Understanding the particularities of pasture inclusion on cows' diets and their subsequent impact on the digestive processes, together with possible differences in the nutrient utilization of cows managed under grazing conditions, are challenges that must be elucidated in order to design strategies to improve the cows' productive performance. The objectives of this dissertation were: 1) to review the existing literature on ration formulation for dairy cows in pasture-based systems, identifying limitations and potential improvement areas, 2) to evaluate the adequacy of the Molly model predictions of ruminal fermentation, nutrient digestion, and performance from cows consuming fresh ryegrass-based diets, identifying mechanisms that could be used to direct further model improvements, 3) to evaluate the model predictions of milk, fat and protein production using data from Holstein-Friesian and Jersey cows from Chile managed under pasture-based systems, identifying mechanisms that could be used to direct further model improvements, 4) to identify the different dairy breeds and their crosses that are used in the Chilean dairy population, determining if there are specific breed and heterosis effects on productive and some functional traits, and 5) to characterize the ruminal degradation dynamics of crude protein (CP) and individual amino acids (AA) from ryegrass (Lolium perenne) at vegetative stage, generating information to improve the ration formulation in dairy cows in pasture-based systems. From the literature revision in objective 1, different factors that could help to create a more specific classification of dairy pasture-based systems were identified. Maximizing grass inclusion seems to leads to an oversimplification of diets, potentially limiting the performance of medium and high producing cows. Despite the low N use efficiencies reached in pasture-based systems, there is a lack of information in studies that delve into the ruminal degradation of CP and AA, as well as their intestinal absorption, and subsequent post-absorptive utilization. Advances in the understanding of these areas could help to create strategies to face this problem. There is evidence suggesting that cows can perform different under different productive systems, but various breeds, strains, and crossbreds are used in pasture-based systems, being needed first a better characterization of them. To achieve the second objective, a total of 25 studies (n = 115 treatments) including dairy cows consuming ryegrass predominant diets, published from 1970 through 2020, were collected from the literature and used to assess the model accuracy and precision based on root mean squared errors and concordance correlation coefficients (CCC). Predictions of protein and fiber digestion and fiber and organic matter fecal excretion were improved after model reparameterization, while body weight and body condition score predictions were improved after model modifications and reparameterization. Although digestion of nutrient was better represented by the new set of parameters derived, the accuracies of milk, protein, and fat production remained low (CCC of 0.13, 0.12, and 018, respectively), with moderate slope bias. To achieve the third objective, a dataset including 180 group cows' diets (153 from Holstein Friesian and 27 from Jersey cows) from 18 commercial dairy farms with different inclusion of ryegrass was compiled. Chemical composition of feeds ingredients, group intakes and animal performance records, were provided by the Chilean cooperative Colun. Separately model mammary reparameterization of Holstein Friesian and Jersey cows' data, improved both milk production (CCC values of 0.69 and 0.90, respectively) and milk solids predictions (CCC values of 0.68 and 0.92 for milk protein and 0.65 and 0.80 for milk fat, for Holstein Friesian and Jersey cows, respectively). This indicates that there seems to be some differences in mammary cells and cells activity between breeds evaluated, translated into different lactation curves and milk solids synthesis patters. To achieve the fourth objective, a dataset considering 1,429,132 records from 586,624 cows that calved between 1998 and 2018 was compiled. Pedigree information, milk, milk protein, and milk fat, as well as somatic cell score and calving interval records were provided by the Chilean cooperative COOPRINSEM. The proportion of each breed according to the different country origin (strain) was calculated for all the animals, being identified eight genetic strains with enough information to perform separated genetic evaluations: Chilean Friesian, French Holstein-Friesian, US-Holstein, US-Jersey, French Montbeliarde, New Zealander Holstein-Friesian, Swedish Red and White, and British Friesian. Four different genetic models, increasing in complexity (considering breed or strain classification, crossbreeding proportion, and heterosis effects) were tested. Specific effects for some genetic strains, as well as heterosis effects between some strains with Chilean Friesian were identified, so these effects should be considered when performing genetic evaluations in the Chilean dairy population. Also, they can be used to direct future selection programs. To achieve the last objective, an in situ study using three cannulated cows was carried out at the Agricultural Research Station of the Austral University