Dissertations / Theses on the topic 'Dairy analysis'

Master of Agribusiness
Department of Agricultural Economics
Kevin Dhuyvetter
The size of our dairy operation increased from 300 milk cows to 1,700 milk cows in 2003. Once the dairy operation increased, the dependency on milk price to support the entire operation also increased. This was due to the fact that the cropping side of the operation became more devoted to growing feed for the livestock as opposed to producing cash crops. Thus, the increase in the number of milk cows led to decreased diversity in our income potentially increasing the financial risk of the operation. The purpose of this thesis is to study different risk management tools and strategies to aid in the formulation of a risk management plan for milk sales in our operation. Risk management strategies using forward contracts, futures, put options, and cash were analyzed at different time periods and various minimum price levels. The strategies were analyzed over the last ten years (2001-2010) of available price data. Twenty-five risk management strategies were analyzed both with and without set minimum milk prices. Minimum price levels ranged from $14/cwt to $17/cwt in $1 increments. The time frame for the transaction ranged from zero to twelve months prior to production in three-month increments. Based on historical data, risk management strategies can be used to decrease the price risk faced by an operation. The risk management strategies did not affect the average price received at statistically significant levels typically considered. Different risk management opportunities are highlighted that need to be analyzed before fully implementing a risk management plan for dairy operations.

Thesis (M.A. in economics)--Washington State University, August 2009.
Title from PDF title page (viewed on Sept. 15, 2009). "School of Economic Sciences." Includes bibliographical references (p. 18-20).

Master of Agribusiness
Department of Agricultural Economics
Kevin Dhuyvetter
Dairy Farmers of America (DFA) is national milk marketing cooperative. DFA’s primary focus is to market the milk of the cooperative’s 17,000 members. In addition, DFA offers its membership a number of farm services. The sole purpose of these services is to make it easier for DFA members to operate their businesses. One of the services offered provides members access to forward contracting alternatives for pricing their milk. The objective of this research is to utilize demographic and other information related to the characteristics of individual dairy producers and determine how these characteristics impact the use (or lack thereof) of risk management marketing tools. More specifically, the focus of this research is to identify what types of dairy producers are most likely to use the DFA’s forward contracting program. The logit model estimated indicated that regional and demographic differences impact the use of DFA’s forward contracting program. Members in the Mountain Area are most likely to use the program followed by members in the Central Area. Demographic differences that significantly impacted the use of forward contracting include age (older producers use forward contracts less than younger operators) and the size of operation, as measured by milk produced per year (larger operators were more likely to use forward contracting services). While the estimated logit model did identify several factors related to the use of forward contracting services, relationships are not particularly strong and the percent of producers using the services is relatively low. Thus, the model is limited in its ability for identifying key factors and thus it will be difficult for DFA to base a targeted marketing effort at certain producers. DFA would need additional information about their members to successfully target for this farm service.

This study was an extension of a study submitted in April 2014 by Sheldon D. Holt entitled “Ambient Temperature, Calf Intakes, and Weight Gains on Preweaned Dairy Calves”. A major component in a profitable dairy operation is the raising of female calves as replacement heifers; but since no direct income is generated by calf raising alone, it is often overlooked as a potential profit area on a dairy farm. Calf management practices that ultimately impact milk productivity and reproductive performance during a heifer’s lifetime begin at birth. This study examines the effect of calf starter intake on calf growth, measuring specifically calf weight. How calf starter intake affected production costs was also examined. Other factors included in the study were seasonal change, hip height, days since birth, and weather conditions. The cost of calf starter is one of the main contributors to total production cost in raising dairy calves. Since the amount of starter intake consumed by the calves in this study was measured by Holt, a cost analysis can be performed using these data. Therefore, the first two objectives of this study are to 1) develop a model which minimizes cost of starter feed (which is a variable controlled by the dairy producer) and 2) use the model developed under objective 1) to find the breakeven point (where the cost of an input is less than or equal to the value gained from that input) and conduct sensitivity analysis with respect to this point. Although an analysis was performed on the data at the close of its collection in 2014 by S.D Holt, there are several econometric issues that were not adequately addressed before these analyses were performed. The following problems have been found in the data: functional form, multicollinearity, heteroskedasticity, and serial correlation. Any interpretation or prediction based on these data, without these issues being resolved, is not reliable. In order for interpretations and predictions based on these data to be valid, the last two objectives of this study are to 3) define in detail the econometric problems that existed in Holt’s study and 4) find and implement solutions to econometric problems that existed in that study.

