<0.005). Slaughter weight had no effect on body composition (P<0.05), D%, carcass pH, temperature or days on trial (P>0.05). However, CCW, EMA and SCF depth were greater in heavier lambs (P<0.001 CCW, P<0.05). Between day one and six post slaughter, redness (a*) and Chroma (C) increased in the Longissimus dorsi, regardless of the treatment and sex (P<0.001). Tannin treatment and CaN had no effect on lightness (L*), redness (a*), yellowness (b*) or hue angle (h) on day one (P>0.05). By day six post slaughter CaN had a lower a* (P<0.05). Tannin had no effect on colour on day six (P>0.05). Lightness (L*), a*, b* and C did not differ in the colour of SCF when tannin was supplemented in the diet. Hue angle (h) increased when CaN was supplemented (P<0.05). Ewes had higher L*, a* and C on day one post slaughter (P<0.05) but by day six there was no difference between the sexes (P>0.05). Heavier lambs had an increase in L* and h on day one (P<0.05 and P<0.01, respectively) but by day six there were no differences between the weights for any of the colour parameters (P>0.05). The colour of SCF was not affected by weight (P>0.05), but a* was higher in ewes (P<0.05) and h was higher in rams (P<0.005). Calcium nitrate had no effect on albumin and hematocrit, but it increased cholesterol and blood urea nitrogen (BUN) (P<0.05). The adaption of lambs to the diet was sufficient as there were no morbidities or mortalities during the duration of the trial. The cholesterol was within the South African Mutton merino range published by Akanmu et al. (2020) of between 1.42 and 1.53mmol/L. Tannin did not affect the molar percent (w/w%) or gravimetric concentration (mg/g sample) of total saturated fatty acid (SFA) in subcutaneous fat (SCF), intramuscular fat (IMF), perirenal fat (PRF) and rumen fluid (RF; P>0.05). Monounsaturated fatty acid (MUFA) only decreased gravimetrically in SCF (P<0.05) but not IMF, PRF or rumen fluid (P>0.05). Tannin increased the percent of polyunsaturated fatty acid (PUFA) in SCF and PRF (P<0.05) and increased its gravimetric concentration in IMF and PRF (P<0.05). Tannin increased the PUFA/SFA ratio gravimetrically and as a percent of total fatty acids in IMF, SCF and PRF (P<0.05), apart from the gravimetric concentration in IMF (P>0.05). Fatty acid health indices showed no effect of tannin on the nutritional value of the fatty acid profile of the longissimus dorsi. The gravimetric desirable fatty acids were lower (DFA; P<0.05) due to reduced major fatty acid, C18:0 (P<0.05). Both hypercholesterolaemic (h) and hypocholesterolaemic (H) fatty acids were also lower (P<0.05). A lower gravimetric concentration of fat in the SCF could describe these lower indices (P<0.05). Rumen fluid was analysed for fatty acid composition to get an indication of how the treatments were affecting the microbial activity and biohydrogenation patterns. No affect in the biohydrogenation ratios (P>0.05) suggest that rumen microbes were unaffected by the supplementation of Acacia mearnsii. No affect of Acacia Mearnsii on ezyme indices suggest there was no physiological response to fatty acids within the muscle and fat. Calcium nitrate did not decrease SFA in SCF, IMF or rumen fluid (P>0.05), but CaN did decrease the SFA percent in IMF (P<0.05). Monounsaturated fatty acids increased as a percent in IMF and gravimetrically in PRF (P<0.05). Calcium nitrate did not affect PUFA in any of the fatty acid depots (P<0.05). The PUFA/SFA ratio only increased as a molar percent on IMF (P<0.05). There was no affect on any of the health indices in SCF or PRF (P>0.05). Calcium nitrate deceased the atherogenic and thrombogenic fatty acids in IMF resulting in a lower atherogenic index (AI) and thrombogenic index (TI) index (P<0.05 and P<0.001, respectively). Only the molar percent showed a higher hypocholesterolaemic fatty acid index (h) and lower hypercholestrolaemic fatty acid index (H; P<0.05). The h/H index was better in the CaN based diet (P<0.05). An increase in the delta-9 desaturase index suggests the lower percent and concentration of C18:0 in the CaN based diet (P<0.05). A change in the Vaccenic acid /stearic acid ratio in the rumen fluid of CaN supplemented lambs suggests that the microbes in the last step of biohydrogenation were affected by NPN source. Rams had a lower percent and gravimetric concentration of SFA in IMF and SCF. Monounsaturated fatty acid decreased as a gravimetric concentration in IMF and SCF (P<0.05). Polyunsaturated fatty acid increased as a percent in IMF, SCF and PRF and as a gravimetric concentration in PRF (P<0.05). The PUFA/SFA ratio was higher in all the fatty acid depots (P<0.05). The atherogenic and cholesterolaemic fatty acids decreased AI and H in all fatty acid depot sites (P<0.05). The desirable fatty acid index (DFA) was higher in ewe IMF, lower as a gravimetric concentration in SCF and increased in PRF as a percent (P<0.05). The molar percent h index was higher in IMF and SCF in ewe lambs but lower as a gravimetric concentration in rams (P<0.05). Sex affected the elongase index in IMF and PRF (P<0.05) and delta 9 desaturase activity in IMF, SCF and PRF (P<0.05). Weight did not affect the nutritional value of the fatty acid profile. There were no changes to the SFA, MUFA or PUFA percent or gravimetric concentrations (P>0.05). Of the individual important fatty acids, C16:0 was consistently lower as a percent and gravimetric concentration in lighter lambs in all the fatty acid depot sites. The elongase activity index suggests that elongase may have reduced C16:0 (P<0.05). The health indecis were not affected by weight (P>0.05). Rams were superior in both carcass characteristics and fatty acid profile. Weight affected CCW, EMA, SCF depth and individual fatty acids. This indicated the importance of the date and weight at which ewes and rams are slaughtered. Using condensed tannin and CaN (to reduce methane emissions in lamb) influenced some carcass characteristics and the fatty acid metabolism of lamb. Although tannin increased days on feed and decreased CCW and D%, and CaN decreased D%, overall, they can be recommended for their acceptable fatty acid profile.
