Thesis (MScAgric)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Little research has been done on natural feed additives which enhance milk production in dairy animals. Fenugreek (Trigonella foenumgraecum) is a member of the legume family and is found in India, Middle East, North Africa and South Europe. Fenugreek is used as an herb in traditional medicine to promote lactation in lactating women. It also influences the lactation performance in ruminants such as dairy cows, water buffaloes and dairy goats. Diocin is a natural saponin found in Fenugreek and has structural similarity to oestrogen, which leads to an increased release of growth hormone (GH) and ultimately milk production. Three different trials were carried out to investigate Fenugreek’s effects. Each trial consisted of three treatment groups where dairy goats were randomly assigned. Nutrifen®, NutrifenPlus® and a control treatment served as the three treatments used in this study. Forty-eight goats per treatment group were used in the first trial where the main objective was to evaluate Fenugreek’s effect on milk production and milk composition. The second trial consisted of eight goats per treatment group, where Fenugreek’s effect on the in vivo and in vitro digestibility of the feed served as the main objective of this study. In the final part of the study, growth hormone found in plasma was subsequently investigated using the same goats from trial two. Fenugreek’s effect on elevating GH levels was the objective from the third part of the study. The first trial showed promising results in terms of an increase in milk production (P = 0.01) from dairy goats using the Nutrifen® treatment and an increase in milk lactose (P = 0.03) using the NutrifenPlus® treatment. Blood cholesterol and cholesterol content found in the milk did not differ between treatments used. Apparent digestibility of the total digestible nutrients (TDN) from the feed did not increase and did not differ between treatments and therefore concluded that the dairy goats digested the different treatments with similar efficiency regardless of the additive added to the feed. Growth hormone levels found in plasma also did not differ between treatments used in the third part of the study. Variation was found in GH plasma levels and this was expected as GH levels are known to have variation within ruminants. It appears that Fenugreek used as a natural feed additive can increase the milk yield from dairy goats, which would be beneficial to the commercial dairy goat farmer. However, the process on how Fenugreek exerts its effect on milk production still remains unclear. / AFRIKAANSE OPSOMMING: Tot datum is min navorsing gepubliseer wat die invloed van natuurlike voer bymiddels op melkproduksie aanspreek. Fenugreek (Trigonella foenumgraecum) is ‘n peulgewas en kom voor in Indië, die Midde Ooste, Noord Afrika en Suid Europa. Fenugreek word in tradisionele medisyne gebruik om sodoende melkproduksie in lakterende vroue te verhoog. Dit verhoog ook melkprodukise in melkkoeie, waterbuffels en melkbokke. Diocin is ‘n natuurlike saponien, met sterk oestrogeniese strukturele ooreenkomste, wat in Fenugreek voorkom. Diocin lei tot die verhoogde afskeiding van groeihormoon (GH) en uiteindelik ‘n toename in melkproduksie. Drie proewe is uitgevoer ten einde die effek van Fenugreek te ondersoek. Elke proef het bestaan uit drie behandelingsgroepe en melkbokke is ewekansig aan die groepe toegedeel. Nutrifen®, NutrifenPlus® en ‘n kontrole sonder enige additief is gebruik as behandelings. Agt-en-veertig bokke is per behandeling gebruik in die eerste proef. Die doel van hierdie proef was om die invloed van Fenugreek op melkproduksie en melksamestelling te bepaal. Die tweede proef het agt bokke per behandelingsgroep gehad en het ten doel gehad om te bepaal wat die invloed van Fenugreek op die in vitro en in vivo verteerbaarheid van die voere was. In die derde proef is dieselfde bokke as die in proef twee gebruik en hier is groeihormoon vlakke in sirkulerende bloedplasma gemeet om die invloed van Fenugreek op hierdie parameter te bepaal. Resultate van die eerste proef het getoon dat melkproduksie van bokke wat Nutrifen® ontvang het betekenisvol verhoog het (P = 0.01) terwyl NutrifenPlus® gelei het tot ‘n verhoging (P = 0.03) in melk laktose vlakke. Bloed cholesterol en melk cholesterol vlakke was onveranderd. Skynbare verteerbaarheid van die totale verteerbare voedingstowwe (TVV) van die voer het nie verander (P = 0.34) met die insluiting van Fenugreek nie. Plasma groeihormoonvlakke was nie betekenisvol verskillend (P > 0.05) tussen behandelingsgroepe nie en die gebrek aan verskille kan waarskynlik toegeskryf word aan die variasie wat binne behandelings groepe opgemerk is vir hierdie parameter. Sodanige variasie in plasma groeihormoon word as algemeen beskou in herkouers. Gevolglik kan aanvaar word dat die natuurlike voerbymiddel, Fenugreek, gebruik kan word om melkproduksie in lakterende melkbokke te verhoog. Hierdie praktyk behoort voordele in te hou vir die kommersiële melkprodusent. Die proses waardeur hierdie verhoging plaasvind is egter steeds nie duidelik nie.