of Chile (Valdivia, Chile). Samples from a perennial ryegrass pasture were collected during winter, spring and summer at vegetative stage. Duplicate bags were ruminally incubated for 4, 8, 12, 24, and 96 h. CP and AA profile of original samples and from incubation residues were determined. Ryegrass samples presented a high crude protein content (averaging 25.8%), however, the RUP content was ~15 to 20% of CP. Significant differences were observed for ryegrass CP and individual AA ruminal degradation kinetics, this seems to be associated to some specific AA. / Doctor of Philosophy / The used of pasture-based systems in dairy production are an important alternative in countries were local environmental and climatological conditions, as well as soil properties are suitable for the growth of high-quality grasslands. The main advantages attributed to the use of pasture-based system are the reduction in the production costs, and potentially improving the nutrition quality of dairy products as well as the cows' welfare. However, they have some important limitations as the natural variation in the quantity and quality of available herbage. Also, there is a lack of information on fundamental nutrition of pasture nutrients digestion and utilization by the cows manage and selected under these environmental conditions. The first two objectives of this dissertation consisted in using the Molly nutritional model, which represents the biology of the whole cow, in order to identify key aspects to better understand the cows manage under pasture-based systems and develop strategies to precise their nutrition. Particularly, topics such as prediction of ruminal fermentation and digestive processes, mobilization of body reserves, mammary glands metabolism, and potential differences between Holstein-Friesian and Jersey cows were analyzed. Overall, work on these objectives resulted in improvements to the Molly model for making predictions of diets that include grass. The diversity of breeds and their country of origin, as well as different crosses in the Chilean dairy population were explored. A more comprehensive genetic model was proposed in this work to precise the calculation of breeding values in the country. Furthermore, our findings could be used as inputs to direct future selection programs. The last objective explored the ruminal degradation of crude protein and each individual amino acid in ryegrass. We demonstrate that indeed there are differences in the degradation parameters for some amino acids. Due to the high degradability of fresh ryegrass, there could be some potential limitations in the supply of some essential amino acids, especially in high producing cows consuming predominant ryegrass diets.

The objectives of this study were to evaluate the effect of Leptospirosis on reproductive and productive performance for dairy breeds cows and to identify the inheritance of this disease by estimating the coefficient of heritability. There were used 1,788 test day milk records, measured in 115 Holstein, 16 Jersey and 18 crossbred cows, daughters of 51 bulls, collected between June/2007 and February/2008 in six herds raised in the Western Region of Santa Catarina State. The file contained the following information: identification of animal (cow) and his father, date of the cow birth, date of the last delivery, test day milk production; reproductive history, Leptospirosis serology, nutrition and health management and outcome of treatment. The effect of Leptospirosis on milk production was evaluated by comparing the performance of serum positive animals, before and after the treatment, through the Test PDIFF, while the effect on the reproductive characteristics were evaluated through the test of the "Qui" Square, relating the serology for Leptospirosis and the reproductive history of animals. The Leptospirosis inheritance probability was evaluated by the coefficient of heritability for serology and for this, there were used 125 records measured in 97 Holstein, 10 Jersey and 18 crossbred cows, daughters of 27 bulls. The results of this study show that Leptospirosis causes reproductive problems, since 70.67% of the animals with positive serology for the disease showed reproductive problems such as repetition of estrus, abortion and prolonged anestrous. Leptospirosis also causes reduction in milk production, since the serum positive animals yielded an average 20.09 liters/day before being treated and, 22.01 liters/day after the treatment, difference equivalent to 1.92 liters/day. The coefficient of heritability of 36% shows that it is possible to produce a population more resistant to the disease by selection. / Os objetivos do presente estudo foram avaliar o efeito da Leptospirose sobre o desempenho reprodutivo e produtivo de vacas de raças leiteiras e identificar o tipo de herança desta enfermidade através da estimativa do coeficiente de herdabilidade. Foram utilizados 1.788 registros de produção de leite no dia do controle, mensurados em 115 vacas da raça Holandesa, 16 Jersey e 18 Mestiças, filhas de 51 touros, coletados entre os meses de junho de 2007 a fevereiro de 2008 em seis rebanhos na Região Oeste do Estado de Santa Catarina. O arquivo continha as seguintes informações: identificação do animal (vaca) e do seu pai; data de nascimento da vaca, do último parto e dos controles leiteiros; histórico reprodutivo, manejo