Development of guidelines for improvement of reproductive management of smallholder beef cattle in five provinces of South Africa
(University of Pretoria, 2024-02) Van Marle-Koster, Este; Makgahlela, Mahlako Linky; nkadimenglm@gmail.com; Nkadimeng, Marble
Smallholder beef cattle farming in South Africa is characterized as an important free-range farming system with the potential to alleviate poverty and up-lift the economy of rural communities. In this farming system, reproductive performance has been identified as poor with substantial influence on herd growth and profitability. Understanding reproductive performance in smallholder farms in this study required an integrated research approach that first focused on the current farming practices to provide insight into smallholder beef production and constraints, secondly outlining reproductive norms, and finally defining achievable targets and factors associated with reproductive performance to provide guidelines for improvement. A structured questionnaire was used to capture the current beef cattle constraints and herd reproductive management practices. To evaluate reproductive performance, a multilevel-sampling approach was used to identify study sites, beef cattle herds and breeding cows. A total of 3694 cow records were collected from 40 smallholder herds between 2018 and 2019 over two seasons: in Autumn (March to May) for pregnancy diagnosis and in Spring (September to November) for monitoring of confirmed pregnancies. Data on animal and herd management factors such as body condition score (BCS), cow age class, breed type, lactation status, culling non-productive cows, record keeping, and breeding and calving months were recorded to evaluate associations with performance indicators. Farmers demographics showed that the majority of farmers were males over the age of 60 whose farming objective is mainly for sales from informal markets. The major constraints in smallholder beef cattle farms included lack of farming knowledge, understanding of farm business and information communicated by government agencies. The preferred 25th quartile was used to describe the performance benchmark and the GLIMMIX procedure of SAS was utilized to determine animal and management factors influencing reproductive performance. The SAS frequency procedure was used to show average reproductive performance levels. Measures of reproductive performance highlighted that 50% pregnancy rate, 12% fetal and calf loss, extended calving interval (608) and days open (304) currently defines reproductive performance in smallholder farms. However, achievable benchmarks of 54% pregnancy rate, 1.4% fetal and calf loss, days open and calving interval of 152 and 425 days, respectively were established. Poor management practices such as lack of knowledge on body condition scoring prior breeding, culling of old and non-productive cows, record keeping and low bull to cow ratio (p < 0.05) were identified as a standard practice in smallholder farms. Major factors determining reproductive norms included BCS, breed type, breeding and calving months, with breeding month December to March having high likelihood of obtaining pregnant cows and autumn calving season with high fetal and calf loss, extended calving interval and days open. The outcomes of the study were compiled into a set of recommended guidelines for improving reproductive performance in smallholder farms that can be applied by extension and advisory services for improved farm management strategies to enhance reproductive performance in smallholder farms.
Use of lipid encapsulated tannin to replace ionophore in mitigating enteric methane emission and manipulating dietary protein bypass in SA mutton merino sheep
(University of Pretoria, 2024) Hassen, Abubeker; abumubarak480@gmail.com; Ibrahim, Shehu Lurwanu
The significant contribution of the livestock subsector to global warming and dietary energy loss as a result of enteric methane emission has drawn the attention of contemporary ruminant nutritionists to engage in more research to reduce methane production while ensuring viable livestock production. Tannins have been documented to suppress methanogenesis and facilitate dietary protein utilization, though depending on the source of tannin and level of its inclusion in the diet may adversely affect feed consumption and nutrient digestion. The objectives of this study are: to assess the effect of pentanol and ethyl acetate purified Acacia mearnsii tannins on methane, gas and in vitro organic matter digestibility of Eragrostis curvula hay; to evaluate the morphology, density, encapsulation efficiency and tannin release rate of A. mearnsii tannin encapsulated in sunflower and palm oils; to evaluate the capacity of palm and sunflower oils based encapsulated A. mearnsii tannins to bind and release protein in buffers simulating gastrointestinal tract; to determine the effect of various doses of A. mearnsii tannin encapsulated in sunflower oil on methane, gas, in vitro organic matter digestibility, ammonia nitrogen and volatile fatty acids concentrations of total mixed ration and Eragrostis curvula hay; and lastly to evaluate the influence of