Thesis (PhD (Animal Sciences))--University of Stellenbosch, 2005. / Milk production records of all grade and registered Saanen dairy goats from the Milk Recording and Performance Testing Scheme of the Animal Improvement Institute of the Agricultural Research Council of South Africa and pedigree information of these animals from SA Studbook were analyzed to obtain specific genetic parameters. Records of goats with lactations exceeding 60 days in milk were used. A sufficient number of records only became available from 1985 onwards. Reproduction records were determined from milk recording data. The number of milk production records for the British Alpine and Toggenburg breeds was too small to warrant a genetic evaluation. In total, 3190 lactation records of 1413 Saanen does were available for the initial analysis. First and second parity records, 1190 and 775 records, respectively, were subjected to a separate genetic analysis. Milk production records (2319) of one commercial herd providing more than 70% of all the records in the national herd, were also subjected to a separate genetic analysis. The fixed effects identified as having a significant (P<0.05) effect on all traits studied were production year, age of dam, lactation length, parity number, herds (owners) and year of birth. Although some significant interactions were found, they were ignored as their effects were very small. Additive genetic variances and heritability estimates were obtained by ASREML procedures fitting three models. Estimates were generally in accordance with values found in the literature although estimates for fat and protein percentage were lower than expected when compared to dairy cow data. This could be explained by pedigree information lacking in the data set. The h2 estimate for milk yield using all records, first parity records, second parity records and records from a commercial herd were 0.21±0.05, 0.32±0.08, 0.20±0.10 and 0.31±0.06, respectively. Heritability estimates for fat percentage showed a large variation and were 0.19±0.05, 0.67±0.08, 0.34±0.12 and 0.12±0.05, respectively for similar data sets as previously mentioned. In contrast to this protein percentage varied little between data sets and were 0.30±0.06, 0.32±0.00, 0.24±0.11 and 0.28±0.07, respectively. Genetic and phenotypic correlations among production traits were positive and high for all data sets. As for dairy cows, milk fat and protein percentages were negatively related to milk yield. Genetic correlations between milk fat and protein percentages were positive and moderate to high. Increasing milk volume would have a negative effect on fat and protein percentages although it would increase fat and protein yields. Reproduction parameters, i.e. age at first kidding (AFK), age at last kidding (ALK), productive life (PL) and number of lactations (NL) were derived from milk recording data. Mean values for these parameters were 457±171 days, 1046±718 days, 19.3±13.9 months and 2.24±1.37 kiddings, respectively. Kidding interval had no genetic basis and is controlled by management. Heritability estimates were in accordance with literature values and were 0.25±0.04, 0.28±0.04, 0.08±0.04 and 0.05±0.03 for AFK, ALK, PL and NL, respectively. The genetic correlation between AFK and ALK was as expected positive and high, i.e. 0.61±0.10, although the correlation between AFK and PL was negative indicating similar to dairy cows that PL is shortened by a later AFK. The genetic trend for milk, fat and protein yield were positive, although it did not differ from zero. Large variations were observed between years (R2 <0.13). Genetic trends for fat and protein percentages were positive and negative (P<0.05), respectively. These trends are in contrast to trends observed in other countries such as France, The Netherlands and the USA where positive trends were generally observed. This may indicate a higher selection emphasis on milk yield parameters or more complete data sets in terms of pedigree information. The dairy goat industry in South Africa should address some of the problems that were encountered in the analysis of the data. These include factors such as a large number of small herds, many short lactations, a large number of animals lacking production data linked to pedigree information, incomplete pedigrees, few does that have completed three or more lactations, little genetic ties between herds and a small number of progeny for bucks. Some organizational and logistic issues concerning pedigree and milk recording need to be addressed by the South African Milch Goat Society to enable the accurate estimation of the genetic merit of animals in the national herd.

Submitted by PAULA LETICIA CAMPELLO null (paulacampello@hotmail.com) on 2017-03-09T14:56:18Z No. of bitstreams: 1 Tese_ Paula_Leticia_Campello.pdf: 1806399 bytes, checksum: 0fa98c824e9bf65929115ecb89e76258 (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-03-16T19:26:11Z (GMT) No. of bitstreams: 1 campello_pl_dr_jabo.pdf: 1806399 bytes, checksum: 0fa98c824e9bf65929115ecb89e76258 (MD5) / Made available in DSpace on 2017-03-16T19:26:11Z (GMT). No. of bitstreams: 1 campello_pl_dr_jabo.pdf: 1806399 bytes, checksum: 0fa98c824e9bf65929115ecb89e76258 (MD5) Previous issue date: 2017-02-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A periodontite e o desgaste dentário excessivo são duas das síndromes mais importantes que afetam o periodonto e os dentes de pequenos ruminantes. Frequentemente relatadas em rebanhos em diversas regiões do mundo, são enfermidades multifatoriais e estão envolvidas com diminuição da produtividade de rebanhos, decorrente das dificuldades de preensão, mastigação e ruminação. O presente estudo, em forma de capítulos, teve como objetivos relatar a ocorrência de periodontite, biofilme dentário supragengival e desgaste excessivo da coroa dental em 150 cabras em lactação de rebanho estabulado. Adicionalmente, foi avaliada pela reação em cadeia da polimerase (PCR) a microbiota subgengival de sítios periodontais sadios e com bolsa periodontal frente a 23 iniciadores de espécies de bactérias com potencial patogênico no homem e em outras espécies animais. A ocorrência de lesão periodontal, avaliada pela recessão gengival, foi observada em 70,66% (106) das 150 cabras, das quais 28% (42/150) apresentaram lesões em dentes incisivos e 62% (93/150) em dentes mastigatórios. Todos os animais avaliados apresentaram algum escore de biofilme supragengival, representando um fator de risco para o desenvolvimento de periodontites. O desgaste excessivo da coroa dental foi observado em 40% (60/150) dos animais em graus variados, nos dentes incisivos e mastigatórios conjuntamente; 37,3% (56/150) somente em dentes mastigatórios e 18,6% (28/150) apenas em dentes incisivos. Na avaliação da microbiota da bolsa periodontal (n=22) e do sulco gengival (n=22) de cabras pôde-se associar a ocorrência da periodontite com Tannerella forsythia, Porphyromonas gingivalis, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, Fusobacterium necrophorum, Prevotella buccae Treponema denticola, Prevotella