In this study whole-genome SNP data from 1977 animals, originating from thirteen sheep breeds in South Africa was analysed. The animals were classified into three production types: dual-purpose (Afrino, Dohne Merino, Dormer, Merino, SA Mutton Merino), meat (Black Headed Persian, Damara, Dorper, Meatmaster, White Dorper) and indigenous (Fat-tailed, Namaqua Afrikaner, Pedi). All animals were genotyped using the Illumina Ovine 50K SNP BeadChip. The aim was to investigate the genetic diversity and inbreeding levels of both indigenous and commercial sheep breeds in South Africa. The populations were first investigated individually to analyse within population diversity, whereafter they were merged in order to perform between population diversity analysis. During sample-based quality control, a total of 207 animals were removed due to low call rates. The number of SNPs remaining after marker-based quality control ranged from 32 422 to 44 778. Average observed heterozygosity values of 0.360, 0.355 and 0.340 were observed for dual-purpose, meat and indigenous populations respectively. Average linkage disequilibrium (LD) estimates were highest for dual-purpose populations at 0.277, followed by meat type populations at 0.259, and the lowest LD was observed for indigenous populations at 0.255. Dual-purpose, meat and indigenous populations showed average minor allele frequencies (MAF) of 0.393, 0.427 and 0.444 respectively. Principal component analysis (PCA) and ADMIXTURE results showed a clear differentiation between the dual-purpose populations, and the meat and indigenous populations. Average inbreeding coefficient (Fis) estimates of 0.008, -0.029 and 0.003 was observed for dual-purpose, meat and indigenous populations respectively. All populations showed a decline in effective population size (Ne) across generations. For all populations, the highest percentage of ROH was found in the shortest length category (1-3.99 Mb), and the largest number of ROH were observed on the first ten chromosomes. The average FROH estimates was highest for dual-purpose populations at 0.015, followed by the meat type and indigenous populations at 0.011 and 0.005 respectively. An unrooted phylogenetic tree based on pairwise Fst estimates showed a divergence of the dual-purpose populations from the meat and indigenous populations. Results from this study indicated lower variation within dual-purpose populations, and higher variation within indigenous populations. High population differentiation was observed between the various production types. / Dissertation (MSc Agric) (Animal Science: Animal Breeding and Genetics))--University of Pretoria, 2020. / Animal and Wildlife Sciences / MSc Agric) (Animal Science: Animal Breeding and Genetics) / Unrestricted

This study aimed to identify genomic regions of significance that are associated with body weight traits and reproduction traits in sheep by using estimated breeding values in a genome wide association study (GWAS). The following traits were investigated: body weight recorded at selection age of 14 months (BW), number of lambs born (NLB), number of lambs weaned (NLW) and total weight of lamb weaned (TWW). A total of 411 animal were genotyped using the Illumina® Ovine SNP50 BeadChip, and consisted of 152 Afrino, 129 Cradock Merino and 130 Grootfontein Merino sheep. Quality control (QC) were implemented using PLINK v1.07 where the parameters were set as 90% for individual call rate, 95% for SNP call rate, minor allele frequency of less than 2% and P <0.001 for Hardy-Weinberg equilibrium. Population parameters were calculated per dataset. The average MAF values estimated for the populations were 0.252, 0.372 and 0.372 for the Afrino, Cradock Merino and Grootfontein Merino, respectively. Inbreeding coefficients were estimated at - 0.025 (Afrino), - 0.025 (Cradock Merino) and 0.002 (Grootfontein Merino). The expected heterozygosity was 0.363 for the Afrino and 0.369 for both Merino populations. All three sheep populations had low inbreeding levels and moderate genetic variation. The population genetic substructure, ancestry proportion and genetic relatedness between the populations were investigated via principal component analysis (PCA) and admixture plots. These plots corresponded to the populations’ selection practises and breeding programs as well as to the geographical locations where the individuals were kept. The GWAS was applied to each dataset separately and per trait using the efficient mixed model association eXpedited (EMMAX) software and visualised by Manhattan plots. Nine suggestive SNPs were identified to be in possible association with the traits. Of these nine, seven SNP were identified to be in close proximity or linked to previously annotated genes. Seven genes were identified which were in association with growth and reproduction traits. The genes SIX6, C14orf13 and TRPS1 showed the most promise for body weight and growth traits. For reproduction and fertility traits the genes LIG1, CABP5, GRIK3 and HDAC9 warrants further investigation. / Dissertation (MScAgric (Animal Science))--University of Pretoria 2020. / Grootfontein Agricultural Development Institute / Animal and Wildlife Sciences / MScAgric (Animal Science) / Unrestricted

The aim of this thesis was to evaluate alternative management options for the smallholder dairy cattle production system in South Africa (SA). Specific objectives included, were to benchmark cow performance in the smallholder (SH) against their counterparts in a high-input system (H), to develop a SH herd model, and to evaluate alternative management options for the improvement of smallholder dairy herd profitability. Data on production (305-day yields of milk, fat and protein), lactation length, somatic cell count (SCC), and reproductive traits (age at first calving (AFC), and calving interval (CI) obtained from the South African National Dairy Animal Improvement scheme (NDAIS) were used in a benchmarking study. Least squares means per trait were compared between the two systems, and lactation curves for roduction traits and SCC were plotted. Results revealed that mean yields of milk, fat and protein were significantly (P<0.05) lower in the SH (4 097±165, 174±5.1 and 141±4.5 respectively) compared to the H system (6 921±141, 298±4.7, and 245±4.1, espectively). Mean lactation length was significantly (P<0.05) shorter for the SH (308±15.1) compared to the H system (346±12.8). Log-transformed SCC was significantly (P<0.05) higher in the SH (2.41±0.01) relative to the H system (2.27±0.01). Cows in H herds exhibited typical lactation curves, in contrast to flat and low-peaking curves obtained for the SH system. SH cows had significantly (P<0.05) older AFC (30±0.5) than those in the H system (27±0.5). There was no significant difference (P<0.05) in CI between the two systems. A bio-economic SH herd model was developed by adapting a previously developed model for the H system in SA. Parameters used were obtained from NDAIS, survey data, personal communications, and literature. The model integrated herd dynamics, outputs, nutrient energy requirements, management, and their associated economics. Nutrient energy requirements were estimated for maintenance, growth, reproduction, and lactation. The developed SH herd model was used to evaluate alternative herd management options, using the partial budget approach. Milk yield (MY), live weight (LW), AFC, and CI were used as indicators of cow performance. Herd management practices studied were herd size (HS), replacement rate (RR), feeding system (FS), breeding methods (natural service vs artificial insemination), and source of replacement heifers (raising vs. buying in). Improvements in profitability were attained by increasing MY or increasing herd size, using small to medium sized cows, or reducing AFC, CI or RR. Break-even points were 3 687.4 l/year, 500 kg, 29 months, 420 days and 25% for MY, LW, AFC, CI, and RR, respectively. Profitability was mostly sensitive to the prices of milk and feed. A drop in the price of milk below R4.50/l or increase in the cost of feed above R5.60/kg DM generally resulted in non-profitability. Relying on pasture only for feed was non-viable, and supplementation of pasture with concentrate was the most profitable feeding system. Feeding systems based on supplementation of pasture with concentrate, and silage were resilient to fluctuations in the price of milk, remaining profitable even when the price dropped to R4.10/l. Using artificial insemination or buying-in replacement heifers are additional management strategies that increase SH dairy farming profitability. These recommended management options should be used in combination for achieving maximum herd profitability. / Thesis (PhD (Animal Science))--University of Pretoria, 2020. / UP Postgraduate/Doctoral Research Bursary / Animal and Wildlife Sciences / PhD (Animal Science) / Unrestricted

Com o aumento da produtividade na área agropecuária, houve um aumento na busca por sistemas de produção mais eficientes e competitivos. Neste contexto, o melhoramento genético animal tem proporcionado avanços na obtenção de produtos de origem animal, principalmente na seleção de touros. A superioridade genética de touros para produção de leite não pode ser medida diretamente nos animais, assim, o valor genético é medido pelo desempenho de produção de leite de suas filhas pelo teste de progênie. A seleção de touros pelo teste de progênie pode ser considerada como método ideal quando temos características de baixa herdabilidade, populações grandes e um grande número de progênies, que hoje são obtidas pelo uso de inseminação artificial. O correto parentesco entre reprodutores é um pré-requisito para um eficiente programa de melhoramento genético animal. Muitas das questões de parentesco podem ser resolvidas pelos testes convencionais, como grupos sanguíneos e proteínas do soro. Entretanto em alguns casos, esses polimorfismos não são suficientes para esclarecer a correta paternidade e, em função disso outros métodos passaram a ser utilizados, como os marcadores moleculares microssatélites. Esta metodologia tem sido descrita para resolver com maior eficiência os casos de verificação e determinação de parentesco, inclusive em bovinos, devido ao alto polimorfismo que apresenta, aliado a resultados de clara interpretação. Para a investigação de paternidade, foram utilizados os marcadores microssatélites BM8246, BMS963, CSFM50, INRA112. Foram verificadas as paternidades de nove touros da raça Gir leiteiro em teste de progênie, calculada a taxa de erro de paternidade e o efeito que esta teria na estimativa do valor genético dos touros. Foi verificado que das 74 filhas analisadas, houve exclusão para 27 delas, correspondendo a um erro de 36% na identificação de paternidade. No entanto, a mudança observada na classificação dos touros devido à correção das paternidades incorretas e consequente mudanças nos valores genéticos dos touros, não foi significativa quando as duas avaliações foram comparadas pelo método de correlação de Spearman. / Increased production in agribusiness has intensified the search for more efficient and competitive production systems. In animal production, advances are achivied primarily through sire selection. Genetic superiority of bulls for milk production cannot be directly measured in the animal; therefore, genetic value is measured by the milk production of its daughters by a progeny test. Selection of bulls by the progeny test could be considered an ideal method when the following characteristics are present: low hereditability, large productions and a large number of progenies. However, the method presents two drawbacks that limit its use: 1) high cost and 2) increase in generation intervals. Nevertheless, these obstacles can be overcome when a large number of progenies are obtained with artificial insemination (A.I.). Correct relationship among sires is essential for an efficient animal-breeding program. Many questions about relationship can be solved by conventional tests, such as blood type and serum proteins. In some cases these polymorphisms are not enough for accurate results; consequently, other methods are used such as microsatelitte molecular markers. This methodology has been described to determine and verify parentage including bovines with high efficiency due to its greater polymorphism and easily interpreted results. Microsatelitte markers BM8246, BMS963, TEXAN15, BMS483, CSFM50, INRA112 were used to investigate paternity. Paternity of nine Gir dairy sires participating in a progeny test was verified. The paternity error rate was calculated and its effect on estimation of the genetic value of the sires determined. Of the 74 daughters analyzed 27 were excluded, which corresponds to a 36% error in paternity identification. However, the change observed in bull classification due to correction of inaccurate paternity and consequent changes of genetic value of the sires was not significant when the two evaluations were compared by the correlation method of Spearman.

