Doctoral Degrees (Animal, Wildlife and Grassland Sciences)
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Browsing Doctoral Degrees (Animal, Wildlife and Grassland Sciences) by Author "Cloete, S. W. P."
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Item Open Access Comparison of genetic and immunological responses to tick infestation between three breeds of sheep in South Africa(University of the Free State, 2016) Thutwa, Ketshephaone; Van Wyk, J. B.; Cloete, S. W. P.; Dzama, K.𝑬𝒏𝒈𝒍𝒊𝒔𝒉 The study investigated genetic parameters and immunological responses to tick infestation in three South African sheep breeds (Namaqua Afrikaner [NA], Dorper and SA Mutton Merino [SAMM]). The study aimed to estimate genetic and crossbreeding parameters for tick count (TC) and weaning weight (WW), to examine the histology of tick attachment and control sites, to select reference genes for normalizing gene expression data in this study, to compare cytokines gene expression at tick attachment and control sites and finally to compare cutaneous hypersensitivity reactions to unfed larvae extracts (ULE) of Rhipicephalus evertsi evertsi between NA, Dorper and SAMM sheep. Genetic parameters for WW and TC were estimated using data of lambs maintained on the Nortier Research Farm from 2010 to 2015. Firstly, data of purebred commercial Dorper and SAMM lambs were combined with data of their reciprocal crosses to assess breed effects and the possible effect of non-additive genetic variation on WW and TC. In the second analysis, data of purebred commercial Dorper lambs were combined with data of the unimproved, indigenous NA and the NA x Dorper cross. In Analysis 1 the coefficient of variations (CV) were 24%, 95% and 50% for WW, untransformed total TC and square root transformed total TC, respectively. Genotype affected WW but not TC. A heterosis estimate of approximately 4% was derived for WW. A single-trait h² estimate for TC was 0.11±0.09. A model analysing across-genotype h² yielded a slightly lower h² estimate of 0.08 ± 0.07. In Analysis 2 the CV were 27% and 55% for WW and square root transformed total TC, respectively. WW and TC were affected by genotype. WW exhibited heterosis amounting to 8.5% while the corresponding value for TC amounted to -23%. The single-trait h² estimate for TC was 0.06±0.05. A model analysing across-genotype h² yielded a substantially higher h² estimate of 0.27±0.07. These results suggest that genetic variation in TC was primarily associated with differences among genetic groups while differences between individual animals within genetic groups were not as important. Heterosis estimates for WW were variable between two analyses, but within ranges reported in the literature. This study established significant variation in TC between sheep genotypes when the indigenous NA breed formed part of the analysis. The NA x Dorper cross resembled the improved Dorper breed for WW but the unimproved, resistant NA for TC and exhibited worthwhile levels of heterosis for both traits. Indigenous ovine genetic resources may be instrumental in providing genetic material for adaptive traits in environments susceptible to high levels of tick infestation. Further research is required to elucidate the role that adapted indigenous ovine genetic resources may play in an integrated tick management strategy under conditions characterised by high levels of tick challenge. A histological study was conducted to assess histological features at tick attachment and control sites in pure breeds. Skin biopsies were examined using routine histological techniques for immunological cell infiltration and skin reactions. Marked variation in immunological responses to tick attachment within and between sheep breeds was observed. There were differences between the attachment and control sites in most of the skin changes (defects) except for four skin defects in the NA. However, all breeds had similar frequencies of skin defects at tick attachment sites. Tick attachment sites were more likely to be infiltrated by cells within as well as across breeds. The NA and SAMM breeds tended to demonstrate greater cellular infiltrations of specific leukocytes at tick attachment sites compared to Dorpers. Basophils, mast cells and eosinophils were increasingly recruited at tick attachment site in NA ewes compared to the Dorper and, occasionally, the SAMM breeds. These results suggest the importance of these cells in sheep resistance to tick infestation. Tick genera influenced the recruitment of neutrophils to tick attachment sites. Tick gender, sampling site as well as tick engorgement level did not affect the number of immunological cells. Further studies should be done with one tick species at a time to better comprehend the species-specific impact of tick attachment to animals belonging to divergent sheep breeds. Five genes (18S, GAPDH, YWHAZ, B2M and SDHA) were tested for their stability. SDHA, YWHAZ and B2M were the most suitable reference genes recommended by geNorm analysis for normalizing gene expression data in sheep skin. These findings will assist in normalizing data in gene expression studies at tick attachment and control