The Canadian supply managed dairy sector is likely to face more competitive pressure from challenges through the World Trade Organization (WTO) and the changing global trade environment. Therefore, it is highly prudent for Canadian dairy producers to focus their concern on their level of competitiveness and how to improve it. This study investigated the competitiveness of Ontario dairy sector based on a sample of farm level data with a Box-Cox transformed econometric cost model. The data were gathered by the Ontario Dairy Farm Accounting Project, for the years 2005, 2006, and 2007. The impacts of output, yield per cow and several farm-specific characteristics on the average cost of milk production were examined. Results support the presence of significant size economies and yield economies within Ontario milk production. Minimum costs were achieved for farms with approximately 125 cows. The results also indicated that some farm-specific characteristics, breed and region, also had significant impacts on the cost of Ontario milk production. However, it appears that Ontario farms may find it difficult to survive if they are forced to face international competition. Even at their minimum, average costs were above an indicator international dairy price.

Bovine Somatotropin (BST) is a naturally occurring hormone in dairy cows which affects milk production levels (Chalupa and Galligan, 1988). The effects of BST have been known since the 1930's but limited supply of this hormone made any large scale commercial use impossible. Recently a low cost source of BST became available through recombinant DNA technology. This low cost availability of the hormone has led to research experiments which show that recombinant BST can significantly increase a cow's ability to produce milk (Peel and Bauman, 1987; Burton et al, 1987; Soderholm et al, 1988; De Boer et al, 1988). A number of studies have examined the firm level impacts of BST on the Canadian dairy industry. This present work will build upon these earlier studies by examining the impacts of BST at the both the firm and aggregate levels for all of the dairy producing regions in Canada. To facilitate this analysis at an aggregate level a linear programming model of the Canadian dairy industry was used. This model describes the dairy sector for each province, including the production, processing, trade and marketing subsectors, and is incorporated into the Canadian Regional Agricultural Model (CRAM), (Webber et al, 1986). Several scenarios were examined representing different government policy responses with the introduction of BST to the Canadian dairy industry. These scenarios are compared to a 1986 "base case" situation of the dairy industry. The first scenario examined represents a "no policy change" situation. Provincial quota levels, producer prices, levies and subsidies all remain unchanged and BST adoption rates are assumed for each province. In order to maintain existing milk production levels with BST a 5% reduction in the national cow herd results. This lower number of animals producing the same amount of milk as in the base case results in a 5% increase in dairy producer income at the national level. In the second scenario the impact of BST on quota values is examined. As in the first scenario all dairy policy instruments remain at 1986 base levels. The decrease in marginal costs for a producer fully adopting BST is then estimated. Using a marginal cost estimate of $32 per hi, the fall in marginal cost was nearly 6% or $2.00 per hi on average for Canada. This results in an 18% increase in what these producers can pay for quota. Using lower marginal cost estimates would result in a greatre increase in this variable and smaller quota increases. In scenario 3 some of the benefits of BST adoption are passed on to consumers. This is done by allowing production levels to expand such that the difference between farm-gate price and supply price remains the same as prior to the introduction of BST. Quota values remain at their base case level. This resulted in a 2% increase in the national supply of raw milk. In the fluid milk market the supply of standard milk increased by 2% and lowfat milk production increased by approximately 3 percent. In the industrial market cheese production increased by 6%, butter production increased by 2% and skim milk powder production fell by approximately 4 percent. In the final scenario the benefits of BST adoption are passed on to the taxpayers. This is accomplished by reducing the dairy subsidy by an amount which just offsets the cost savings in each province as a result of BST adoption. This leads to a decrease in the dairy subsidy of $80 million at the national level or approximately 30% of the 1986 subsidy payment. At the firm level, given the assumptions of this study, the main impacts of BST are a fall in marginal costs of $2 per hi and an increase in quota values of 18%. While these estimates of firm level changes resulting from BST adoption are not trivial they are much less than would be expected with earlier results of milk yield increases of over 25 to 3 5% accompanied by dry matter feed increases of only 10 to 15 percent (Bauman et al, 1985; Soderholm et al, 1988) . Given the assumed Canadian adoption rates of approximately 50% the aggregate level impacts of BST are more moderate. The national herd size falls by 5% and dairy producer incomes are increased by 5% to produce at the base case 198 6 production levels.
