Artificial insemination (AI) is a widely used part of the modern agricultural industry, with the number of animals inseminated globally being measured in the millions per anum. Crucial to the success of AI is that the sperm sample used is of a high Quality. Two factors which determine the quality of the sample are the number of sperm present and their motility. There are numerous methods used to analyse the quality of a sperm sample, but these are generally laboratory based, expensive and in need of a skilled operator to perform the analysis. It would, therefore be useful to have a simple and inexpensive system which could be used outside the laboratory, immediately prior to the insemination of the animal. Presented in this thesis is work developing a time of flight (ToF) technique which makes use of a quartz crystal microbalance (QCM), operating at 5 MHz, as the sensing element. Data is shown developing a device where a 50 μl sample of boar sperm is added to a liquid filled swim channel, which the sperm are allowed to self-propel down and attach to the surface of a QCM at the end. The attachment of the sperm to the surface causes a measurable frequency decrease in the QCM, aproximately 50 Hz. An average effective mass measurement was made using a QCM and gave a value of 8 ± 5 pg per sperm, which was used in conjunction with the frequency change to determine the number rate of sperm reaching the QCM. Additional data is presented to investigate the effect of environmental temperature on the ToF of the sperm, showing a decrease in ToF between 23 0C to 37 0C. The system was also used to investigate increasing the swim speed of the sperm by chemical means. A range of 20 μmol to 100 μmol of progesterone was added to the swim medium and the ToF was shown to decrease as a result. To further develop the system, large commercial electronics were replaced by smaller circuits built in-house. An oscillator circuit based on a Pierce oscillator was used to drive the QCM and a frequency counter circuit making use of a universal frequency to digital converter (UFDC-1) was used to measure the frequency of the QCM. ToF experiments were performed which showed these pieces of equipment to be effective for performing the analysis of sperm samples. The swim cell itself was also refined, resulting in a compact, modular design. Work was performed developing layer-guided, single-port acoustic resonators to replace the QCM as the sensing element in the sperm analysis device. A maximum mass sensitivity of 1110 Hzμg-1cm-2 was found for devices on a LiTaO3 substrate with a 6 μm guiding layer. While viscosity-density sensing experiments found a maximum sensitivity of 488 KHz Pa-1/2 kg1/2 for a 4 μm guiding layer.

Thesis (M.Sc.) (Agriculture) --University of Limpopo, 2007 / The objectives of this study were to evaluate the effect of pre-weaning selection on estimates of genetic parameters for post-weaning average daily gain in Phases C (ADG-C) and D (ADG-D) and to estimate genetic relationships between average daily gain in the two phases. Performance records of the South African Angus cattle breed was used in the analysis. (Co)variance components and genetic parameters for weaning (WWT), AGD-C and ADG-D were estimated by REML procedures fitting three different models (Models 1, 2 and 3) that differed in how they integrated sequential selection in the analysis of post-weaning traits. Model 1 was a univariate model of WWT, ADG-C and ADG-D. Model 2 was a two trait model of WWT and either ADG-C or ADG-D. Model 3 was a three trait model of WWT, ADG-C and ADG-D. Estimates of heritability for ADG-C were 0.39±0.08, 0.42±0.06 and 0.44±0.01 from Model 1, 2 and 3 respectively. Corresponding estimates of heritability for ADG-D were 0.18±0.021, 0.19±0.021 and 0.21±0.02 respectively. An estimate of genetic correlation between ADG-C and ADG-D was 0.58± and it suggested that the two traits may not necessarily be under the same genetic control. Rank correlations for all bulls based on ADG-C estimated breeding values (EBV’s) were 0.92, 0.83 and 0.94 for Model 1 vs. Model 2, Model 1 vs. Model 3 and Model 2 vs. Model 3 respectively. Corresponding ADG-D EBV’s rank correlations were 0.88, 0.84 and 0.93. Rank correlations for top and bottom 1%, 5% and 10% were lower than those for all bulls in both ADG-C and ADG-D. Low rank correlations showed that the difference in magnitude of genetic parameters from different models was enough to alter bull rankings based on EBV’s of ADG-C and ADG-D. Hence it was concluded that inclusion of pre-weaning information in genetic analysis for post-weaning average daily gain is necessary to account for selection at weaning. / the THRIP (Technology and Human Resource for Industry Project) and NRF (National Research Foundation).