Com o aumento da produtividade na área agropecuária, houve um aumento na busca por sistemas de produção mais eficientes e competitivos. Neste contexto, o melhoramento genético animal tem proporcionado avanços na obtenção de produtos de origem animal, principalmente na seleção de touros. A superioridade genética de touros para produção de leite não pode ser medida diretamente nos animais, assim, o valor genético é medido pelo desempenho de produção de leite de suas filhas pelo teste de progênie. A seleção de touros pelo teste de progênie pode ser considerada como método ideal quando temos características de baixa herdabilidade, populações grandes e um grande número de progênies, que hoje são obtidas pelo uso de inseminação artificial. O correto parentesco entre reprodutores é um pré-requisito para um eficiente programa de melhoramento genético animal. Muitas das questões de parentesco podem ser resolvidas pelos testes convencionais, como grupos sanguíneos e proteínas do soro. Entretanto em alguns casos, esses polimorfismos não são suficientes para esclarecer a correta paternidade e, em função disso outros métodos passaram a ser utilizados, como os marcadores moleculares microssatélites. Esta metodologia tem sido descrita para resolver com maior eficiência os casos de verificação e determinação de parentesco, inclusive em bovinos, devido ao alto polimorfismo que apresenta, aliado a resultados de clara interpretação. Para a investigação de paternidade, foram utilizados os marcadores microssatélites BM8246, BMS963, CSFM50, INRA112. Foram verificadas as paternidades de nove touros da raça Gir leiteiro em teste de progênie, calculada a taxa de erro de paternidade e o efeito que esta teria na estimativa do valor genético dos touros. Foi verificado que das 74 filhas analisadas, houve exclusão para 27 delas, correspondendo a um erro de 36% na identificação de paternidade. No entanto, a mudança observada na classificação dos touros devido à correção das paternidades incorretas e consequente mudanças nos valores genéticos dos touros, não foi significativa quando as duas avaliações foram comparadas pelo método de correlação de Spearman. / Increased production in agribusiness has intensified the search for more efficient and competitive production systems. In animal production, advances are achivied primarily through sire selection. Genetic superiority of bulls for milk production cannot be directly measured in the animal; therefore, genetic value is measured by the milk production of its daughters by a progeny test. Selection of bulls by the progeny test could be considered an ideal method when the following characteristics are present: low hereditability, large productions and a large number of progenies. However, the method presents two drawbacks that limit its use: 1) high cost and 2) increase in generation intervals. Nevertheless, these obstacles can be overcome when a large number of progenies are obtained with artificial insemination (A.I.). Correct relationship among sires is essential for an efficient animal-breeding program. Many questions about relationship can be solved by conventional tests, such as blood type and serum proteins. In some cases these polymorphisms are not enough for accurate results; consequently, other methods are used such as microsatelitte molecular markers. This methodology has been described to determine and verify parentage including bovines with high efficiency due to its greater polymorphism and easily interpreted results. Microsatelitte markers BM8246, BMS963, TEXAN15, BMS483, CSFM50, INRA112 were used to investigate paternity. Paternity of nine Gir dairy sires participating in a progeny test was verified. The paternity error rate was calculated and its effect on estimation of the genetic value of the sires determined. Of the 74 daughters analyzed 27 were excluded, which corresponds to a 36% error in paternity identification. However, the change observed in bull classification due to correction of inaccurate paternity and consequent changes of genetic value of the sires was not significant when the two evaluations were compared by the correlation method of Spearman.