intermedia, Porphyromonas melaninogenica, Treponema maltophilum, Prevotella loeschii, Dialister pneumosintes e Aggregatibacter actinomycetemcomitans. Os dois problemas sanitários coocorreram no rebanho, sugerindo que, embora de etiologias distintas, provavelmente elas tenham algum fator de risco comum. Parte da microbiota avaliada e associada à periodontite diferiu, pela frequência de detecção, daquela dos sítios periodontais sem a doença, sugerindo a participação desses patógenos potenciais na etiologia da periodontite caprina. / Periodontitis and excessive dental wear are considered two of the most important syndromes that affect the periodontium and the teeth of small ruminants. Often reported in herds in different regions of the world, they are multifactorial diseases and are involved with decreased herd productivity due to difficulties in gripping, chewing and rumination. The present study, in the form of chapters, had as objective to report the occurrence of periodontitis, supragingival dental biofilm and excessive wear of the dental crown in 150 lactating goats. In addition, the subgingival microbiota of healthy sites and periodontal pockets were evaluated by the polymerase chain reaction (PCR) using 23 primers of bacterial species with pathogenic potential in man and other animal species. The occurrence of periodontal lesion, evaluated by gingival recession, was observed in 70.66% (106) of the 150 goats, which 28% (42/150) presented lesions in incisor teeth and 62% (93/150) in masticatory teeth. All animals evaluated had a supragingival biofilm score, representing a risk factor for the development of periodontitis. The excessive wear of the dental crown was observed in 40% (60/150) of the animals in varying degrees, in the incisors and masticatory teeth together; 37.3% (56/150) only in masticatory teeth and 18.6% (28/150) only in incisors. In the evaluation of the microbiota of periodontal pockets (n = 22) and gingival sulcus (n = 22) of goats, the occurrence of periodontitis can be connected to Tannerella forsythia, Porphyromonas gingivalis, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, Fusobacterium necrophorum, Prevotella buccae, Treponema denticola, Prevotella intermedia, Porphyromonas melaninogenica, Treponema maltophilum, Prevotella loescheii, Dialister pneumosintes and Aggregatibacter actinomycetemcomitans. The two sanitary problems cooccurred in the herd, suggesting that although they have different etiologies, they probably have some common risk factors. Part of the microbiota evaluated and associated with periodontitis differed, by frequency of detection, of periodontal sites without the disease, suggesting the participation of these putative pathogens in the etiology of caprine periodontitis.

This thesis was to determine the prevalence and distribution of paratuberculosis in the Ontario dairy sheep and dairy goat industries, identify potential risk factors for herds which tested positive, evaluate the accuracy of seven commercially available individual and two bulk tank diagnostic tests in these two populations, and determine the circulating strains of Mycobacterium avium ssp. paratuberculosis in faecal isolates obtained. A cross-sectional study was conducted between October 2010 and August 2011 in 29 goat herds and 21 sheep flocks located in Ontario. On each farm, 20 lactating animals over the age of two years were randomly selected and faeces, blood, and milk were sampled from each animal, and a bulk milk sample from each herd. A questionnaire inquiring about herd management and biosecurity behaviours was also completed. The seven individual animal tests evaluated were: faecal culture using the BACTEC® MGIT™ 960 liquid culture system, direct faecal PCR (Tetracore®, Rockville, MD) based on the hspX gene, the Prionics® ELISA on serum and milk, the IDEXX® ELISA on serum and milk, and the agar gel immunodiffusion (AGID) test on serum. The test evaluations used both frequentist (faecal culture - reference test) and Latent Class Analysis/Bayesian (LCA/BM) methods (no reference test). In goat herds, faecal culture demonstrated the highest sensitivity (Se), 81.1% (LCA/BM). In sheep, while faecal culture demonstrated the highest Se, 49.5%, there was a small probability it was higher than faecal PCR Se at 42.4%. The bulk tank tests evaluated were the 'Hyper-ELISA' test and real-time PCR test based on IS900 (AntelBio®). While PCR did not demonstrate sufficiently high Se to be used as a herd-level test, the Hyper-ELISA performed well as a herd-level test identifying farms with high prevalence when the cut-off was reduced to 0.05. Overall herd-level apparent prevalence was 79.3% in goat herds and 57.1% in sheep flocks when faecal culture was the reference standard and true herd-level prevalence (LCA/BM) was 83.0% and 66.8% in each population respectively. This high prevalence reveals a need for the implementation of a small ruminant paratuberculosis control program in Ontario, Canada based on testing, improving youngstock management, and strengthening biosecurity practices. / AHSI, OMAF

Made available in DSpace on 2015-03-26T13:47:31Z (GMT). No. of bitstreams: 1 texto completo.pdf: 342345 bytes, checksum: 80e5d84706ce69760a37ae144547d6fc (MD5) Previous issue date: 2007-08-10 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / This work deals with the reproductive behavior of Alpine and Saanen female goats submitted to artificial bioclimatic conditions similar to those of the the Brasilian Equatorial Region, when compared to female goats raised under normal typical bioclimatic conditions of regions where they demonstrate seasonality. The study was conducted during the reproductive season for goats (April to July of 2007), consisting of an adaptation period of 30 days (Phase 1) and an experimental period (Phase 2) of 60 days, in the bioclimatic chamber. Two groups of animals were used in this study. Group 1 (n = 4) remained in the bioclimatic chamber with temperature and air humidity control (8:00 - 12:00 hours - 30 ºC; 12:00 - 18:00 - 36 ºC; 18:00 - 8:00 - 26 ºC; with 60 % of average humidity; and a 12 hour fotoperiod), thus simulating bioclimatic conditions of the northern region of Brazil (next to the Equator line), whereas group 2 (n = 4) was kept under influence of the natural climatic variations of the season. The physiological parameters of respiratory (FR) and cardiac frequencies (FC), rectal temperature (TR) and rumination behavior (MR) were measured twice a day, with daily follicular dynamics accompaniment, besides blood collection twice a week for triiodotironine (T3), tiroxine (T4), cortisol, total cholesterol, total proteins (PT), albumine (ALB), progesterone (P4) and estrogen (E2) dosages. The average values for water consumption were different (p < 0.05) as a function of group and time, showing that the animals of group 1 consumed more than the double (4,386.3 mL/day) than those of group 2 (1,663.2 mL/day). In relation to the ration consumption, there was a difference both between groups and periods (499.0 and 490.8 g/day, for groups 1 and 2, respectively). There was