encapsulated A. mearnsii tannin in sunflower oil on methane, nutrient utilization, growth changes and rumen fermentation characteristics of South African mutton Merino ram lambs. A series of in vitro and/or in vivo experiments were carried out at the Department of Animal Science Nutrition Laboratory and University of Pretoria Experimental Farm, Hatfield, Pretoria, Republic of South Africa to examine the possibility of enhancing dietary tannin utilization as a feed additive in ruminant nutrition by adopting Sheep as a model experimental animal. Tannin purification with pentanol and ethyl acetate improved the proportion of condensed tannin and decreased gas and methane production with slight reduction on digestibility at dose of 30 g/kg feed DM. Moreover, lesser dosage of purified tannin extracts showed similar impact on gas and methane comparable with higher inclusion level of non-purified tannin. Tannin encapsulation with sunflower oil and palm oil exhibited excellent encapsulation efficiencies, smaller particles sizes, lighter in density and delayed tannin release in the gastrointestinal tract simulated buffers compared to unprotected tannin. However, non-encapsulated tannin bound and released more protein in the buffers simulating rumen and abomasum. Whereas, the encapsulated tannin in sunflower and palm oils released more protein in small intestine simulated buffer. Among the two oils, sunflower oil microparticles bound and released more protein than palm oil microcapsules. Addition of encapsulated and non-encapsulated acacia tannin at dose of 20 g/kg feed DM decreased methane and total gas yield without affecting ammonia nitrogen, volatile fatty acids and in vitro organic matter digestibility. Moreover, encapsulated tannin reduced more methane yield compared to equivalent dosage of free tannin. Nevertheless, 30 g/kg feed DM inclusion of encapsulated tannin reduced feed digestibility. In vivo results showed that A. mearnsii tannin encapsulated in sunflower oil at a dose of 20 g/kg feed DM reduced methane emitted by sheep while increasing the intake of dry matter, organic matter and fibre without decreasing the digestibility of dry matter, organic matter and crude protein compared to the unencapsulated tannin and monensin treatments. Feed conversion ratio was unaffected by inclusion of tannins and was comparable to those animal on monensin additive. Thus, supplementation of encapsulated acacia tannin at the dose of 20 g/kg feed DM could be adopted as safer natural alternative and eco-friendly approach of ruminant animal production to replace the use of ionophore.
Selection signatures in geographically separated Hereford populations
(University of Pretoria, 2023-08-30) Van Marle-Koster, Este; chantellec31399@gmail.com; Croucamp, Chantelle
Genomic differences between geographically separated Hereford populations may be characterised by using genomic diversity parameters, providing insight into different genes responsible for variation in traits of economic importance and adaptability to each population’s relevant production environment. This study aimed to develop a better understanding of the local adaptation and selection of South African, Irish, Uruguayan, and New Zealand Hereford populations in their respective environments. A total of 1 538 individuals for the four populations remained after quality control for further downstream data analyses. Descriptive genomic diversity parameters were estimated as HE, HO, FIS, MAF, and LD using PLINK v 1.9. All populations showed a moderate level of heterozygosity with HE values ranging from 0.359 to 0.391, and HO values ranging from 0.352 to 0.388. FIS values were -0.00475 to 0.0189 with MAF values ranging from 0.24 to 0.29 and LD ranging from 0.41 to 0.70. Population structure was visualised through principal component analysis. Each population showed to have a distinct cluster with some overlap between clusters. Intra-population genomic relatedness was determined through ROH. The detectRUNS package was used in R and a consecutive runs method was applied. The Irish and New Zealand populations showed to have the lowest degree of intra-population relatedness. A high level of genetic differentiation was observed in all populations. Selection signatures and candidate genes were identified using ROH for an intra-population approach and Pairwise Wright’s FST for an inter-population approach. Most notably, intra-population candidate genes related to traits of adaptation where the KDR and KIT genes were identified. Inter-population comparisons revealed 60 candidate genes related to traits of adaptation, production, and quality. The most common trait identified was that of bovine respiratory disease susceptibility. Five candidate genes, namely ARL6, ENOPH1, PPARGC1A, SCD5, and SNCA, were found to overlap between four of the six inter-population comparisons. Production and quality-related traits aligned with the breeding objectives of each population. The candidate genes related to adaptability traits showed that each population is adapted to its environment. Overall, each population showed to be genomically diverse and adapted to its geographically separated production region.