sites of the NA, Dorper and SAMM breeds. This study suggested that no reference gene is stably expressed in different experimental conditions. The expression of IL-1β, IL-8, CCL2 and CCL26 was quantified in real-time qPCR. IL-1β and IL-8 were more highly expressed at tick attachment than at control sites. NA ewes expressed IL-1β more at tick attachment sites than Dorpers. The NA breed was also more likely to upregulate the expression of the CCL2, CCL26 and IL-8 genes at tick attachment sites compared to control sites than the other breeds. This indicates that IL-1 β, CCL26 and IL-8 may play a part in resistance or susceptibility of sheep to tick infestation. The differences in expression of the two chemokines between the resistant NA and more susceptible SAMM and Dorper imply that the NA breed could be able to overcome the anti-chemokine activity of tick saliva. ULE of R. evertsi evertsi induced hypersensitivity reactions in all the breeds. The indigenous NA displayed stronger reactions, immediate and delayed, than the commercial breeds. The results suggest that cell-mediated immune responses are invoked to fight against tick infestation in the NA. The hypersensitivity reaction may be used as a phenotypic marker to select animals or breeds that are more resistant to tick infestation. It is well-known that challenge-based research for promoting resistance to pathogens is under scrutiny from an ethical and welfare perspective. The methods employed here could be refined to enable routine evaluation of valuable animals without resorting to more invasive strategies, such as allowing adequate natural challenge to accrue over time in selection candidates. Overall, the component studies reported in the thesis increased the present understanding of ovine tick-host interactions and factors contibuting to breed differences in tick loads. ___________________________________________________________________Item Open Access The genetic and environmental modelling of production and reproduction in ostrich females within and across breeding seasons(University of the Free State, 2012-01) Fair, Michael Denis; Van Wyk, J. B.; Cloete, S. W. P.English: Pedigree and performance data of a well-documented ostrich breeding resource flock was used to (1) investigate the flock structure, (2) estimate variance and (co)variance components for egg and day-old chick weight (individual traits), (3) estimate genetic and environmental parameters for egg and chick production, mean egg and day-old chick weights and hatchability within breeding seasons (hen traits) and (4) investigate early identification of superior animals using random regression models for repeated measures (longitudinal) data over years. The average level of pedigree completeness of 40 074 birds of a pair-breeding ostrich flock maintained from 1978 to 2005 at the Oudtshoorn Research Farm, South Africa was high (99.3%) in the first generation and the average level of inbreeding (F) was low at 0.51%. The estimated measures of variability were: effective genome equivalents = 47.3, effective number of founders = 59 and the effective number of ancestors = 58. The numbers of ancestors responsible for 100%, 50% and 20% of the variation in the reference population (birds with both parents known), were equal to 254, 21 and 6 respectively. The generation interval in years calculated as the average age of parents when their offspring which were kept for reproduction were born, amounted to 7.72 ± 4.79 years. The linear regressions of rate of inbreeding on year of hatch for the two distinct periods, 1995-2002 and 2003-2005, were 0.08% and -0.07% per year respectively. The estimate of effective population size (Ne) computed via the increase in the individual rate of inbreeding was 112.7 animals. The results of this study indicated that the population under study was at an acceptable level of genetic variability. Pedigree and performance data for 71 147 individual egg records collected between 1991 to 2005 were used to estimate genetic parameters for egg weight (EWT), live day-old chick weight (CWT) and hatchability (H). Heritability estimates (±SE) were 0.12 ± 0.02, 0.14 ± 0.04 and 0.09 ± 0.04 for EWT, CWT and H. Corresponding estimates for maternal genetic effects were 0.27 ± 0.08, 0.38 ± 0.08 and 0.13 ± 0.02. The effects of common environment, permanent environment and breeding paddock were significant but relatively low for all traits. Egg weight and CWT were highly correlated at all levels, while H was mostly independent of the weight traits. These results indicated that genetic improvement in these traits would be feasible. Data involving monthly records of egg production (EP), chick production (CP), hatchability (H), mean egg weight (MEW) and mean day-old chick weight (MCW) were analysed as hen traits. Heritability estimates amounted to 0.04 ± 0.02 for EP, 0.05 ± 0.03 for CP, 0.44 ± 0.04 for MEW, 0.02 ± 0.02 for H and 0.67 ± 0.02 for MCW. Permanent environmental effects as a ratio of phenotypic variance (c2 pe) ranged from 0.08 ± 0.03 to 0.11 ± 0.02 for the first four traits (MCW did not exhibit a significant c2 pe effect). Monthly EP and CP were highly correlated at all