Land and Food Systems, Faculty of
Graduate

A key challenge facing dairy farming is to meet the increasing demand for dairy products from a growing and more affluent global population in a period of unprecedented socio-economic and environmental change. In order to address this challenge, policies are currently placing emphasis on ‘sustainable intensification’ (SI), i.e. producing ‘more’ outputs and services with ‘less’ resources and environmental impacts. Determining whether or not SI can deliver greater yet sustainable dairy production requires understanding of the relationships between sustainability pillars (environmental; economic; and social) and farm aspects (e.g. on-farm management; and animal productivity) under particular farming systems and circumstances (e.g. regional bio-physical conditions). Trade-offs between pillars and aspects is inevitable within a farming system. Many widely-used assessment methods that aim to measure, scale and weight these pillars and aspects are unable to fully capture trade-offs between them. The objectives of this thesis are: 1) to identify key trade-offs in dairy farming systems to inform greater yet sustainable food production; and 2) to introduce models and methodologies aiming at a more holistic measurement and better understanding of dairy farm sustainability. This thesis assesses the sustainability of French and UK dairy farming systems via a farm efficiency benchmarking modelling framework coupled with statistical analyses. It explores the relationships between pillars, aspects and technical, economic and environmental performance; and identifies important drivers/differentials in dairy farm efficiency. Importantly, it also suggests ways in which farm inputs and outputs can be adjusted so that improvements in environmental, technical and economic performance become feasible. Efficiency benchmarking was performed with the multiple-input – multiple-output productive efficiency method Data Envelopment Analysis (DEA). DEA calculates single aggregated efficiency indices per farm by accounting for several farm inputs and outputs which the DEA model endogenously scales and weights. In this work, the notion of farm inputs and outputs was extended to also include ‘undesirable’ outputs (greenhouse gas emissions) and environmental impacts (e.g. eutrophication, acidification etc.) of dairy farming. The DEA models employed belong to the family of ‘additive’ models, which have several advantages over ‘traditional’ DEA models. These include their ability (i) to simultaneously increase outputs and reduce inputs, undesirable outputs and environmental impacts; (ii) to identify specific sources of inefficiency. These ‘sources’ represent a farm’s shortfalls in output production and its excesses in input use and/or in undesirable outputs and environmental impacts, relatively to the other farms; (iii) to position undesirable outputs in the output set rather than consider them as inputs or ‘inverse’ outputs; and (iv) to rank farms by efficiency performance. Importantly, this thesis also proposes a new additive model with a ranking property and high discriminatory power. In a second stage, DEA was coupled with partial least squares structural equation modelling (SEM) so as to develop and relate latent variables for environmental performance, animal productivity and on-farm management practices. The results suggested that the efficacy of SI may be compromised by several on-farm trade-offs between pillars, aspects and farm inputs and outputs. Moreover, trade-offs depended on particular farming systems and circumstances. Increasing animal productivity did not always improve farm environmental performance at whole farm-level. Intensifying production at animal and farm-levels, coupled with high reliance on external inputs, reduced farm environmental performance in the French case, i.e. a significant negative relationship was found between intensification and environmental performance (SEM path coefficients ranged between -0.31 and -0.57, p < 0.05). Conversely, in the UK case, systems representing animal-level intensification (via genetic selection) for increased milk fat plus protein production performed better, on average, than controls of UK average genetic merit for milk fat plus protein production in terms of technical efficiency (DEA scores between 0.91– 0.92 versus 0.78–0.79) and environmental efficiency (scores between 0.92–0.93 versus 0.80), regardless of whether on a low-forage or high-forage diet. The levels of inefficiency in (undesirable) outputs, inputs and environmental impacts varied among farming systems and depended on the regional and managerial characteristics of each system. For instance, in France, West farms had higher eutrophication inefficiencies than East farms (average normalized eutrophication inefficiencies were, respectively 0.141 and 0.107), perhaps because of their more intensive production practices. However, West farms were more DEA-efficient than East farms as the former benefited from bio-physical conditions more favourable to dairy farming (mean DEA score ranks were 97 for West and 83 for East). Such findings can guide policy incentives for SI in different regions or dairy systems. The proposed modelling framework significantly contributes to current knowledge and the search for the best pathways to SI, improves widely-used modelling approaches, and challenges earlier findings based on less holistic exercises.