The assessment of the genetic improvement of South African composite breeds and their respective foundation breeds
(University of Pretoria, 2023) Van Marle-Koster, Este; Lashmar, Simon Federick; u21771970@tuks.co.za; Sithole, Phillipine
South Africa (SA) has a diverse climate that poses potential challenges for future beef production. Different composite breeds that combine the superior growth and beef-producing potential of the European Bos taurus breeds with the adaptive traits of Bos taurus africanus and Bos indicus breeds have been well established over the past century. Even though composite breeds have been used extensively in SA livestock production, research efforts focusing on these breeds have been sparse. The aim of this study was to utilize phenotypic and genotypic data to characterize the genetic status of three SA composite beef breeds (Braford, Santa Gertrudis, and Simbra) in comparison to their selected founder breeds namely, Brahman and Simmentaler. The phenotypic data for the different breeds consisted of pedigree data from the establishment of the herdbook (1957 – 1997) up to 2020. Based on PopReport analysis pedigree completeness (PIC) between composite breeds over six generations was higher than 90% and across breeds PIC in the six-generation depth varied from 24.90% for the Braford to 88.00% for both the Simmentaler and Brahman breed. The average inbreeding coefficient per year was low across all the breeds ranging from 0.011% (Braford) to 0.054% (Simmentaler). The effective population size (Ne) across the breeds varied from 152 in the Santa Gertrudis breed to 750 in the Braford breed respectively. The average genetic change calculated by averaging the estimated breeding values (EBVs) from 2000 to 2020 was investigated for reproduction, growth, and carcass traits. Genetic trends for reproductive trends were favorable in all the breeds varying from -0.088 in days to calving (DC) to +0.020 in scrotal circumference (SC) trait. The Santa Gertrudis breed had a slightly higher birth weight (BW) compared to the Braford and Simbra breeds. Across the breeds, the overall genetic trends for growth traits varied from +0.007 (BW) in the Simmentaler to +0.737 (MCW) in the Simbra breed. Carcass weight (CW) based on real-time ultrasonic records (RTU) across the breeds ranged from 9.80 kg in the Braford breed to 19.12 kg in the Brahman breed in 2020. A total of 5 210 (Illumina® Bovine 7K) and 103 646 (Genomic ProfilerTM Bovine 150K SNP) SNPs after quality control (QC) were available for genomic analysis. Results of the study across the breeds indicated that the Simbra breed had the highest level of genetic diversity (HO = 0.427; 0.413) for both panels and the Brahman had the lowest level of genetic diversity (HO = 0.291; 0.016). Principal component analysis (PCA) and model-based clustering algorithms distinguished the breeds according to their ancestral origin with the Santa Gertrudis animals clustered separate from the other breeds. Admixture analysis revealed that the Simbra is a composite breed composed of 58.1% (Simmentaler) and 26.4% (Brahman) genetic composition. The estimated Ne in the last 12 generations ago across the breeds ranged from 215 (Santa Gertrudis) to 316 (Simmentaler) indicating a higher risk of inbreeding for the Santa Gertrudis if not managed carefully. The results of the study indicated genetic improvement in composite breeds compared to its selected founder breeds over the years, indicating that these breeds have the potential for sustainable beef production in both commercial and non-commercial beef production systems.
Characterisation of muscle calpain system SNPs and associations with production and beef quality traits in South African beef cattle following electrical stimulation and extended ageing
(University of Pretoria, 2023) Webb, E.C. (Edward Cottington); Frylinck, L.; Strydom, P.E. (Phillip Evert); veefluisteraar@gmail.com; Basson, Annie
The genes of the muscle calpain system are the most important genes that affect beef tenderness and research on associations of these genotypes with beef quality traits in South African beef cattle is limited. Beef quality traits often have a large environmental component and it is important to minimize environmental biases for accurate analyses, while shorter distances between single nucleotide polymorphisms (SNPs) enable the identification of more informative variants across breeds. We therefore used the Illumina BovineHD (777K) SNP array to genotype bulls from five selected South African purebred beef breeds (Angus, Bonsmara, Brahman, Charolais and Nguni) for the capn1, capn2, capn3 and cast genes. Detailed carcass and beef quality traits were determined, while maintaining a constant environment for finishing, carcass handling and sample analyses. Characterization of the calpain system genes revealed a high proportion of alleles favourable for tenderness in Bonsmara cattle (originally a Sanga-type composite) and an opportunity to improve the average frequency of tender alleles in Nguni cattle (Sanga, Bos taurus africanus). Extensive linkage was identified in the cast and capn2 genes with regions of high linkage disequilibrium between breeds. This presents an opportunity for across-breed selection for candidate SNPs in overlapping haplotype blocks. The identification of candidate SNPs with mixed model association analyses (GCTA software) identified 62 putative associations with Warner-Bratzler shear force (WBSF) or myofibril fragment length (MFL), while only six of these SNPs (especially in the cast and capn2 genes) affected these tenderness phenotypes over extended meat ageing periods. Most candidate SNPs (>80% of associations) affected certain stages of the meat ageing period and were unable to sustain the genetic effect over the entire meat ageing period of 20 days, confirming that the altered physiological mechanisms of extended aging are subject to effects from different genetic markers. Several quantitative trait nucleotides (QTNs) were identified in both the non-electrically stimulated (NS) and the electrically stimulated (ES) treatment groups using a different mixed model approach, more suited to these data (GAPIT package in R software). Associations of SNPs with tenderization, estimated by MFL at various stages of meat ageing, were closely linked to associations of SNPs with decreased calpastatin inhibitory effects on proteases (in linkage blocks). All four genes of the calpain system contained QTNs for calpastatin inhibition of proteases (ten in total) and the tenderizing effects of the SNPs in these genes were primarily found for MFL, where 13 QTNs were identified in both control and ES groups, with some SNPs sustaining effects for extended meat ageing periods. The effects of electrical stimulation on SNP associations with traits failed to demonstrate a universal effect across SNPs or traits. Although many SNP effects were only slightly affected by treatment, other SNP effects were observed in only one of the treatment groups, where electrical stimulation either enhanced or eliminated genetic associations. Novel QTNs for intermediary energy metabolism were identified, with four of these SNPs located in the capn2 gene that could explain previous data linking pH to these genes. This provides the link between calpain protease activity (through energy metabolic pathways) and pH decline that will favour sarcoplasmic Ca2+ release, facilitating more rapid tenderization. These results validate the SNPs of the calpain-calpastatin system for selection to improve myofibril fragmentation in South African beef bulls and highlight the importance of tenderizing interventions, when determining genomic associations. Furthermore, these data confirmed the complex effects of calpain protease activity in cellular homeostasis that can also alter metabolic processes, though pleiotropic effects of these genetic markers.