nutricional e sanitário, sorologia para a Leptospirose e resultado de tratamento. O efeito da Leptospirose sobre a produção de leite foi avaliado comparando o desempenho dos animais soropositivos, antes e após o tratamento terapêutico, através do Teste PDIFF, enquanto que o efeito sobre as características reprodutivas foi avaliado através do Teste do Qui Quadrado, relacionando a sorologia para Leptospirose e o histórico reprodutivo dos animais. A probabilidade de herança da Leptospirose foi avaliada pelo coeficiente de herdabilidade da titulação sorológica e para isto foram utilizados 125 registros mensurados em 97 vacas da raça Holandesa, 10 Jersey e 18 Mestiças, filhas de 27 touros. Os resultados do presente trabalho mostram que a Leptospirose causa problemas de ordem reprodutiva, visto que 70,67% dos animais com sorologia positiva para a doença apresentaram problemas reprodutivos, tais como, repetição de cio, aborto e anestro prolongado. A Leptospirose também provocou redução na produção de leite, uma vez que os animais soropositivos produziram, em média, 20,09 litros/controle antes de serem tratadas e, após o tratamento terapêutico, produziram 22,01 litros de leite/controle em média, uma diferença equivalente a 1,92 litros de leite por vaca/dia. O coeficiente de herdabilidade de 36% mostra que é possível produzir uma população mais resistente a esta doença através da seleção.

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.

IT-system kan delas upp i två huvudgrupper: Enterprise Resource Planning (ERP)-system och Best of Breed (BoB)-system. Ett ERP-system definieras som ett system vars funktioner använder en gemensam databas och kan därigenom binda ihop olika IT-system. Användaren kan då enkelt komma åt data inom den egna organisationen från sin egen arbetsstation utan att söka igenom flera olika system, jämfört med system som arbetar parallellt och inte samlar data i en gemensam databas. BoB-system är inriktade på en specifik tjänst, men är utvecklade för att klara av att utföra den så bra som möjligt. De är inriktade på sina specifika uppgifter och använder inte någon gemensam databas, eftersom de är byggda av olika utvecklare och leverantörer. När ett företag ska investera i ett system finns det flera aspekter att ta hänsyn till, exempelvis om värdet systemet väntas ge kommer överstiga utvecklings- samt driftkostnaden och/eller vilken systeminvestering som kommer effektivisera arbetet mest. I denna uppsats presenteras en fallstudie som genomförts på Swedbank Robur AB, Sveriges största fondförvaltningsbolag. Fallstudien utfördes med syftet att påvisa centrala aspekter och problem vad gäller systemmiljö och val av systemtyp i relation till detta. Tre personer med olika positioner och arbetsuppgifter har intervjuats på Robur, för att erhålla en helhetsbild av systemmiljön från flera perspektiv, vilket säkerhetsställs genom det faktum att de personer som intervjuats har olika roller och ansvar i samband med systemnyttjandet. En mer generell intervju utöver fallstudien, har även genomförts med Microsofts utvecklingschef för att uppnå jämförbarhet med andra system och användare. Baserat på de fakta studien redovisat har det blivit uppenbart att det är mycket svårt för företag att enbart använda sig av ERP-system då viss funktionalitet är specifik för företaget. Studien har även funnit att begreppet ERP är väldigt vagt och kan tolkas på många sätt. / IT-systems can be divided into two distinct groups, Enterprise Resource Planning (ERP) systems and Best of Breed (BoB) systems. An ERP-system is defined as a system where a number of functions are brought together and use a common database, in order to link different IT-systems. It makes it easier to access data within the organization from the users own workstation without looking through several different systems, compared to systems that work in parallel and do not collect data in a common database. BoB-systems are geared towards a specific service and are developed to be able to perform their tasks as good as possible. They are focused on their specific tasks and are not joined together through a common database, since there are different developers or vendors for the different systems. When a company is going to invest in a system there are many aspects to consider, for example whether the expected value will exceed the associated development and operating costs, and/or which system will increase the efficiency of the tasks the most. This thesis presents a case study done at Swedbank Robur AB, Sweden’s largest fund management company. The case study was carried out with the aim to find central aspects and problems with different IT-environments and the choice of systems in relation to these. Three persons with different positions and work tasks were interviewed at Robur, to give their individual opinions and a good overall picture of their system environment. A more general interview was also carried out with Microsoft’s development manager to achieve comparability with other systems and users. This thesis shows that it is not possible for large companies to only use ERP-systems, when certain functionality is specific to the company. We have also seen that the concept of ERP is very vague and can be interpreted in different ways. It is also concluded that the definition of ERP is very vauge and can thus be interpreted in several ways.