Cooling systems used to reduce heat stress in dairy operations require high energy, water usage, or both. Steady increases in electricity costs and reduction of water availability and an increase in water usage regulations require evaluation of passive cooling systems to cool cows and reduce use of water and electricity. A series of experiments were conducted to evaluate the use of heat exchangers buried as components in a conductive system for cooling cows. In the first experiment six cows were housed in environmentally controlled rooms with tiestall beds, which were equipped with a heat exchanger and filled with 25 cm of either sand or dried manure. Beds were connected to supply and return lines and individually controlled. Two beds (one per each kind of bedding material) constituted a control group (water off), and the other 4 (2 sand and 2 dried manure) used water at 7°C passing through the heat exchangers (water on). The experiment was divided in 2 periods of 40 d, and each period involved 3 repetitions of 3 different climates (hot and dry, thermo neutral, and hot and humid). Each cow was randomly assigned to a different treatment after each repetition was over. Sand bedding remained cooler than dried manure bedding in all environments and at all levels of cooling (water on or off). Results from this experiment demonstrated that bed temperatures were lower and heat flux higher during the bed treatment with sand and water on. We also detected a reduction in core body temperatures, respiration rates, rectal temperatures, and skin temperatures of those cows during the sand and water on treatment. Feed intake and milk yield numerically increased during the bed treatment with sand and water on for all climates. No major changes were observed in the lying time of cows or the composition of the milk produced. The efficiency of conductive cooling as a heat abatement technique in dairy production is highly correlated with the distance between the cooling system and the skin of the cow and the type of bedding material used. A second experiment was conducted to identify possible improvements in the utilization of conductive cooling for cooling cows. Heat exchangers buried 12.7 cm below the surface as components in a conductive system ware evaluated in this study. Six cows were housed in environmentally controlled rooms with tie-stall beds, which were equipped with a heat exchanger and filled with 12.7 cm of either sand or dried manure. Beds were connected to supply and return lines and individually controlled. Two beds (one per bedding material type) constituted a control group (water OFF), and the other four (two sand and two dried manure) used water at 7°C passing through the heat exchangers (water ON). The experiment was divided into two periods of 40 days and each period involved three repetitions of three different climates hot dry (HD), thermo neutral(TN) and hot humid (HH). Each cow was randomly assigned to a different treatment after each repetition was over. The sand and water on treatment was the most efficient treatment under heat stress conditions (humid or dry heat). Cows in stalls with the sand and water on treatment demonstrated lower rectal temperatures, respiration rates, skin surface temperatures and core body temperatures compared to the other three treatments. Additionally, the sand and water on treatment increased milk yield and resting time of cows under heat stress. Also, the sand and water on treatment had the lowest bed surface temperatures and highest heat exchange compared to the other treatments. From these two experiments we confirm that heat exchangers are a viable heat abatement technique that could reduce the heat load of heat stressed cows; however, this system should be paired with additional cooling systems (e.g. fans and or misters) to most efficiently reduce the negative effects of heat stress on dairy production. Additionally, Sand was superior to dried manure as a bedding material in combination with heat exchangers. To make further recommendations of the use of heat exchangers in commercial dairy farm, a third study was developed. Based on the data obtained in the previous experiments, a comprehensive energy balance was developed to fully understand conductive cooling in two different environments (HD and HH), two bedding materials (sand and dried manure) and two depths between cows and the heat exchangers (25 vs. 12.5 cm). The energy balance estimates indicated that sand is the most efficient bedding material when utilized as bedding material with conductive cooling in both hot dry and hot humid environments. In the hot-dry environment there was an increase in the conductive heat exchanged with the reduction in bedding depth to 12.5 cm, however this did not result in a reduction in the heat storage of cows. In the hot-humid environment when heat exchangers were placed 12.5 cm from the top of the bed there was an increase in both the