A landscape genomic approach to investigating growth performance in South African Bonsmara cattle
(University of Pretoria, 2023) Van Marle-Koster, Este; Visser, Carina; charnevisser00@gmail.com; Visser, Charné
This study utilized a landscape genomic approach to investigate growth performance in Bonsmara cows from three South African provinces, Eastern Cape, Free State and North-West. Landscape genomics seeks to investigate potential associations between the genotype of an animal and a specific environment. Genotype and phenotypic growth trait data from 4679 Bonsmara cattle were obtained for analysis. The cattle were grouped according to province, ownership, population size per province, and sex. After editing and pruning, the final list of animals included 766 cows from the Eastern Cape (418), Free State (224), and North-West (124) provinces. The genotypic data originated from four SNP array panels; GGP 80k (GeneSeek Genomic Profiler™), GGP 150k (GeneSeek Genomic Profiler™), IDB version 3 (International Beef and Dairy), and VersaSNP 50k (Weatherbys Scientific). The common SNPs across these panels were identified and quality control was conducted with PLINK software; 25272 SNPs remained for downstream analysis. The population structure of the cows was analyzed through PCA plots and admixture plots, using GCTA64 and ADMIXTURE software respectively. Weather data for the three provinces included summer and winter month temperatures, relative humidity, and average annual precipitation, from 2016 to 2021. Landscape genomics analysis was conducted on the weather variables and the 25272 common SNPs, using the latent factor mixed model (LFMM) landscape ecology association (LEA) software package in RStudio. The output results consisted of candidate loci that the LEA identified to be associated with the environmental variables included in the weather datasets. The Fst values for each candidate loci list (three lists in total; one per province) were calculated and the 20 SNPs (20 SNPs per candidate loci list; 60 SNPs in total) with the highest values were chosen for gene annotation. The objective of gene annotation was to determine if any of the associated genes were linked to growth performance in cattle. Nine out of the 60 annotated SNPs were found to be associated with genes that had previously been reported in cattle and linked to growth performance. A genome wide association study (GWAS) was also conducted to identify candidate loci associated with eighteen-month weight (18MW) phenotypes. The GWAS was conducted using PLINK and the results were plotted on Manhattan Plots using RStudio software packages. The GWAS results were used comparatively to the candidate loci results from the LEA analysis. There were no commonly associated loci identified between the GWAS and the LEA. Further studies on larger and more informative data sets will be needed for confirmation of the LEA results.
Profiling the determinants of food insecurity in households keeping livestock in the Limpopo province
(University of Pretoria, 2023) Van Marle-Koster, Este; Schonfeldt, H.C. (Hettie Carina); mamphasha.mdaka@up.ac.za; Mdaka, Mamphasha Phina
South African smallholder farmers help reduce rural poverty and famine. Smallholder farmers in remote places have several obstacles that limit their growth and food security contributions compared to commercial farmers. Land, funds, infrastructure, and markets are some of these obstacles. About 50 to 80% of rural South African households face food insecurity. Households keeping livestock were also included in the definition of smallholder farmers based on economic variables, thus, the study examined livestock-keeping households' food availability. The study analysed data from 600 families in Limpopo's Capricorn, Mopani, Sekhukhune, Vhembe, and Waterberg districts. To achieve each objective, House Dietary Diversity Score and Household Food Insecurity Access Scale scores were used to assess food insecurity. Food insecure households were characterized using a 2-step cluster analysis, Analysis of Variance, and t-tests. Multilinear regression determined household food insecurity factors. Food security indicators for the Province of Limpopo were calculated using data collected from a sample of 301 households (those who kept livestock and poultry). The results in this study shows that in Sekhukhune District, a greater proportion of households are food secure compared to other districts, whereas in Waterberg District, a greater proportion of households are food insecure. Only 29.3 % of residents in Fetakgomo, a municipality in the district of Sekhukhune, are food secure. Yet, in Mookgopong, a municipality in the Waterberg district, only 10.3% of households appear to be food secure. Moreover, it is demonstrated that 67.2% of households in Mookgopong are highly food insecure. A municipality in the Mopani district, Maruleng, also has a significant proportion of severely food insecure households (65%). The majority of livestock smallholders depend on animals for food and revenue. However, lack of land, funding, and infrastructure hampers livestock smallholder expansion in Limpopo province. Thus, the department of agriculture and other government and non-government organization initiatives must create and implement programs to provide smallholder farmers with facilities, advanced technology, land, and other livestock outputs.