no variation in the average values for corporal weight and corporal score condition (ECC) as a function of time, however, during the experimental period, there was a difference in the weight of the animals between groups (50.5 and 41.5 kg, for groups 1 and 2, respectively). During the experimental period, a difference was observed (p < 0.05) for the studied physiological parameters between the morning and the afternoon, being the afternoon values always higher than the ones in the morning. With regard to cholesterol, ALB and PT concentrations behavior as a function of the days, in the different groups and experimental and adaptation periods, no difference was registered between the obtained average values during the observation period (p > 0.05). With regard to T3, T4 and cortisol concentrations behavior as a function of the days, in the different groups and experimental and adaptation periods, no difference was registered between the obtained values during the experimental period (p > 0.05). There was no difference (p > 0.05) in the duration of estral cycle and estrus for the animals of groups 1 and 2. There was no difference (p > 0.05) in relation to the number of follicles observed in the day of the estrus and to the ovulatory follicle diameter, as a function of the groups and number of estrus evaluated, with average values of 4 and 3.5 in the 1st estrus, 5 and 3 in the 2nd estrus, and 4 and 4.5 in the 3rd estrus, for groups 1 and 2, respectively. The number of follicular waves observed varied from 4 to 5 in group 1 and 2, to 4 waves in group 2. The day after the ovulation where the corpus luteum (CL) presented greater diameter was 5.2 ± 2.0; 9.7 ± 2.7 and 7.7 ± 2.6 for the 1st, 2nd and 3rd estral cycles, respectively, and the CL area in the day of its higher diameter was 9.7 ± 3.0; 12.1 ± 4.4 and 7.0 ± 1.3 mm3 for the 1st, 2nd and 3rd estral cycles, respectively. There was no difference (p > 0.05) in any of the studied reproductive parameters, neither as a function of the group nor as of the estrus. Although the animals of group 1 demonstrated higher values of P4 and E2 in relation to the animals of group 2, the endocrine secretion standard of these hormones revealed to be similar for both groups in all the studied estral cycles, as a function of time. Although the number of animals observed in bioclimatic conditions similar to the Eastern Amazon was small, the average values obtained for the physiological parameters, food and water ingestion, metabolic and hormonal, indicated that female goats can be raised under bioclimatic conditions, without modifying the related physiological standards. / Este trabalho estuda o comportamento reprodutivo de cabras das raças Alpina e Saanen submetidas a condições bioclimáticas artificiais semelhantes Zona Equatorial Brasileira, quando comparadas com cabras criadas em condições bioclimáticas normais típicas de regiões onde as mesmas demonstram comportamento poliéstrico estacional. O estudo foi conduzido durante a estação reprodutiva para a espécie caprina (abril a julho de 2007), consistindo de um período de adaptação de 30 dias (Fase 1), e período experimental (Fase 2) de 60 dias, na câmara bioclimática. Foram utilizados neste estudo, dois grupos de animais. O grupo 1 (n = 4) permaneceu na câmara bioclimática com controle da temperatura ambiente e umidade relativa do ar (8:00 - 12:00 horas 30 ºC; 12:00 - 18:00 36 ºC; 18:00 - 8:00 26 ºC; Umidade relativa (UR) média de 60 %; Fotoperíodo de 12 horas), simulando assim condições bioclimatológicas da Região Norte do Brasil (próxima à linha do Equador), enquanto que o grupo 2 (n = 4) foi mantido em gaiolas individuais com influência das variações climáticas naturais da estação. Foram mensurados parâmetros fisiológicos de freqüências respiratória (FR) e cardíaca (FC), temperatura retal (TR) e movimentos ruminais (MR) duas vezes ao dia e acompanhamento diário da dinâmica folicular, além de coleta de sangue 2 vezes por semana para as dosagens de triiodotironina (T3), tiroxina (T4), cortisol, colesterol, proteínas totais (PT), albumina (ALB), progesterona (P4) e estrógeno (E2). Os valores médios para o consumo de água mostraram-se diferentes (p < 0,05) tanto em função do grupo, quanto em função do tempo, sendo que os animais do grupo 1 consumiram mais do que o dobro de água (4.386,3 mL/dia) do que os animais do grupo 2 (1.663,2 mL/dia). Em relação ao consumo de ração, houve diferença entre grupos e fases (499,0 e 490,8 g/dia, para os grupos 1 e 2, respectivamente). Não houve variação nos valores médios para os parâmetros de peso corporal e escore de condição corporal (ECC) em função do tempo, no entanto durante a fase experimental houve diferença entre grupos no peso dos animais (50,5 e 41,5 kg, para os grupos 1 e 2, respectivamente). Durante a fase experimental, observou-se diferença (p < 0,05) para os parâmetros fisiológicos estudados entre os turnos da manhã e tarde, sendo os valores da tarde sempre superiores aos da manhã. Com relação ao comportamento concentrações de colesterol, ALB e PT em função dos dias, nos diferentes grupos e fases de adaptação e experimental, não se registrou nenhuma diferença nos valores médios obtidos durante todo o período de observação (p > 0,05). Com relação ao comportamento das concentrações de T3, T4 e cortisol em função dos dias, nos diferentes grupos e fases de adaptação e experimental, não se registrou nenhuma diferença nos valores obtidos durante todo o período experimental (p > 0,05). Não houve diferença (p > 0,05) para as durações de ciclo estral e estro para os animais dos grupos 1 e 2. Não houve diferença (p > 0,05) em relação ao número de folículos observados no dia do estro e diâmetro do folículo ovulatório, tanto em função dos grupos, quanto no número de estros avaliados, com valores médios de 4 e 3,5 no 1º estro, 5 e 3 no 2º estro, e 4 e 4,5 no 3º estro, para os grupos 1 e 2, respectivamente. O número de ondas foliculares observadas variou de 4 a 5 nos animais do grupo 1, e 2 a 4 ondas nos animais do grupo 2. O dia após a ovulação em que o corpo lúteo (CL) apresentou maior diâmetro foi 5,2 ± 2,0; 9,7 ± 2,7 e 7,7 ± 2,6 para os 1º, 2º e 3º ciclos estrais, respectivamente, e a área do CL no dia de seu maior diâmetro foi de 9,7 ± 3,0; 12,1 ± 4,4 e 7,0 ± 1,3 mm3 para os 1º, 2º e 3º ciclos estrais, respectivamente. Não houve diferença (p > 0,05) em nenhum dos parâmetros reprodutivos estudados, tanto em função do grupo quanto dos estros. Apesar de os animais do grupo 1 terem demonstrado valores mais elevados de P4 e E2 em relação aos animais do grupo 2, o padrão de secreção endócrina desses hormônios mostrou-se semelhante para ambos os grupos em todos os ciclos estrais estudados, em função do tempo. Embora o número de animais avaliados em condições bioclimáticas semelhantes à Zona Equatorial Brasileira seja pequeno, os valores médios obtidos para os parâmetros fisiológicos, ingestão de alimentos e água, metabólicos e hormonal, indicaram que fêmeas caprinas podem ser criadas nas condições bioclimáticas propostas, sem que haja comprometimento nos referidos padrões fisiológicos.