conductive heat loss and heat storage of cows when compared to 25 cm. Additionally, results demonstrated that the efficiency of heat exchangers as measured by heat flux was improved when heat exchangers were at a depth of 12.5 cm. The sensibility analysis indicated that a reduction in the depth and/or an increase in the thermal conductivity of both bedding materials would maximize conductive heat exchange. These results should be utilized as recommendations for the utilization of heat exchangers and conductive cooling in commercial dairy farms. Evaporative cooling is widely used in dairy farms located in arid environments. Even though, these cooling systems have been shown to effectively reduce the heat stress of lactating dairy cows, a growing shortage of water and rising cost of electricity compromise its future usage. An experiment was developed to compare two evaporative cooling systems, their interaction with lactating dairy cows and their usage of natural resources. The efficacy of 2 evaporative cooling systems (Korral Kool, KK, Korral Kool Inc., Mesa, AZ; FlipFan dairy system, FF, Schaefer Ventilation Equipment LLC, Sauk Rapids, MN) was estimated utilizing 400 multiparous Holstein dairy cows randomly assigned to 1 of 4 cooled California-style shade pens (2 shade pens per cooling system). Each shaded pen contained 100 cows (days in milk = 58 ± 39, milk production = 56 ± 18 kg/d, and lactation = 3 ± 1). Production data (milk yield and reproductive performance) were collected during 3 months (June–August, 2013) and physiological responses (core body temperature, respiration rates, surface temperatures, and resting time) were measured in June and July to estimate responses of cows to the 2 different cooling systems. Water and electricity consumption were recorded for each system. Cows in the KK system displayed slightly lower respiration rates in the month of June and lower surface temperatures in June and July. However, no differences were observed in the core body temperature of cows, resting time, feed intake, milk yield, services/cow, and conception rate between systems. The FF system used less water and electricity during this study. In conclusion, both cooling systems (KK and FF) were effective in mitigating the negative effects of heat stress on cows housed in arid environments, whereas the FF system consumed less water and electricity and did not require use of curtains on the shade structure. Results of this research indicate that effective use of conductive cooling in combination with efficient evaporative cooling systems offer opportunities to reduce both water and electricity consumption on dairy farms under both hot dry and hot humid environments.

This study investigated the hypothesis that the particulate content of milk, as monitored with particle counters, is correlated to the health status of lactating dairy cows, in particular the condition mastitis. Twenty Holstein cows were monitored from the very first day of clinical mastitis outbreak until complete recovery from the disease. During the experiment, the changes in particle behaviour in all four quarters and mixture of milk from all of them were measured. For each sample the following parameters were measured: somatic cell count, fat content, lactose and protein concentration, number and size distribution of milk particles, electric conductivity and diameter of milk fat globules. In total over thirty mastitis outbreaks were observed and monitored throughout, including the first phase of this study when over three thousand samples of foremilk were collected and examined. An operational protocol and particle monitoring device were designed with the help of a commercial company Facility Monitoring Systems Ltd (FMS), Malvern. A particle counter and Peak Height Analyser (PHA) were used to monitor particulate content of milk and a compound phase contrast microscope was used to identify milk particles by photographic visualisation and to establish their diameter. It was observed that the number of particles, milk fat globule diameter and somatic cell counts were stable during periods without udder inflammation. Mastitis caused great changes in these parameters. Both milk particulate size and number were significantly affected by clinical and subclinical form of inflammation (change to the particulate behaviour). It was observed that the changes to the volume median diameter (VMD) of fat globules became evident a few days before clinical signs were present. Results obtained from a particle counter and the PHA were in agreement with data obtained by microscopy. Major changes were recorded in the number of total particles in milk before and during the outbreak of mastitis. Further research showed that changes took place in the pattern of particulate behaviour without visible signs of disease; additional data established that subclinical mastitis can be also identified through the monitoring of particles in