levels, ranging from 0.74 for the temporary environmental correlation to unity for the genetic correlation. Hatchability was highly correlated with EP and CP at the genetic level (>0.94). Genetic correlations of EP and CP with MEW and MCW were variable and in some cases antagonistic. Genetic correlations of H with MEW and MCW were positive (0.52 and 0.47, respectively). Results indicate that selection for improved reproduction (reproductive output and product quality traits) is feasible. Selection for production is unlikely to be complicated by unfavourable correlations with H, MEW and MCW. Hen traits defined above were further analysed in single-trait mixed models with a random regression fitted as an intercept for the direct animal (a) and a quadratic polynomial with intercept for the permanent environmental (p) effect peculiar to each hen. Heritability (h2) estimates were moderate and remained relatively constant for EP and CP ranging from 0.13-0.14 and 0.07-0.08 respectively for 3- to 10-year old hens. Quality traits MEW and MCW had moderately high h2 estimates ranging from 0.49-0.61 and 0.37-0.45 respectively. Hatchability had h2 estimates ranging from 0.11-0.13 for the 10 hen-ages. Permanent environment variance ratio for EP, CP, MEW, MCW and H ranges were 0.28-0.42, 0.29-0.41, 0.17-0.33, 0.21-0.35 and 0.14-0.24 respectively. Selection of superior hens from three years onwards seems possible. Hens older than eleven years should be replaced with younger, genetically superior hens which would reduce the generation interval and improve EP and CP genetically, without adversely affecting MEW, MCW and H.Item Open Access Studies on the behavioural and genetic aspects of ewe rearing ability and lamb survival in South African sheep flocks(University of the Free State, 2002-11) Cloete, S. W. P.; Erasmus, G. J.; Van Wyk, J. B.; Schoeman, S. J.English: The dissertation is based on a number of separate trials conducted since 1989. The central theme is ewe rearing ability and lamb survival, and the study includes 15 papers prepared over an 11-year period from 1992 to 2002. These papers are all linked by their emphasis on sheep production as influenced by lambing and neonatal behaviour and its interface with breeding and management. The papers demonstrate the various phases the study went through, and how it eventually transpired into an account of genetic change in lamb output achievable through rigorous selection. The individual papers already contain abstracts. This summary is intended to provide readers with a broad overview of the most important outcomes of the study. The study was organised in three parts, as follows: Part 1:Background Initially, two papers provided the background for the investigations into lamb survival and ewe rearing ability. The first paper dealt with the average reproductive performance of sheep in the Southern Cape, and with levels of reproductive wastage in a number of flocks. It demonstrated that approximately one in four breeding ewes did not care for at least one lamb at lamb marking. Losses were more or less evenly distributed between barrenness and rearing failure. It was impossible to identify managerial practices conclusively associated with a good reproductive performance. Evidence was provided that an improvement in the reproduction of the current flock can be achieved by a simple method of selection that can be practiced by commercial farmers with minimal record keeping. The second paper considered rearing ability in four experimental flocks of the Merino, SA Mutton Merino and Dormer breeds. A minority of ewes was shown to contribute markedly to the observed levels of rearing failure. Animals classified as being "good" or "poor" mothers on their lamb rearing history were shown to differ in one or more pelvic dimensions in two Merino flocks and the SA Mutton Merino flocks. Ewes classified as "good" had larger dimensions. Rearing ability was also demonstrated to be repeatable in the Tygerhoek Merino flock, where sufficient data were available. Part 2: The dynamics of behaviour in lambing flocks This part of the dissertation included four papers. The first paper detailed aspects of parturition and separation from one or more lamb in Dormer and SA Mutton Merino ewes. Length of parturition was found to be dependent on breed, with Dormer ewes having shorter parturitions than SA Mutton Merinos. They also were less likely to be assisted and Dormer lambs were less likely to die during or shortly after parturition. Across years, length of parturition was also repeatable in ewes. Early movement (within two hours) of ewes from the lambing site and high concentrations of lambed ewes in the same paddock were found to result in higher levels of separation from one or more lambs, resulting in lamb mortality. The second paper detailed neonatal progress in lambs and related it to birth weight and lamb survival. Survival was affected by neonatal progress as well as by live weight gain from birth to 3 days in lambs. No breed differences were found for the interval from birth to standing or from standing to apparently suckling in Dormer and SA Mutton Merino lambs. It was, however, found