The prevalence of high rigor mortis temperature beef carcasses at abattoirs across South Africa
(University of Pretoria, 2022) Webb, E.C. (Edward Cottington); Hope-Jones, Michelle; jasminemasemola29@gmail.com; Masemola, Nthabiseng Innocentia
High rigor mortis temperature carcass conditions occur when the pH drops below 6.0 while the temperature is still above 35ﹾC. The aim of this research was to find out if there is an increase in the prevalence of high rigor mortis temperature carcasses in abattoirs across South Africa (SA). With the increase in the production of larger and heavier carcasses in the SA beef industry, it is essential to investigate the factors that might contribute to the increased occurrence of carcass conditions that might affect the supply of beef of consistent quality to consumers. A total of 12 abattoirs, across most of the 9 provinces of SA, were visited. The pH and temperature readings (at 1 hour and 2 hours post mortem) were taken on a total of 180 carcasses (90 per day) over a period of 2 days per abattoir. The beef carcasses were from both grain fed and grass-fed cattle, with additional data collected being whether the abattoir makes use of electrical stimulation (ES) or not, the cold and warm carcass weight, the age, and the fat code and the use of beta-agonists. The temperature at pH6 was measured to check for the proportion of carcasses with high rigor mortis temperature conditions. The frequency of occurrence of high rigor temperature carcasses across the 12 abattoirs was 65.64 %, with most of these carcasses falling under the weight category of 200-300 kg (40.09%). Carcass weight had an effect on the occurrence of rigor at a high temperature (p< 0.001) with an increase in carcass weight leading to an increase in the occurrence. The carcasses that went into rigor mortis at a high temperature, had an average weight of 283kg, while those at risk of going into rigor at high temperature had an average weight of 251kg. The group that did not go into rigor at high mortis temperature, had an average weight of 242kg. In general, it can therefore be said that carcasses that have a weight of over 250kg, are likely to go into rigor mortis at high temperatures. There was a significant effect of age and fat code on the incidence of high rigor (p<0.001 for both). The incidence of occurrence of high rigor temperature increased with an increase in fat code and increase in age. It must be noted however that the majority of the carcasses were fat code 2 and A age carcasses (the data was therefore skewed), which is what the majority of the SA abattoirs produce in terms of their carcasses. The use of beta-agonists (leading to an increase in carcass weight) and the use of ES on heavier carcasses, contribute towards the occurrence of high rigor temperature. Most abattoirs if not all in SA, make use of ES, hence it will be a requirement to manage the duration and timing of the ES correctly. The chiller rooms will also need to be re-adjusted and updated to accommodate the heavier carcasses produced in today’s market so that adequate chilling of the carcasses occurs.
Bromelain as a feed additive to promote broiler performance, nutrient digestibility and health
(University of Pretoria, 2023) Jansen van Rensburg, Christine; u17018308@tuks.co.za; Sarrimanolis, Emmanuela
The broiler industry faces a growing pressure to reduce antibiotic growth promotors (AGP) from broiler feed due to public concern and the threat of antibiotic resistance. This has caused an upsurge in studies relating to natural alternatives to antibiotic growth promoters. Some such alternatives are exogenous proteases, which improves the digestibility of dietary protein. Bromelain, a natural protease found in pineapple, may be beneficial in livestock, however, there exists little literature on the effect of bromelain on broiler production specifically. This study aimed at determining the effects of supplementation of bromelain on broiler health and performance. Two trials were conducted: a performance trial and a digestibility trial. The performance trial was carried out to determine whether bromelain supplementation would improve broiler gut health and therefore broiler growth and performance. The aim of the digestibility trial was to determine whether bromelain supplementation would have any effect on the crude protein and dry matter digestibility of feed. Two-thousand four hundred male Ross 308 chicks were used in the performance trial and were reared in standard commercial conditions. All birds received a standard maize-soya based diet and were separated into 12 treatments of a combination of three levels of bromelain (0, 0.125, 0.75 g/kg), two levels of crude protein (standard or high) and either in the presence or absence of an AGP (zinc bacitracin) and there were 8 replicates per treatment. The trial lasted 34 days and birds were weighed weekly to determine body weight, body weight gain, feed intake and feed conversion ratio. On day 34, duodenum, jejunum and ileal samples of 16 birds from each treatment were analysed for villi height, crypt depth and villus height-to-crypt depth ratio. Bromelain had a significant effect on intestinal crypt depth, where a high level of bromelain lead to a lower crypt depth. Birds that received a standard crude protein diet without an AGP performed the best, and birds that received an AGP showed shorter villi and crypt depths. Bromelain did not have a significant effect on body weight, feed intake or FCR. For the digestibility trial, Ross 308 chicks were reared in floor pens receiving the same maize-soya based diet. On day 14, 180 birds with a body weight closest to the average were transferred to 30 metabolic cages with six birds per cage. From day 15 to 21, the birds received either a negative control diet, a diet supplemented with bromelain, or a diet supplemented with a commercially available protease that served as a positive control. On day 21, all birds were euthanised and ileal digesta was removed and analysed. Neither bromelain, nor the commercial protease product improved crude protein digestibility compared to the negative control. However, both bromelain and iii the commercial protease significantly increased dry matter digestibility, compared to the control. This study found that the performance and gut morphology of the birds that received supplemental bromelain was not significantly better than birds that did not receive supplemental bromelain, even though dry matter digestibility was improved. Thus, there might be room for bromelain in poultry production as it was seen to improve digestibility and gut health in this trial. Its benefits could perhaps be more attainable in different conditions, for example if a larger gut challenge was presented.