milk. In summary monitoring of the behaviour (changes to size and number) of milk fag globules (MFG) can be used as an early indicator of the onset of mastitis. In addition data collected during study produced strong evidence supporting the theory of the interdependence of the quarters within the udder. It was found that the coefficient of correlation for size and number of particles for all four quarters within the udder was statistically significant. Particle counts and the VMD values behaviour were similar for the four quarters. This relationship was observed for all monitored animals. Moreover, the same relationship was also observed during both clinical and subclinical outbreaks of mastitis. Somatic cell count was affected only in an infected quarter while particulate content of milk ―responded‖ to disease in all four quarters within the udder (even if only one was infected). These results were the most surprising and unexpected outcome, suggesting that four quarters within the udder work together as one organ not four separate units. It was observed that the mean MFG cannot be used as a baseline to test individual animal deviations due to the unique particle profile of each observed animal. In all monitored animals particle counts obtained from PHA was found to be in the range of 1011 to 1013 with an average of 1012 particles per ml. The number of particles recorded in mastitis for one animal was at the healthy level for another. The particle pattern became a finger print for each animal and therefore MFG behaviour cannot be compared between animals. Following the first phase of the study the monitoring period was set at 15 to 20 days. This protocol allowed for minimising the influence of any other parameters on particles, which may influence the outcome of an experiment e.g. the number of particles in single samples detected by the particle counter. It was also essential to understand how the age, nutrition and stage of lactation might influence the particles and affect the results. Therefore two animals were chosen to be examined during their lactation. The analysed data did not present enough evidence to establish the relationship between nutrition and milk fat globules size and number. However to better understand this association additional studies should be carried out. Further work is required to optimise the monitoring device and build a fully automated system which will allow collecting and analysing data from the whole herd. This study proposed that particle pattern is unique for each animal – like a finger print. More research is needed to better understand the mechanism behind milk fat globules synthesis during inflammation. The results obtained during this study provide new evidence with regard to physiological changes within the udder before and during mastitis outbreak and supported the theory of interdependence between quarters within udder. The particle count in milk can be used as an indicator of the health status of the single animal. Combined the PHA and microscope can be used as a new tool to determine and monitor the particle count in milk. The understanding of the particulate behaviour will help to minimise the chance of mastitis outbreak by early detection and also to reduce the chance of the cross-contamination between animals during the milking process. Milk fat globule size and number can be used as an efficient indicator of the onset of mastitis.

This thesis deals with the use of Geographic Information Systems (GIS) in the transport of raw fluid milk from its origin on the farm to the processing plant. Current applications of GIS in transportation planning are discussed. Spatial, physical, administrative and legal constraints affecting the shipment of fluid milk are outlined, especially the roles of government legislation and dairy cooperatives. GIS is used to evaluate milk hauling efficiencies on both local and regional scales. The case study focuses on Rockingham and Augusta counties in northwestern Virginia and the surrounding hinterland. On the local scale GIS network functions are used to determine optima] routes for milk trucks between dairy farms in these counties and the processing plant in Mt. Crawford, Virginia. Comparisons are made between the results achieved by GIS and the results obtained through traditional methods of route planning. A regional scale case study uses GIS allocation functions to evaluate the effect of government regulations (Federal and State Order Markets) on the efficiency of hauling fluid milk from farms in the study area to plants outside the region. Results indicate that government regulations and cooperative decisions shape the morphology of fluid milk shipment and that GIS is a useful tool for regional milk marketing. Finally, a mail survey assesses the present use of automated systems and GIS among dairy cooperatives, and the possibility of future implementation of such systems in the dairy industry.