that the traits were moderately heritable, using paternal halfsib methods on a relatively small data set. The mechanisms of difficult births were subsequently investigated in Dormer and SA Mutton Merino ewes, since the two breeds were markedly different in this respect. The etiology of difficult births in the breeds was found to differ vastly. Dystocia and feto-pelvic disproportions commonly led to prolonged parturitions and assistance in SA Mutton Merinos. Uterine inertia were more likely to be observed in Dormers. The ability of factors associated with birth difficulties (pelvic dimensions, litter size and weight, ewe live weight and conformation) to predict length of parturition within breeds was, however, limited. In the final paper of this part of the dissertation, it was possible to partition the genetic variances for behaviour traits observed during lambing in Dormer and SA Mutton Merino ewes. Maternal additive variance ratios for length of parturition were moderate and significant in both breeds. Neonatal progress (time intervals from birth to standing and from standing to apparently suckling) was lowly heritable in both breeds. The interval from standing to suckling was also influenced by the maternal permanent environmental variance in SA Mutton Merinos. Direct and maternal breeding values for behavioural traits differed significantly between lambs that survived and those that died in most cases. This result suggested a genetic association of lamb mortality with lambing and neonatal behaviour. Part 3: Responses to selection for ewe multiple rearing ability This part of the dissertation was based on observed responses in two Merino lines that were divergently selected for ewe multiple rearing ability since 1986. The line selected in an upward direction for multiple rearing ability is referred to as the High (H) line. The line selected downwards is referred to as the Low (L) line. This part of the study consists of nine papers. In the first paper, separation of ewes from one or more lambs was studied in the Merino lines referred to above. Ewes in the H line were more likely to be separated from one or more lambs because of interference, and they tended to be more interested in other parturient ewes. Ewes in the L line tended to be more likely to desert their lamb(s). Ewes that left their birth sites within two hours of birth were more likely to be separated from one or more offspring. The ability of ewes and lambs from the Hand L lines to recognize each other were investigated next. Ewes in the H line were able to find their lambs sooner after the lamb being tethered 20 m away, compared to their L line contemporaries. They were also able to establish contact with all litter members in multiples sooner after finding a tethered lamb. Lambs in the H line tended to be more likely to bleat and tug on the tethering rope when tethered. They also followed their dams more closely when chased away with their dams at three days of age. The paper allowed the estimation of preliminary genetic parameters for mutual recognition of one another by ewes and lambs, although it was not the primary objective. Significant maternal genetic variances were found for most of the traits. The following paper demonstrated a better lamb survival in H line lambs, despite a higher multiple birth rate. Line differences were reported, mostly involving behavioural adaptations conducive to lamb survival in the H line. Ewes in the H line generally experienced shorter births, and H line lambs were less likely to succumb during or soon after parturition. Ewes in the H line showed better cooperation with the first suckling attempts of their lambs, and H line lambs apparently suckled sooner after standing than L line contemporaries. This line difference remained after correction for the better cooperation of H line ewes. A marked advantage in terms of weight of lamb weaned per breeding ewe in the H line was demonstrated for the five years of this study, when compared to the L line. It was found that a substantial proportion of births will not be supervised if the supervision of Merino ewes in South Africa was confined to daylight hours in intensive systems. A larger than expected frequency of very short intervals between subsequent onsets of parturition was observed. If the contention that births would trigger each other could be substantiated, it could be of benefit to quantify the mechanism involved. Knowledge of this would facilitate the synchronisation of natural births in pasture lambing flocks, where it is impractical to alter the distribution of births by nutrition. Relatively few line differences were found in this paper. The distribution of birth sites within paddocks could not be related to selection line. Ewes in the H line ewes were more likely to groom their lambs shortly after birth, while L line ewes commenced grazing sooner after birth. These behavioural adaptations in the H line would generally facilitate lamb survival. Behavioural data from the H and L lines were recorded over a lO-year period and subjected to a genetic analysis. The line differences obtained earlier could be confirmed in this study. Genetic