The aim of this study was to develop and examine the validity of using a phenotype scoring system (PTS), a new concept, in evaluating milk yield and constituents in different goat genotypes (Indigenous, British Alpines, Saanen and Toggenburg) raised in small scale production systems. Strategic decisions of small scale African farmers are mostly based on visual appraisal or body condition scoring (BCS) of their animals. BCS has been highly recommended as a means to evaluate both the energy and the health status of animals, especially in beef farming, but this method has been criticized for being too simple and too subjective because its evaluation is often done too late after the damage has already happened. Phenotype scoring (an approach which includes breed, udder size and BCS of the animal) is presented in this study as a better tool to evaluate milk yield in different goat genotypes raised under free range conditions. This has also been a good opportunity firstly to indicate which, among the three dairy breeds of goat under discussion, can adapt best to the African small scale farming system; secondly to review the relevance of some blood metabolites in characterizing milk production in different goat breeds and thirdly to study the milking capacity of the indigenous compared to the dairy goats raised under small scale production systems in South Africa. Thirty-two goats (8 Indigenous, 8 British Alpines, 8 Saanen and 8 Toggenburg) were raised in a free range system at the ARC-Irene experimental farm close to Pretoria. The experiment was a completely randomized experimental design with eight replicates per treatment group. Blood samples were collected by jugular venipuncture into 10 ml heparinised tubes in the morning before feeding on a weekly basis over a period of two months. Blood plasma was immediately aspirated after centrifugation (3000G), kept on ice and brought to the laboratory for the analysis of glucose, cholesterol, urea nitrogen (BUN) and free fatty acid (FFA) concentrations. Immediately after, all does were entirely milked (followed by 1ml oxytocin IM injection and the kids taken away for a period of four hours) before a second milking session took place to measure the daily milk yield of the does. Milk samples were analyzed for lactose, milk proteins, milk fat, milk urea-nitrogen (MUN) and milk somatic cell count (SCC). In addition body condition score (BCS), age and data related to the goat genotype (breed, udder characteristics) were recorded. Results confirmed that milk yield from dairy goats was higher (p<0.001) than the milk yield of indigenous goats during the entire period of study. Milk lactose values recorded in this study (between 3.9 and 4.9%) were the most stable constituent in goat’s milk. Milk protein concentration (between 3.1 and 4.5%) was significantly higher in the indigenous than in dairy breeds, especially in week one and from week four onwards. Milk fat values (between 3.3 and 7.7%) displayed a decline in all breeds; but as from week three, the fat in milk of indigenous does increased and from week five onwards, it remained significantly higher (p<0.001) compared to that of dairy breeds. In conclusion, the superiority of dairy breeds in milk yield was proven while the quality of indigenous goat milk was recognized. Studies on the characterization of milk production in different breeds revealed that the Toggenburg was superior to the other breeds, followed by the British Alpines and the Saanen; but the British Alpines showed a better adaptability to the environment followed by the Toggenburg and the Saanen. The latter could not produce milk without feed supplementation and lost most body condition as compared to the other breeds. Statistical analyses indicated that breed influenced milk yield, milk fat and the protein content of milk (especially in the Saanen and Toggenburg goats). BCS influenced fat content, lactose, milk proteins, MUN and SCC and also milk yield. Udder size influenced milk proteins and milk yield while udder attachment was associated with milk yield only. These results show that PTS, because it takes into account BCS, breed and udder size, is a better tool for predicting milk yield of goats herded in small scale farming systems. Africans interested in dairy goat farming should adopt PTS as a means to evaluate milk yield especially since milk is sold per volume and not by quality in Africa. Finally, milk from the indigenous goats is superior in terms of lactose, fat and protein content. The latter quality attributes can be used as selection criteria since the milk industry pays premiums for the fat and protein content of milk. / Thesis (PhD)--University of Pretoria, 2012. / Animal and Wildlife Sciences / unrestricted

La sélection génomique, qui a révolutionné la sélection génétique des bovins laitiers notamment, est désormais envisagée dans d’autres espèces comme l’espèce caprine. La clé du succès de la sélection génomique réside dans la précision des évaluations génomiques. Chez les caprins laitiers français, le gain de précision attendu avec la sélection génomique était un des questionnements de la filière en raison de la petite taille de la population de référence disponible (825 mâles et 1945 femelles génotypés sur une puce SNP 50K). Le but de cette étude est d’évaluer comment augmenter la précision des évaluations génomiques dans l’espèce caprine. Une étude de la structure génétique de la population de référence caprine constituée d’animaux de races Saanen et Alpine, a permis de montrer que la population de référence choisie est représentative de la population élevée sur le territoire français. En revanche, les faibles niveaux de déséquilibre de liaison (0,17 entre deux SNP consécutifs) de consanguinité et de parenté au sein de la population, similaires à ceux trouvés en ovins Lacaune, ne sont pas idéaux pour obtenir une bonne précision des évaluations génomiques. De