Master of Science

Amb l'objectiu d'obtenir nous coneixements sobre la base molecular de la lactació en cabres de la raça Murciano-Granadina (MUG), hem dut a terme una anàlisi RNA-Seq de mostres de la glàndula mamària (N=7) obtingudes en tres punts temporals diferents: 78 dies (T1, lactació primerenca), 216 dies (T2, lactació tardana) i 285 dies (T3, període sec) després del part. Aquest experiment ens va permetre identificar 1654 gens expressats diferencialment (DE), les funcions dels quals estaven relacionades principalment amb el metabolisme de les proteïnes, lípids i carbohidrats, homeòstasi del calci, mort cel·lular programada, remodelació tissular i immunitat. A més, vam realitzar un estudi d'associació del genoma complet (GWAS) que va incloure 822 cabres amb registres per set fenotipus lleters mesurats durant la primera lactació amb la finalitat de contribuir a dilucidar l'arquitectura genòmica de la producció i la composició de la llet. Aquest estudi ens va permetre detectar 24 quantitative trait loci (QTL). No obstant això, només tres QTL van mostrar significació estadística a nivell genòmic, és a dir, QTL1 (cromosoma 2, 130,72-131,01 Mb) per al percentatge de lactosa de la llet, QTL6 (cromosoma 6, 78,90-93, 48) Mb) per al percentatge de proteïna i QTL17 (cromosoma 17, 11.20 Mb) per als percentatges de proteïna i matèria seca. Mitjançant l'anàlisi del patró de segregació de polimorfismes d'un sol nucleòtid (SNP) dels genes de les caseïnes en bezoars (ancestre de la cabra domèstica) i cabres domèstiques d'Europa, Àfrica, Pròxim Orient i Extrem Orient, es va determinar que del 36,1% (CSN2) al 55,1% (CSN1S2) dels SNPs són compartits entre bezoar i cabra domèstica. Així mateix, més del 50% dels SNP dels gens de les caseïnes van ser compartits per 2 o més poblacions de cabra doméstica situades en diferents continents, i del 18 al 44% dels SNP van ser compartits per les quatre poblacions domèstiques esmentades anteriorment. Aquests resultats ens permeten concloure que una part important de la diversitat existent en els gens de les caseïnes caprines va emergir abans de la domesticació de les cabres. Un altre objectiu de la Tesi va ser caracteritzar la variació del nombre de còpies (CNV) en una població de 1036 cabres MUG. Mitjançant l'ús del programari PennCNV i QuantiSNP, vam identificar 4617 i 7750 CNV autosòmics, respectivament, que posteriorment van ser acoblats en 486 regions CNV o CNVR. Els gens que mapegen dins de CNV mostren un enriquiment de funcions relacionades amb la transducció olfactiva, els transportadors ABC i el desenvolupament embrionari. Un dels CNVR identificats en el nostre estudi coincideix amb la posició del gen de la proteïna de senyalització agouti (ASIP), que afavoreix la síntesi de feomelanina groga/vermella. En diversos estudis, l'augment del nombre de còpies del gen ASIP va ser associat amb un patró de pigmentació blanc en cabres. No obstant això, al realitzar un experiment de qPCR amb l'objectiu de quantificar el nombre de còpies del gen ASIP en poblacions de cabres amb diferents patrons de pigmentació, vam esbrinar que el CNV de ASIP no solsament segrega en cabres Saanen (blanques), sinó també en cabres MUG (negres/marrons) i cabres Malaguenyes (vermelles/rosses). Aquest resultat indica l'absència d'una relació simple i lineal entre el nombre de còpies del gen ASIP i la diŀlució del patró de pigmentació en cabres. Finalment, hem investigat l'arquitectura genòmica de la coloració de la capa en cabres MUG mitjançant la combinació de diferents tècniques experimentals. Aquesta anàlisi ha revelat l'existència d'una estreta associació entre una mutació aminoacídica (c.801C> G, p.Cys267Trp) al gen de receptor de la melanocortina 1 (MC1R) i el color negre/marró de les cabres MUG, la qual cosa implica que l'herència de la pigmentació en aquesta raça és monogènica.