Effect of extraction solvents and encapsulation on the efficacy of certain medicinal plant extracts to inhibit enteric methane emission
(University of Pretoria, 2023) Hassen, Abubeker; u17328812@tuks.co.za; Ibrahim, Taofik Adam
A series of in vitro and in vivo experiments were conducted to evaluate the antimethanogenic properties of four medicinal plants (Aloe vera, Jatropha curcas, Moringa oleifera, and Piper betle) extracts as alternative rumen modifiers to antibiotics to modulate rumen fermentation and inhibit methane production. In the first study, two solvents (methanol and water) were used in three different combinations (70, 85, and 100%) to extract bioactive compounds from the four studied medicinal plants as some of their metabolites have been reported to possess rumen modulation properties and improve nutrient utilization in ruminants, thereby reducing enteric methane emission per unit of animal product. The extracts were evaluated at 50 mg kg-1 DM feed as an additive to Eragrostis curvula hay substrate in vitro. Results showed an increase in extract yields with increasing water content in the extraction solvents. The effect of extraction solvents was also observed in the concentration of the bioactive compounds in each plant extract when analysed with UPLC-MS, these plant bioactive compounds showed different solubility values. Subsequently, promising plant extracts were selected based on yield and methane inhibition potentials for subsequent encapsulation with alginate as wall material. The encapsulated products were scanned using electron microscope for morphological characterisation and later their methane inhibition attributes were investigated using both in vitro and in vivo studies. The particle characterization of the encapsulated extracts was carried out using a scanning electron microscope (SEM) and images were generated for a morphological study. Gas measurements were taken at regular intervals of 3, 6, 12, 24, and 48 h during the incubation period. Methane emission was determined for each gas sample with the use of gas chromatography. During the first phase of the in vitro study, the plant extract treatments were incubated with feed samples to test their methane inhibition potentials, their effect on total gas production (TGP), and their organic matter digestibility (IVOMD). In the second phase of the in vitro study, Aloe vera and Moringa oleifera extracts were encapsulated with alginate and/or alginate-chitosan wall materials and the final product is incubated with feed samples to evaluate their methane inhibition potentials, their effect on TGP, and IVOMD. The results from the first in vitro study indicated that the four plant extracts from three aqueous-methanol extractions (70%, 85%, and 100%) generally reduced methane emission in different proportions at 50 mg kg-1 DM without adversely affecting TGP and IVOMD of E. curvula hay. However, the methane inhibition potentials of the tested plant extracts were not influenced by the extraction solvents. For the second in vitro study, alginate encapsulated and alginate-chitosan encapsulated plant extracts were also tested together with non-encapsulated plant extracts on E. curvula hay and also reduced methane production. Higher methane inhibitions were noted for the alginate encapsulated and alginate-chitosan encapsulated extracts as against the non-encapsulated extracts, without negatively affecting the TGP and IVOMD. Finally, encapsulated M. oleifera plant extract was selected for in vivo evaluation to determine its effect on enteric methane production, rumen fermentation parameters, growth performance, feed intake, apparent digestibility, and nutrient utilization of South African Mutton Merino (SAMM) lamb. A total of thirty (30) SAMM lambs were first ranked according to their body weight and divided into three groups with approximately equal body weight measurements. The three treatment groups were randomly allotted to one of the three treatments (two plant extract treatments and control). The plant extract treatments included non-encapsulated M. oleifera extract (NME) and encapsulated M. oleifera extract (EME) additives. These additives were provided to the lambs at 50 mg kg-1 feed DM intake by incorporating them into a ball-like molasses mix and presented at 7:30 am daily to the experimental lambs. All treatments were placed on the same total mixed ration formulated with a 42% roughage component. The growth performance study lasted for 14 weeks, including adaptation, and the feed digestibility study lasted for 14 days. The lambs were moved into the open circuit respiratory chambers for methane emission measurements in six batches. The methane emission measurements and digestibility study were done concurrently with the growth performance study. For the in vivo study, both the NME and EME reduced (p < 0.05) enteric methane emission by approximately 22.61% and 20.06%, respectively; reduced rumen ammonia nitrogen (NH3-N), urinary nitrogen excretion and feed conversion ratio but increased nitrogen retained as a percentage of intake without adverse effect on nutrient intake, apparent digestibility, and performance of SAMM lambs. Supplementation of SAMM lambs with NME and EME as dietary additives did not affect the rumen fermentation parameters. The alginate encapsulation of MO plant extract is safe and did not reduce the efficacy of MO plant extracts compared to non-encapsulated plant extracts, and is therefore recommended for practical use as antimethanogenic dietary additives in the feeding system of ruminant animals. Further study needs to be conducted to determine the effect of alginate encapsulated MO plant extracts on the rumen microbial populations and meat quality of the lambs. Also, other wall materials that can act as good carriers of active compounds in rumen medium should be evaluated for methane inhibition in livestock production.
