Animal, Wildlife and Grassland Sciences
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Browsing Animal, Wildlife and Grassland Sciences by Advisor "Cloete, S. W. P."
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Item Open Access Breed effects and non additive genetic variation in indigenous and commercial sheep in an extensive environment(University of the Free State, 2019-06) Kao, 'Mamolleloa A.; Van Wyk, J. B.; Cloete, S. W. P.The first part of the study compared a commercial, the Dorper as an arguably adapted commercial breed to the Namaqua Afrikaner as an unselected, indigenous, far-tail breed. The Dorper conclusively outperformed the Namaqua Afrikaner with reference to live weight and growth traits. On the other hand, Namaqua Afrikaner lambs were superior to Dorpers for an adaptive trait like total tick count. Lamb survival was unaffected by breed. When meat traits were considered, it was evident that Dorper lambs outperformed their Namaqua Afrikaner contemporaries for important attributes associated with size and meat yield, namely carcass weight and dressing percentage. Dorper carcasses also attained better grades and were more tender according to instrumental measurements (Warner Brazler equipment). Dorper lambs were fatter than Namaqua Afrikaner lambs, as derived from the backfat thickness at the 13th rib and the rump. While leaner meat would be preferred by health-conscious consumers, it is important to note that, under the conditions of the study, Dorper carcasses were more likely to be in the preferred grades. In the second part of the study, Dorpers were evaluated against the SA Mutton Merino (SAMM; the most numerous dual-purpose breed in South Africa), as well as the reciprocal cross between the two breeds. No conclusive breed differences were found for weight traits, lamb survival, tick counts or meat traits. However, there was a suggestion that lamb survival of Dorpers was higher than that of their SAMM contemporaries (P = 0.08), but significance could not be demonstrated. Crossbred progeny outperformed the midparent value by 6.3% for weaning weight. The corresponding study on meat traits was constrained by low numbers. However, it was evident that the observed heterosis for weaning weight was also present a later growth stage. Direct heterosis estimates amounted to 7.7% for slaughter weight and 7.1% for carcass weight. These estimates were consistent with the literature for the expected level of heterosis for early growth when assessed in fairly divergent sheep breeds. This outcome once again reiterated that crossbreeding may have a definite role to play at the commercial level in the South African sheep industry. Further studies on the comparison of indigenous genetic resources with commercial breeds, as well as crossbreeding studies with the variety of available breeds were recommended.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 A genetic evaluation of the Dohne Merino breed in South Africa(University of the Free State, 2006-05) Swanepoel, Jan Willem; Van Wyk, J. B.; Delport, G. J.; Cloete, S. W. P.English: Genetic (co)variances for yearling body weight (BW), clean fleece weight (CFW) and mean fibre diameter (MFD) in the SA Dohne Merino population were estimated using records of 107 389 animals recorded between 1992 and 2004. The data include records of 1 530 sires and 45 178 dams. An animal model with direct and maternal additive, maternal permanent and temporary environmental effects was fitted for all traits. Sire-flock (SF) and sire-flock-year-season (SFYS) was included as additional random effects. Fixed effects were (FYSSM) (1594 classes), type of birth (singles, multiples), age of dam (2 to 7+ years) and average age (± SD) at measurement fitted as a linear covariate (385 ± 12 days). Estimates obtained by single -trait analyses were used as starting values in three-trait analyses. The direct genetic heritability estimates for FD, CFW and BW obtained from the three-trait analysis were 0.447 (0.009), 0.216 (0.008) and 0.277 (0.008) respectively. The genetic correlations were 0.050 between BW and CFW, 0.100 between BW and FD and 0.139 between FD and CFW. The phenotypic correlations were 0.318 between BW and CFW, 0.129 between BW and FD and 0.180 between FD and CFW. Direct genetic correlations of BW, CFW and MFD were positive, which suggest that selection for bigger and heavier sheep would generally lead to a stronger MFD and higher CFW. Because these values are very low the subsequent effect of this phenomenon would be that the effect of selection for body traits on fleece traits would be very small and vice versa. Genetic trends were calculated using the annual average breeding value estimates (EBV) for each trait. According to the genetic trends derived, the selection policy followed did cause genetic change in the traits studied, even though it was slow. The level of inbreeding (F) in the South African Dohne Merino sheep population is very low. The proportion of animals that was inbred to some extent increased from 0% (average F=0) in 1980 to 38% in 2003 (average F=1.22%). No significant inbreeding depression on BW, CFW and MFD could be found. In general the results suggest that inbreeding at present is not a serious problem in the South African Dohne Merino breed.