L'efficacité de la sélection génomique étant principalement dépendante de la taille de la population de référence, seules les principales races laitières françaises bénéficient aujourd'hui d'évaluations génomiques. Pour contourner cette contrainte et développer des évaluations génomiques pour les races régionales, il a été proposé de créer une population de référence commune entre races.Cependant, utiliser une population de référence multiraciale nécessite que le lien entre QTL et marqueurs soit conservé entre races, ce qui implique, sauf cas particulier, l'utilisation d'une puce haute densité. Les taux d'erreur d'imputation des génotypes haute densité à partir de génotypes moyenne densité (classiquement utilisés en bovins) ont été étudiés. La précision d'imputation étant supérieure à 99% dans la majorité des races laitières, l'imputation des génotypes des animaux des populations de référence des principales races laitières a été réalisée. Cette population de référence « haute densité » a ensuite été utilisée pour le développement d'évaluations génomiques multiraciales. Plusieurs stratégies d'évaluations génomiques (intra-race ou multi-race, à partir de génotypes moyenne ou haute densité) ont été comparées pour différentes tailles de populations de référence. Les évaluations multiraciales basées sur la puce haute densité permettent d'améliorer la précision des évaluations génomiques dans le cas d'une population de référence de 500 taureaux ou moins. L'efficacité d'une troisième stratégie utilisant des évaluations génomiques multiraciales à partir de la puce moyenne densité pour un groupe de races proches a donc été étudiée. L'augmentation de la précision des évaluations génomiques observée dans ce cas était trois fois supérieure à celle qui avait été observée dans le cas des principales races laitières. Par ailleurs, dans les deux cas étudiés ici, la précision des évaluations génomiques intra-races est relativement élevée, même dans le cas d'une population de référence réduite, lorsque les pères des candidats à la sélection sont inclus dans la population de référence.Les résultats obtenus suggèrent donc que la mise en place d'évaluations génomiques dans les races régionales est envisageable. Il faudra toutefois poursuivre les travaux pour déterminer quelle stratégie optimale peut/doit être utilisée dans chacune des races. / Within-breed genomic selection is now implemented in a number of large cattle breeds. However, building reference populations large enough remains a major challenge for smaller breeds. Combining reference populations and implementing a multi-breed approach appears to be an appealing alternative for small breeds.Such an approach requires conserved linkage disequilibrium across breeds to maintain the association between QTL and markers. Therefore, the use of a high density chip is generally needed. Error rates for high density imputation from medium density genotypes, classically used in cattle, were estimated. The mean error rate was below 1% in most dairy cattle breed which implies that a large high density imputed reference populations can be available for genomic selection at low cost. Reference populations from the three major French dairy breeds were imputed to high density and used to develop a multi-breed genomic evaluation.Several alternative genomic selection approaches (within-breed or multi-breed, based on medium or high density genotypes) were compared for breeds with different sizes of reference population. Improvement of genomic prediction accuracy due to the multi-breed evaluation was observed for breeds with 500 animals or less in their reference population. Accuracy of a third alternative using multi-breed evaluation based on medium density genotypes of closely related breeds was investigated. The benefit of multi-breed genomic evaluation was then three times higher in this situation than in the one where populations from major dairy cattle breeds were pooled. It can be noted that in both situations, using within-breed genomic information allowed a significant gain in accuracy compared to pedigree-based evaluations even for a small breed, when all sires of selection candidates belong to the reference population.These results suggest that implementation of genomic selection is feasible in small dairy cattle breeds. However further work is required to determine which optimal strategy can/must be implemented in a given breed.

Actuellement en France et aux Etats-Unis, seules 30 à 35 % des premières inséminations artificielles chez la vache Holstein aboutissent à un vêlage. Les échecs de gestation ont lieu le plus souvent au cours du développement embryonnaire (Non-Fécondation-Mortalité Embryonnaire Précoce (NF-MEP) entre 0 et 16 jours, Mortalité Embryonnaire Tardive (MET) entre 16 et 45 jours après insémination). Ces échecs précoces de gestation expliquent en grande partie les différences de fertilité observées en France entre la race Holstein et les autres races plus fertiles. Les facteurs de risque de l'interruption de la gestation sont multiples : liés à l'animal, à l'environnement et à la conduite de l'élevage. Trois facteurs cependant ont évolué au cours du temps pour les vaches Holstein : le potentiel génétique, les anomalies de reprise de la cyclicité après vêlage, le déficit énergétique en début de lactation. Notre objectif a été d'identifier l'influence de ces trois facteurs sur les échecs précoces de gestation après première insémination postpartum chez la vache de race Holstein. Le potentiel génétique a été associé à l'incidence de NF-MEP et de MET. Les phases lutéales prolongées sembleraient être à l'origine d'une augmentation d'incidence de MET. Le déficit énergétique a eu un effet sur la NF-MEP et sur la MET. L'effet du déficit énergétique postpartum sur la qualité des ovocytes au moment de la mise à la reproduction reste hypothétique. Notre travail sur les échecs précoces de gestation a permis de contribuer à fournir des outils d'amélioration de conduite d'élevage aux professionnels. / Currently, in France and the United States of America, only 30-35 % of first artificial inseminations in Holstein cows result in a calving. Pregnancy failure mainly occurs during embryonic development (fertilization failure - early embryonic mortality (FF-EEM) between D0 and D16 or late embryonic mortality (LEM) between D16 and D45 after insemination). Early pregnancy failure explains the majority of the differences in fertility between the Holstein breed and the other breeds in France, which are more fertile. There are numerous risk factors which cause pregnancy failure: animal, environmental and farm management factors. There are however, three factors which have been modified over time in Holstein cows: genetic merit, abnormal patterns of resumption of cyclicity and negative postpartum energy balance (NEB). Our objective was to identify the relationships between these three factors and early pregnancy failure after first postpartum insemination in Holstein dairy cows. Genetic merit was related to the incidence of FF-EEM and LEM. Prolonged luteal phases seemed to increase the incidence of LEM. The NEB was associated with FF-EEM and LEM. The impact of NEB on oocyte quality during the breeding period remains unclear. Our early pregnancy failure studies have helped to provide some tools to improve farm management.