plus, malgré l’origine commune des races Alpine et Saanen, leurs structures génétiques suggèrent qu’elles se distinguent clairement d’un point de vue génétique. Les méthodes génomiques (GBLUP ou Bayésiennes) « two-step », basées sur des performances pré-corrigées (DYD, EBV dérégressées) n’ont pas permis une amélioration significative des précisions des évaluations génomiques pour les caractères évalués en routine (caractères de production, de morphologie et de comptages de cellules somatiques) chez les caprins laitiers. La prise en compte des phénotypes des mâles non génotypés permet d’augmenter les précisions des évaluations de 3 à 47% selon le caractère. L’ajout des génotypes de femelles issues d’un dispositif de détection de QTL améliore également les précisions (de 2 à 14%) que ce soit pour les évaluations two steps ou les évaluations basées sur les performances propres des femelles (single step). Les précisions sont augmentées de 10 à 74% avec les évaluations single step comparées aux évaluations two steps, ce qui permet d’atteindre des précisions supérieures à celles obtenues sur ascendance. Les précisions obtenues avec les évaluations génomiques multiraciales, bicaractères et uniraciales sont similaires même si la précision des valeurs génomiques estimées des candidats à la sélection est plus élevée avec les évaluations multiraciales. La sélection génomique est donc envisageable chez les caprins laitiers français à l’aide d’un modèle génomique multiracial single step. Les précisions peuvent être légèrement augmentées par l’inclusion de gènes majeurs tels que celui de la caséine αs1 notamment à l’aide d’un modèle « gene content » pour prédire le génotype des animaux non génotypés. / Genomic selection which is revolutionizing genetic selection in dairy cattle has been tested in several species like dairy goat. Key point in genomic selection is accuracy of genomic evaluation. In French dairy goats, gain in accuracy using genomic selection was questioning due to the small size of the reference population (825 males and 1 945 females genotyped). The aim of this study was to investigate how to reach adequate genomic evaluation accuracy in French dairy goat population. The study of reference population structure (Alpine and Saanen breeds) showed that reference population is similar to the whole population of French dairy goats. But the weak level of linkage disequilibrium (0.17 between two consecutive SNP), inbreeding and relationship between reference and candidate population were not ideal to maximize genomic evaluation accuracy. Despite their common origin, genetic structure of Alpine and Saanen breeds suggested that they were genetically distant. Two steps genomic evaluation (GBLUP, Bayesian) based on performances corrected for fixed effect (DYD, deregressed EBV) did not improve genetic evaluation accuracy compared to classical evaluations for milk production traits, udder type traits and somatic cells score classically selected in French dairy goat. Taking into account phenotypes of ungenotyped sires increased genomic evaluation from 3 to 47% depending on the trait considered. Adding female genotypes also improved genomic evaluation accuracies from 2 to 4% depending on the method (two steps or single step) and on the trait. When using gemomic evaluation directly based on female performances (single step), accuracy of genomic evaluation reach the level obtained from ascendance in classic evaluation which was not the case using two steps evaluations. Genomic evaluation accuracies were similar when using multiple-trait model, multi-breed or single breed evaluation. But accuracies derived from prediction error variances were better when using multi-breed genomic evaluations. Genomic selection is feasible in French dairy goats using single step multi-breed genomic evaluations. Accuracies could be slightly improved integrating major gene as αs1 casein especially when using « gene content » approach to predict genotypes of ungenotyped animals.

Suite aux travaux de Céline Carillier (2012-2015), des évaluations ssGBLUP ont été mises en place en 2018 pour les races caprines Alpine et Saanen. L’objectif est d’améliorer les précisions des évaluations pour maximiser le progrès génétique pour les caractères d’intérêt. Pour notre première étude, nous nous sommes intéressés à l’effet de la taille de la population de référence (limitée pour ces races) sur les précisions des évaluations. L’accroissement de la population d’apprentissage ne s’est pas systématiquement accompagné d’une hausse des précisions. Le ssGBLUP présente des biais et tend à surestimer ou sous-estimer les valeurs génomiques. Des hyperparamètres ont été introduits dans la construction de la matrice génomique du ssGBLUP pour limiter ces biais. Ces hyperparamètres (, et ) peuvent améliorer les biais tout en affectant de manière limitée les précisions. Pour les races Alpine et Saanen, les biais sont proches de 1 pour un compris entre 0,1 et 0,3 et un compris entre 3 et 4. L’hyperparamètre a peu d’effet sur les précisions et les biais, sa valeur par défaut (0,95) semble être optimale. Dans une deuxième partie, nous nous sommes intéressés à l’intégration de mutations causales ou de QTLs dans les modèles d’évaluations pour améliorer les précisions. Des mutations causales et des QTLs ont été détectés dans les races caprines. On peut citer le gène de la caséine s1 pour le taux protéique ou DGAT1 pour le taux butyreux. D’autres études ont identifié un QTL, localisé sur le chromosome 19, en Saanen. Il a été détecté pour les caractères : quantités de lait et de matières (grasses et protéiques), la distance plancher-jarret et pour la qualité de l’attache arrière. L’utilisation des génotypes de la caséine s1 ou DGAT1 dans les modèles d’évaluations (gene content) a été inefficace pour améliorer les précisions des évaluations. Le gene content est une méthode multicaractère où le « gene content » est un second caractère corrélé au caractère en sélection. Pour le taux protéique ou butyreux, les précisions avec le gene content sont entre -11 % et 0 % inférieures aux précisions du ssGBLUP. En pondérant les SNPs de manière adéquate avec un ssGBLUP (appelée Weighted ssGBLUP et notée WssGBLUP), les précisions des évaluations ont été améliorées. Cette méthode attribue des poids aux SNPs en fonction de leur association aux caractères. Ces poids sont intégrés dans la construction de la matrice de parenté génomique. Des gains jusqu’à +5 % et +14 % (Alpine et Saanen) ont été observés par rapport au ssGBLUP. Le WssGBLUP est plus adapté pour la race Saanen car des QTLs sont présents sur la majorité des caractères. Pour la race Alpine, le WssGBLUP s’est avéré intéressant pour le taux protéique. Le ssGBLUP reste la meilleure méthode lorsque le caractère a une architecture génétique polygénique. Enfin, nous nous sommes intéressés à des modèles d’évaluation génomiques haplotypiques. Les haplotypes ont été construits en regroupant plusieurs SNPs consécutifs ou en se basant sur le déséquilibre de liaison entre SNPs. Les haplotypes sont utilisés pour construire une matrice de parenté haplotypique ou convertis en pseudo-SNPs, pour construire une matrice de parenté génomique. En Alpine, les précisions du ssGBLUP haplotypiques (ou pseudo-SNPs) ont évolué entre -1 % et 19 % par rapport au ssGBLUP basé sur l’information des SNPs. En Saanen, les précisions ont évolué entre -3 % et +6 % par rapport au ssGBLUP. Nous avons appliqué le WssGBLUP avec des pseudo-SNPs. En Saanen, une amélioration des précisions jusqu’à +16 % par rapport au ssGBLUP a été observée. Les gains les plus forts (supérieurs à +10 %) sont obtenus pour les caractères avec un QTL identifié (lait, matières grasses et protéiques, taux protéique, qualité de l’attache arrière et distance entre le plancher et le jarret). En Alpine, des gains de précision entre -8 % et +5 % ont été observés par rapport au ssGBLUP selon le caractère excepté pour les matières grasses (+19 %). / Following Céline Carillier’s PhD (2012-2015), genomic evaluations based on the ssGBLUP were implemented in 2018 in the dairy goat breeds Alpine and Saanen. The objective of breeders is to improve the accuracy of genomic evaluations in order to maximize genetic gain for traits of interest. In our first study, we looked at the effect of the size of the reference population (limited for these breeds) on the accuracy of genomic evaluations. The increase of the training population was not systematically associated with an increase of genomic accuracies. The ssGBLUP has some biases and tends to overestimate or underestimate genomic value estimates. To avoid these biases, hyperparameters were introduced into the construction of the ssGBLUP genomic relationship matrix. An analysis of these hyperparameters (, and ) was carried out and we found that the choice of them improves bias while having a limited impact on genomic accuracy. For the Alpine and Saanen breeds, the biases are close to 1 for a between 0.1 and 0.3 and a between 3 and 4. The hyperparameter has little effect on accuracy and bias and its default value (0,95) seems to be optimal. In a second part of my thesis, we focused on the integration of causal mutations or QTLs into genomic evaluation models to improve genomic accuracy. Causal mutations and QTLs were detected in the Alpine and Saanen breeds such as the s1 casein gene for protein content or DGAT1 for fat content. Other studies have shown a QTL, located on chromosome 19, in the Saanen breed. It was detected for different traits: milk, fat and protein content, udder floor position and rear udder attachment. The use of genotypes for s1 casein or DGAT1 in genomic evaluation models (gene content) was inefficient in improving evaluation accuracy. The gene content is a multi-trait method where the "gene content" is a second trait correlated to the selected trait. Whether for protein or fat content, accuracies with gene content were between -11% and 0% lower than the ssGBLUP accuracies for the Alpine and Saanen breeds. We have shown by adequately weighting SNPs in an ssGBLUP (approach called Weighted ssGBLUP and noted WssGBLUP), the accuracy of evaluations could be improved. This method assigns weights to SNPs based on their association with traits. These weights are integrated into the construction of the genomic relationship matrix. Gains up to +5% for the Alpine breed and +14% for the Saanen breed were observed compared to the ssGBLUP. The WssGBLUP is more suitable for the Saanen breed because QTLs are present on the majority of traits. For the Alpine breed, WssGBLUP was interesting for the protein content. The ssGBLUP remained the most interesting method when the trait had a polygenic genetic architecture. Finally, in the last study, we focused on haplotype genomic evaluation models. Haplotypes were constructed either by grouping several consecutive SNPs or by using the linkage disequilibrium (LD) between SNPs. The haplotypes are then used to build a haplotypic relationship matrix or converted to pseudo-SNPs to build a genomic relationship matrix. In the Alpine breed, the accuracy of the haplotypic ssGBLUP (or pseudo-SNPs) was increased between -1% and 19% compared to an ssGBLUP based on SNP information. On the other hand, in the Saanen breed, the accuracy was increased between -3% and +6% compared to a ssGBLUP. Finally, we applied the WssGBLUP approach using pseudo-SNPs. In the Saanen breed, an improvement in accuracy up to +16% compared to a ssGBLUP was observed. The highest gains (above +10%) were obtained for traits with an identified QTL (milk, fat and protein yields, protein content, udder floor position and rear udder attachment). In the Alpine breed, accuracy gains between -8% and +5% were observed compared to ssGBLUP depending on the trait except for fat yield and fat content where the gains reach +19%.