Influence of accessions, metabolite ion features, storage and processing conditions on efficacy of Moringa plant extracts to inhibit enteric methane emission
(University of Pretoria, 2023) Hassen, Abubeker; Apostolides, Zeno; Tjelele, Julius; u17408017@tuks.co.za; Zeru, Addisu Endalew
Developing healthier and more practically applicable intervention strategies for methane (CH4) inhibition emitted from ruminants has been a priority issue globally. Among the strategies, the use of natural medicinal plants containing bioactive secondary plant metabolites (SPMs) is increasing owing to the cost-effectiveness, environmental suitability and safety value of producing healthy organic animal products of the interventions. Since multiple complex factors affect their bioactive SPMs and bioactivities, the study of wider influencing factors of the extract activities may probably increase the efficacy and sustainability of the final products during application. Thus, this study was initiated i) to investigate the relationships of agronomic traits and SPMs of Moringa accessions with in vitro gas production characteristics from ruminants, ii) to identify potential bioactive SPMs ion features responsible for high and low CH4 inhibition from ruminants, iii) to investigate the effectiveness of varying proportions of binary Moringa accession extract cocktails on in vitro CH4 inhibition, and iv) to evaluate the effects of postharvest processing and storage conditions on the efficacy of Moringa extracts to inhibit enteric CH4 production from ruminants. For the study, twelve Moringa accessions were raised at the University of Pretoria and transplanted in the field at the Roodeplaat experimental site of the ARC in Pretoria, South Africa. The leaf samples from individual plants from these accessions were harvested in the fifth month of transplanting to the field. Then, a series of studies were conducted to develop Moringa leaf extract products that were effective and consistent when used as additives for mitigating enteric CH4 emission in ruminants. In the study that investigated the relationships of agronomic traits of Moringa accessions with in vitro gas production characteristics, most of the agronomic traits, total flavonoids and total phenolics varied among these accessions of M. oleifera. All accessions reduced the total gas (TGP) and CH4 volume compared with the control, incubated without Moringa plant extracts. Hence, among the twelve accessions, those designated A3 (7633), A8 (7717) and A11 (Pretoria) exhibited superior in vitro antimethanogenesis and organic matter digestibility (OMD) with equivalent or superior performances in adaptability in the field. The subsequent study was aimed at identifying potential bioactive secondary plant metabolite ion features responsible for high and low CH4 inhibition from ruminants. In this study, the m/z ion features (MIFs) 4.44_609.1462 and 4.53_433.1112 were linked with higher CH4 inhibition, whereas the MIF 9.06_443.2317 and MIF 15.00_487.2319 were linked with lower CH4 inhibition. The secondary MIFs associated with higher CH4 inhibition can be considered potential secondary MIFs markers for the standardization of plant extracts and commercialization of Moringa varieties that provide extracts effective in antimethanogenic activity from ruminants. In another study, the effectiveness of varying proportions of binary Moringa accession extract cocktails of the two highest CH4-inhibiting accessions was investigated for their effect on in vitro fermentation parameters and CH4 inhibition. The cocktails were prepared by mixing the selected accessions extracts after freeze-drying, milling, and extracting with methanol as 100:0, 80:20, 60:40, 50:50, 40:60, 20:80, and 0:100 proportions (A3:A11) and applied to anaerobically incubated E. curvula hay with 50 mg extract per kg substrate. Thus, the application of Moringa accession extracts in the form of cocktails provided better inhibition of CH4 with comparable or greater in vitro organic matter digestibility (IVOMD) of the substrate feed compared with those values recorded for single Moringa accessions. Thus, a cocktail of A350A1150 showed favourable associative effects on propionate, CH4 inhibition, total volatile fatty acids (TVFA), CH4/TVFA and acetate to propionate ratio (C2/C3), whereas A360A1140 exhibited associative effects on TVFA, acetate, and CH4/TVFA. Thus, the binary combination of the two selected M. oleifera accession extracts at 50% mix exhibited higher benefits of antimethanogenesis and propionate production with a decrease in C2/C3 ratio than when were used the two Moringa accessions in a single form or other cocktails were mixed in various proportions. In the last study, the effects of various postharvest processing and storage conditions were evaluated for their effect on the efficacy of M. oleifera extract to inhibit CH4 production from ruminants. The studied postharvest factors include drying methods (sun, freeze, oven, and shade), drying temperatures (25, 45, 60, and 80 °C), extraction solvents (absolute methanol, 70% methanol, 70% ethanol, and 70% acetone), storage temperatures (4, 15, 25, and 35 °C) and storage light conditions (light and dark). The TGP, CH4 inhibition, total phenolics and total flavonoids differed significantly among the drying methods, drying temperatures and extraction solvents. The freeze- and sun-drying methods compared with shade- and oven-drying methods, drying temperatures of 25 °C and 45 °C compared with 60 °C and 80 °C, and 70% acetone among the extraction solvents recorded higher total phenolics and total flavonoids with better antimethanogenic activities. Storage temperatures of 4 °C and 15 °C also maintained higher total phenolics, total flavonoids and IVOMD with lower CH4/TGP and CH4/IVOMD than those recorded at 25 °C and 35 °C of storage. Dark storage showed lower TGP and CH4 production with better total phenolics, total flavonoids and IVOMD than light storage. Hence, among the postharvest factors, freeze-drying methods, drying temperature of 45 °C, 70% acetone, the storage temperature of 4 °C and dark storage conditions were preferable processing and storage conditions to maintain higher antimethanogenesis, total phenolics and total flavonoids with equal or improved IVOMD from the Moringa plant extract products. The variation recorded among these Moringa accessions when grown in the same environment in terms of SPMs, agronomic performances, and different in vitro fermentation parameters generally indicate the presence of wider genetic sources among Moringa varieties. These could in turn show that superior accessions can be further improved to develop commercial varieties suitable as a source of plant extract products that can be used for mitigating enteric CH4 production. The total phenolics, total flavonoids and the subsequent antimethanogenic activities are influenced crucially by the various postharvest treatments of Moringa leaf/powder. This infers the need for the establishment of appropriate postharvest processing methods, storage conditions and time for a specific purpose and application to utilize optimally Moringa as a dietary additive effectively throughout the year to inhibit CH4 emission from ruminants. However, further investigations are needed on the relationship of agronomic traits with gas production characteristics using long-term adaptability performance at different agro-ecologies, stages of plant growth, plant density, season of harvesting and parts of the plant. The identified MIFs as potential candidates for higher and lower CH4 inhibition of Moringa accessions needed to be studied for their pathways and mode of action. The different organic solvents with various extraction aqueous levels and each storage temperature for longer storage periods at various time points to fix a cut-off storage time for each storage temperature need also be conducted in the future. Keywords: agronomic traits; acetate to propionate ratio; drying methods; drying temperatures; extraction solvents; in vitro organic matter digestibility; storage light; total flavonoids; total gas; phenolics

Browse

Recent Submissions