The diploma thesis is focused on reproduction and milk yield of a herd of Czech Fleckvieh and Red Holstein cattle on Velká Chyška farm. Milk yield together with the reproduction makes a basement of every breeding and its analysing is very useful for the breeder. The aim of the thesis was to split the herd according to the lactation into four groups (1, 2, 3, 4 and more lactations) and according to the percentage of blood of Czech Fleckvieh and Red Holstein cattle into three groups (C1- C 75-100 %, C2- C 51-74 % and R- R 51-100 %). To observe the indicators of milk yield and especially to observe yield in standardized lactation, index of persistence of the lactation line and whole-life yield of these cows. Next, to focus on the reproductive indicators: the insemination interval, the service period and the interval itself. Gathered information was recorded into tables and then statistically evaluated. Also, all groups were mutually compared. Needed information was gathered from GEA Dairy plan program and the milk cow cards. Milk cows, which started the lactation in period from 10. 10. 2014 to 30. 2. 2015, were included into the analyzed group. Generally, 155 pieces of livestock participated here. The milk yield indicators were evaluated as excellent. The groups of cows C1 and C2 cows with dominant percentage of blood of Czech Fleckvieh breed, showed significantly better-than-average results when compared with the yield check. The group with dominant percentage of blood of Red Holstein breed (R) exceeded the results from the yield check of the Czech republic as well, but not as in such extent as in case of C1 and C2 groups. In comparison of the groups together, no statistically important results were found. Statistically, only influence of lactation order to the yield in standardized lactation and also influence of lactation order to the index of persistence of lactation line was proved. Reproductive indicators were different in comparison from the yield; they were on very low levels. The service period and the period itself were evaluated as unsatisfactory in all groups and a problem with reproductive management was proved. In comparison of the groups together, no statistically important differences were found as well. Based on the found results and their analysis, conclusions for the breeding practice came about.

Milk production has been evaluated not only by genetic potential but there are also a lot of indicators. The potential milk production of the herd depends on the correct link between the genetic potential and the system of selection, feeding and nutrition, reproduction and the breeding environment and health of animals. The aim of the thesis was to produce a literary overview of milk production, milk composition and influences that can influence the composition of milk. For the selected herd to evaluate the effects on the monitored indicators of the milk composition and to statistically evaluate them. For discarded dairy cows to determine the age and reason of culling and lifelong milk production.

In 1869-70 the Métis of the Red River region in Manitoba resisted the transfer of their homeland from the Hudson’s Bay Company to Canada. The Métis people responded to this transfer by blocking Canadian surveyors, government officials, and taking control of the territory through the establishment of representative institutions. Eventually, the Métis negotiated favourable terms with Ottawa which, this thesis argues, represented according to law, and to the Métis, a treaty. This thesis argues that this treaty was intended to protect the Métis homeland and provide political and social protections. The Manitoba Métis Treaty was intended to guarantee the Métis a land base in Manitoba the total size of which was to be 1.4 million acres. The reservation of this land came with protective obligations so that the entire community would receive a benefit from such lands. While Canada has developed a body of treaty law which will be used to interpret the Manitoba Métis Treaty, matters were convoluted by the enshrinement of this treaty agreement in the Manitoba Act of 1870, a document which would gain constitutional status a year later. The impact of this legislative history has led some researchers to link government obligations entirely to the Act, rather than to the negotiated agreement. Indeed, it would seem that the negotiations have been, for the most part, understood as nothing more than conversations. I reject that position and argue that both the negotiations and the Act must be taken into consideration when assessing the obligations undertaken by the Crown. The unique history of the Manitoba agreement means that Canada was under both constitutional and treaty law obligations to uphold the negotiated agreement between itself and the Métis. This thesis argues that not only is the treaty the correct legal interpretation of the events of 1869-70 but that the government of Canada failed to honour its commitments in several meaningful ways. The approach utilized in this thesis is designed to be reliant upon the basic structure and doctrines of Canadian law but to do so in a manner which gives weight to the Métis voice. It is neither a critique which is wholly internal to Canadian law nor is it completely dismissive of Canadian law. Instead, this thesis will illustrate that with only minor adjustments to the application and interpretation of colonial law, the Manitoba Métis Treaty could find a more receptive audience in Canadian legal thought. In the face of a reasonable alternative, such a project can allow other researchers to question why the courts have chosen a path which denies reception of Métis voice, community and culture in Canadian law.