Um inquérito soroepidemiológico foi conduzido para a pesquisa de anticorpos anti-Chlamydophila abortus, anti-Toxoplasma gondii, anti-Neospora caninum e anti-Brucella abortus em caprinos leiteiros do semiárido da Paraíba. A amostragem foi delineada para a determinação da prevalência de propriedades positivas (focos) e de animais soropositivos. Foi realizada uma seleção aleatória de propriedades (unidades primárias) e, dentro dessas, foi escolhido, de forma aleatória, um número pré-estabelecido de fêmeas caprinas (unidades secundárias). Ao todo foi colhido sangue de 974 fêmeas caprinas provenientes de 110 propriedades. Na ocasião da colheita, foi aplicado um questionário epidemiológico por propriedade e as coordenadas geográficas foram obtidas com um aparelho de GPS. Para o diagnóstico sorológico das infecções por C. abortus e B. abortus, foram utilizados os testes de Fixação de Complemento e do Antígeno Acidificado Tamponado (AAT), respectivamente. Para o diagnóstico das infecções por T. gondii e N. caninum foram utilizadas reações de imunofluorescência indireta (RIFI). Uma propriedade foi considerada foco quando apresentou pelo menos um animal soropositivo. As análises realizadas foram: determinação das prevalências de focos e de animais soropositivos e identificação de fatores de risco. As prevalências de focos de C. abortus, T. gondii, N. caninum e B. abortus foram de 50,0% [40,3% - 59,7%], 70,0% [60,5% - 78,4%], 16,4% [10,0% - 24,6%] e 0,0% [0,0% - 3,3%], respectivamente. As prevalências de animais soropositivos para C. abortus, T. gondii, N. caninum e B. abortus foram de 11,9% [8,3% - 16,8%], 18,1% [14,3% - 22,6%], 1,9% [1,0% - 3,4%] e 0,0% [0,0% - 3,8%], respectivamente. Os fatores de risco para a infecção por C. abortus foram: compartilhar reprodutores e/ou sêmen (odds ratio = 2,35) e histórico de abortamentos (odds ratio = 3,06). Presença de plantas tóxicas na propriedade (odds ratio = 5,11) e a caprinocultura não ser a principal atividade (odds ratio = 3,34) foram apontadas como fatores de risco para a ocorrência de focos de infecção por T. gondii. Para a infecção por N. caninum, os fatores de risco associados à ocorrência de focos foram: alugar pastos (odds ratio = 10,34), não usar seringas descartáveis (odds ratio = 3,78) e possuir 25 ou mais caprinos (odds ratio = 6,51). Sugere-se que esforços sejam concentrados na condução de medidas de prevenção e controle das infecções por C. abortus, T. gondii e N. caninum em caprinos leiteiros do semiárido da Paraíba, especialmente aquelas relacionadas à correção de fatores de risco, visando a redução da prevalência e da disseminação desses agentes nesses animais e a possível exposição de seres humanos. / A seroepidemiological study for anti-Chlamydophila abortus, anti-Toxoplasma gondii, anti-Neospora caninum and anti-Brucella abortus antibody research was carried out in dairy goats from the semiarid of Paraíba state. Sampling was delineated for the determination of positive flocks (foci) and seropositive animals prevalences. A random selection of flocks (primary units) was performed and a pre-established number of female goats (secundary units) were sampled in each of these flocks. A total of 975 serum samples from 110 flocks were collected. On the occasion of the blood collection, an epidemiological questionnaire was applied in each flock and the geographical coordinates were obtained with a GPS. For the serological diagnosis of C. abortus and B. abortus infections complement fixation test and Rose Bengal test (RBT) were used, respectively. Indirect fluorescent antibody tests (IFAT) were carried out for detecting anti-T. gondii and anti-N. caninum antibodies. A flock was considered focus when presented at least one seropositive animal. The following analyses were performed: determination of foci and seropositive animals prevalences and identification of risk factors. Foci prevalences of C. abortus, T. gondii, N. caninum and B. abortus were 50.0% [40.3% - 59.7%], 70.0% [60.5% - 78.4%], 16.4% [10.0% - 24.6%] and 0.0% [0.0% - 3.3%], respectively. Seropositive animals prevalences to C. abortus, T. gondii, N. caninum and B. abortus were 11.9% [8.3% - 16.8%], 18.1% [14.3% - 22.6%], 1.9% [1.0% - 3.4%] and 0.0% [0.0% - 3.8%], respectively. Risk factors associated with C. abortus infection were: lend buck and/or semen (odds ratio = 2.35) and history of abortions (odds ratio = 3.06). Presence of toxic plants in the property (odds ratio = 5.11) and goat production do not be the main activity in the property (odds ratio = 3.34) were identified as risk factors for the occurrence of foci of T. gondii infection. For the N. caninum infection risk factors associated with occurrence of foci were: share pasture (odds ratio = 10.34), do not use disposable syringes (odds ratio = 3.78) and flock size 25 goats (odds ratio = 6.51). It was suggested that efforts be concentrated on the application of control and prevention measures for C. abortus, T. gondii and N. caninum infections in dairy goats from the semiarid of the Paraíba state, especially those related to the correction of risk factors, aiming to reduce the prevalence and spread of these agents and possible exposure of humans.

Goat's milk has many great nutritional properties, which arise from its unique composition. The milk composition is however depending on the composition of the feed diet. The aim of this work is to determine how the diet affects the quantity of milk yield and composition. We also made observations to determine how selected herbs affect the intake of feed rations with goats. The experimental part is divided into three parts. In the first part, we evaluated the impact of selected herbs to income ration with goats. We found that the addition of perennial ryegrass (Lolium perenne) increases the amount of food taken. Conversely, an addition of meadow pea (Lathyrus pratensis) decreases the amount of food intake. In the second part, we tested the ribwort plantain (Plantago lanceolata) effect on the milk composition. We found that an addition of this herb in the ration slightly increases daily milk yield. In the third section we monitored a herd of goats on grassland. We evaluated influence of the composition of pasture vegetation and the addition of oats on milk yield and composition. Our conclusion is that the composition of the pasture had a significant impact not only on the basic components of milk, but also on the representation of individual groups of fatty acids. The adding of oats decreases the influence of grazing.