parameters estimated from the data indicated that behaviour traits in lambs and ewes were lowly to moderately heritable. In lambs, a significant heritability estimate was derived for the interval from birth to standing. Maternal heritability estimates were significant for length of parturition and for the interval from birth to standing. Maternal permanent environmental variances were significant for maternal cooperation and the interval from standing to apparently suckling. When behavioural traits were assessed in ewes, length of parturition, maternal behaviour score and the period that ewes remained on or near the birth site were found to be moderately heritable. Genetic divergence was found for the H line compared to the L line. The derived genetic trends indicated changes conducive to lamb survival in the H line. Direct additive, maternal additive and maternal permanent environmental variance ratios were subsequently derived for lamb birth weight, birth coat score and lamb weaning weight. Birth coat score was highly heritable and not influenced maternally. Genetic and phenotypic trends indicated divergence between the H and L lines for weaning weight over the period of assessment. Genetic divergence was particularly strong in the case of direct breeding values for weaning weight. Birth weight and birth coat score were independent of selection line. Genetic parameters were estimated for annual reproduction traits, ewe greasy fleece weight and ewe body weight at joining, using a repeatability model. Heritability estimates for reproduction traits were low, consistently below 10 % of the overall phenotypic variance. Ewe permanent environmental variances were higher, between 7 and 12 %. Genetic correlations of reproduction traits with ewe joining weight were favourable and very high in the case of weight of lamb weaned per ewe. Corresponding genetic correlations with ewe greasy fleece weight were low and variable. Ewe permanent environmental correlations of reproduction traits with ewe joining weight and greasy fleece weight were unfavourable and high in some instances. Phenotypic trends indicated divergence in the expected direction between the Hand L lines in the reproduction traits considered. These tendencies were confirmed by genetic trends based on averaged predicted breeding values within birth years. The results confirmed that genetic progress at a rate of 1-2 % per year was attainable in reproduction traits, despite low additive variance ratios. Genetic parameters were estimated for hogget wool and live weight traits, as well as for testis measurements. Adequate genetic variation for exploitation in a well-structured breeding program was estimated in all traits. Genetic trends indicated change towards heavier and plainer sheep in the H line, while L line contemporaries became smaller and more developed. Genetic trends for testis circumference suggested divergence in the expected direction between lines. This result was, however, associated with the genetic change in live weight, since no line difference was found in testis circumference corrected for live weight. Genetic trends for clean fleece weight and fibre diameter indicated no divergence between lines. Age influences on reproduction, wool traits and live weight were assessed in H and L line ewes subjected to at least 10 years of divergent selection. Genetic parameters derived from this data set were generally consistent with previous estimates, despite the usage of a much smaller data set. The Hand L lines differed markedly for reproduction, but no differences in the shape of age trends were found between lines. Compared to average L line performance, the superiority of H line ewes amounted to 56 % in the case of weight of lamb weaned per ewe. Ewes in the H line were heavier than L line contemporaries at two-tooth age, but the line difference disappeared at later ages. Wool production of L line ewes were heavier than those of their H line contemporaries, particularly in the middle age groups (3 to 6 years), where the highest fleece weights are expected. Fibre diameter increased with ewe age, with no apparent line difference. It was contended that the stress of increased reproduction resulted in the different age trends for the respective selection lines for live weight and greasy fleece weight. In the final instance, this dissertation provides a framework for the genetic improvement of lamb output in pasture-fed sheep by selection for reproductivity. Unwanted correlated genetic changes were minimal, although the stress associated with an increased reproduction impaired live weight and wool traits in mature animals to an extent. The interface between behaviour, lamb survival and ewe rearing ability were clarified for a number of South African sheep breeds, leading to a better understanding of the dynamics involved. These results contributed to the formulation of adapted husbandry and breeding practices, in the context of overall flock productivity. Results pertaining to behaviour appeared to be fairly robust across studies involving different resource populations, and should be appropriate for extension to the broader industry.