This thesis addresses the genetic characterisation of livestock breeds, a key aspect of the long-term future breed preservation and, thus, of primary interest for animal breeders and management in the industry. First, the genetic diversity and structure of breeds were investigated. The application of individual-based population genetic approaches at characterising genetic structure was assessed using the British pig breeds. All approaches, except for Principle Component Analysis (PCA), found that the breeds were distinct genetic populations. Bayesian genotypic clustering tools agreed that breeds had little individual genetic admixture. However, inconsistent results were observed between the Bayesian methods. Primarily, BAPS detected finer genetic differentiation than other approaches, producing biologically credible genetic populations. BAPS also detected substructure in the British Meishan, consistent with prior known population information. In contrast, STRUCTURE detected substructure in the British Saddleback breed that could not wholly be explained. Further analysis of the British Saddleback revealed that the genetic subdivision did not reflect its historical origin (union of Essex pig and Wessex Saddleback) but was associated with herds. The Rainbarrow appeared to be moderately differentiated from the other herds, and relatively lower allelic diversity and higher individual inbreeding, a possible result of certain breeding strategies. The genetic structure and diversity of the British traditional chicken breeds was also characterised. The breeds were found to be highly distinctive populations with moderately high levels of within-breed genetic diversity. However, majority of the breeds had an observed heterozygote deficit. Although individuals clustered to their origin for some of the breeds, genetic subdivision of individuals was observed in some breeds. For two breeds the inferred genetic subpopulations were associated with morphological varieties, but in others they were associated with flock supplier. As with the British Saddleback breed, gene flow between flocks within the chicken breeds should be enhanced to maintain current levels of genetic diversity. Second, the thesis focused on breed identification through the assignment of individuals to breed origin. Dense genome-wide assays provide an opportunity to develop tailor-made panels for food authentication, especially for verifying traditional breed-labelled products. In European cattle breeds, the prior selection of informative markers produced higher correct individual identification than panels of randomly selected markers. Selecting breed informative markers was more powerful using delta (allele frequency difference) and Wright's FST (allele frequency variation), than PCA. However, no further gain in power of assignment was achieved by sampling in excess of 200 markers. The power of assignment and number of markers required was dependent on the levels of breed genetic distinctiveness. Use of dense genome-wide assays and marker selection was further assessed in the British pig breeds. With delta, it was found that 96 informative SNP markers were sufficient for breed differentiation, with the exception of Landrace and Welsh pair. Assignment of individuals to breed origin was high and few individuals were falsely assigned, especially for the traditional breeds. The probability that a sample of a presumed origin actually originated from that breed was high in the traditional breeds. Validation of the 96-SNP panel using independent test samples of known origin and market samples revealed a high level of breed label conformity.

There is a growing market for specialty poultry production using alternative genotypes and management systems. However, producers interested in specialty poultry production face several challenges. One challenge is that little published data exists regarding the growth and production parameters for alternative genotypes like slow-growing meat strains and heritage breeds. To address this challenge, research at the University of Kentucky examined the effect of feed strategies, alternative feedstuffs, and dietary enzymes on the growth and performance of heritage breeds of chicken used for either egg- or meat-production. The first trial documented the growth and nutrient intake of pullets from three heritage breeds (Rhode Island Red, Barred Plymouth Rock, and Black Australorp) and three egg-laying strains (Red Star, Black Star, and ISA Brown) on a self-selection feeding program through nineteen weeks of age. The second trial documented the growth and nutrient intake of males from those same three heritage breeds, a slow-growing meat-type strain (Red Ranger), and males and females from a fast-growing meat-type strain (Cornish Cross). Birds used a self-selection feeding program and were grown to a common weight of 2300 grams. Carcass characteristics of these birds were evaluated in the third trial. The fourth trial evaluated the partial replacement of corn and soybean meal with alternative feedstuffs (field peas, buckwheat, and flax seed) and dietary enzymes on the performance of straight-run commercial broilers and two alternative breeds of chickens: males from a Black Sex-Link cross and straight-run Rhode Island Reds. The fifth trial examined the use of sorghum and field peas to completely replace corn and soybean meal in formulated diets for two heritage breeds (Rhode Island Red and Barred Plymouth Rock). Results of these trials showed that heritage breed pullets had similar growth parameters and nutrient intake as commercial egg-laying strains. Heritage breed cockerels grew significantly slower and exhibited poorer feed efficiency than meat-type birds, but seemed to tolerate low nutrient density diets better. Overall, the findings of these studies could help producers interested in raising slow-growing meat-type chickens and heritage breeds create accurate business plans and determine if they can profitably produce meat and/or eggs for niche markets.

Rumen microbiota enable dairy cattle to breakdown fiber into useable energy for milk production. Rumen bacteria, protozoa, and fungi ferment feedstuff into volatile fatty acids (VFA), the main energy source, while methanogens utilize fermentation by-products to produce methane. Milk fat contains several bioactive rumen-derived fatty acids (FA), including odd-chain FA (OCFA) and branched-chain FA (BCFA), important for maintenance of human health. The overarching dissertation goal was to determine which factors affect rumen methanogen and protozoal community structures and their metabolism products, while defining relationships between rumen microbiota and animal performance. Results presented contribute to the goals of providing new knowledge to dairy farmers, maintaining ruminant health, and enhancing bioactive FA in milk. The first objective was to use next-generation sequencing techniques to determine if lactation stage and dairy breed affect rumen methanogen and protozoal community structures and protozoa cell FA compositions in Jersey, Holstein, and Holstein-Jersey crossbred cows at 3, 93, 183, and 273 days in milk (DIM). A core methanogen community persisted by lactation stage and breed. At 3 DIM, methanogen 16S rRNA gene sequences formed distinct clusters apart from 93, 183, and 273 DIM, reflective of the dietary transition period post-partum. The starch-utilizing protozoal genus Entodinium, was more abundant in Holsteins than in Jerseys and Holstein-Jersey crossbred cows and positively correlated with milk yield. Jerseys had greater iso-BCFA contents in protozoa and milk and protozoa of the genus Metadinium. The second objective was to determine if supplementation of mixed cool-season grasses with annual forages (AF) alters the forage, microbial, and milk FA contents during typical periods of decreased pasture growth in Northeastern US. In short-term grazing (21d) of AF, ruminal VFA and major rumen-derived FA were not altered in bacterial and protozoal cells, suggesting little alteration of biohydrogenation and maintenance of ruminant health. In spring, milk contents of iso-15:0 and 17:0 per serving of whole milk were greater in control (CON)-fed cows, while contents of 12:0 and 14:0 per serving were greater in AF-fed cows. Contents of de novo FA and OCFA per serving of whole milk were greater in summer AF-fed cows than CON-fed cows, while total contents and BCFA did not differ, suggesting post-ruminal FA modifications in adipose tissue and the mammary gland. The third objective was to characterize and relate the rumen microbiota from CON- and AF-fed cows to animal performance. Rumen protozoal taxa were not altered, while less abundant bacterial taxa (< 5%) were different in both periods. The protozoal genus Diplodinium was positively correlated with feed efficiency and milk fat yield. In spring, AF-fed cows had greater abundances of the methanogen species Methanobrevibacter millerae, whereas CON-fed cows had greater abundances of the methanogen species Methanobrevibacter ruminantium, potentially as a result of differences in substrate availability. In conclusion, the work presented identifies several factors that influence rumen microbiota, rumen microbial FA, and milk FA, while providing new information to dairy farmers, researchers, and consumers.