Con el objetivo de obtener nuevos conocimientos sobre la base molecular de la lactación en cabras de la raza Murciano-Granadina (MUG), se llevó a cabo un análisis RNA-Seq de muestras de la glándula mamaria (N=7) obtenidas en tres puntos temporales distintos, es decir, 78 días (T1, lactación temprana), 216 días (T2, lactación tardía) y 285 días (T3, período seco) después del parto. Este experimento permitió identificar 1654 genes expresados diferencialmente (DE), cuyas funciones estaban relacionadas principalmente con el metabolismo de las proteínas, lípidos y carbohidratos, homeostasis del calcio, muerte celular programada, remodelación tisular e inmunidad. Con la finalidad de contribuir a dilucidar la arquitectura genómica de la producción y la composición de la leche, realizamos un estudio de asociación del genoma completo (GWAS) que incluyó 822 cabras con registros para siete fenotipos lecheros medidos durante la 1ª lactación. Este estudio permitió detectar 24 quantitative trait loci (QTL). No obstante, sólo tres QTL mostraron significación estadística a nivel genómico, es decir, QTL1 (cromosoma 2, 130,72-131,01 Mb) para el porcentaje de lactosa de la leche, QTL6 (cromosoma 6, 78,90-93,48) Mb) para el porcentaje de proteína y QTL17 (cromosoma 17, 11.20 Mb) para los porcentajes de proteína y materia seca. Mediante el análisis del patrón de segregación de polimorfismos nucleotídicos sencillos (SNP) de los genes de las caseínas en bezoares (ancestro de la cabra doméstica) y cabras domésticas de Europa, África, Cercano Oriente y Lejano Oriente, se determinó que del 36,1% (CSN2) al 55,1% (CSN1S2) de los SNPs son compartidos por el bezoar y la cabra doméstica. Asimismo, más del 50% de los SNP de los genes de las caseínas fueron compartidos por 2 o más poblaciones de cabra doméstica ubicadas en diferentes continentes, y del 18 al 44% de los SNP fueron compartidos por las cuatro poblaciones domésticas mencionadas anteriormente. Estos resultados nos permiten concluir que una parte importante de la diversidad existente en los genes de las caseínas caprinas emergió antes de la domesticación de las cabras. Otro objetivo de la Tesis consistió en caracterizar la variación del número de copias (CNV) en una población de 1036 cabras MUG. Mediante el uso del software PennCNV y QuantiSNP, identificamos 4617 y 7750 CNV autosómicos, respectivamente, que posteriormente fueron ensamblados en 486 regiones CNV o CNVR. Los genes que mapean dentro de CNVR muestran un enriquecimiento de funciones relacionadas con la transducción olfativa, los transportadores ABC y el desarrollo embrionario. Uno de los CNVR identificados en nuestro estudio coincide con la posición del gen de la proteína de señalización agouti (ASIP), que favorece la síntesis de feomelanina amarilla/roja. En diversos estudios, el aumento del número de copias del gen ASIP fue asociado con un patrón de pigmentación blanco en cabras. Sin embargo, al realizar un experimento de qPCR con el objetivo de cuantificar el número de copias del gen ASIP en poblaciones de cabras con diferentes patrones de pigmentación, averiguamos que el CNV del gen ASIP no sólo segrega en cabras Saanen (blancas), sino también en cabras MUG (negras/marrones) y cabras Malagueñas (rojas/rubias). Este resultado indica la ausencia de una relación simple y lineal entre el número de copias del gen ASIP caprino y la dilución del patrón de pigmentación. Finalmente, hemos investigado la arquitectura genómica de la coloración de la capa en cabras MUG mediante la combinación de distintas técnicas experimentales. Este análisis reveló la existencia de una estrecha asociación entre una mutación aminoacídica (c.801C> G, p.Cys267Trp) en el gen del receptor de la melanocortina 1 (MC1R) y el color negro/marrón de las cabras MUG, lo que implica que la herencia de la pigmentación en dicha raza es monogénico.
In order to obtain new insights into the molecular basis of lactation in Murciano-Granadina (MUG) goats, we carried out a RNA-Seq analysis of mammary gland samples (N = 7) obtained in three different time points, that is, 78 days (T1, early lactation), 216 days (T2, late lactation) and 285 days (T3, dry period) after parturition. This experiment allowed the identification of 1654 differentially expressed (DE) genes, the functions of which were mainly related to protein, lipid and carbohydrate metabolism, calcium homeostasis, programmed cell death, tissue remodeling and immunity. In order to help elucidate the genomic architecture of milk production and composition, we also carried out a genome-wide association study (GWAS) including 822 goats with records for seven dairy phenotypes measured during the first lactation. This study allowed the detection of 24 quantitative trait loci (QTL). However, only three QTL showed statistical significance at the genome-wide level, that is, QTL1 (chromosome 2, 130.72-131.01 Mb) for the percentage of lactose in milk, QTL6 (chromosome 6, 78.90-93, 48) Mb) for the percentage of protein and QTL17 (chromosome 17, 11.20 Mb) for the percentages of protein and dry matter. By analyzing the segregation patterns of single nucleotide polymorphisms (SNPs) mapping to the casein genes in bezoars (ancestor of the domestic goat) and domestic goats of Europe, Africa, the Near East and the Far East, it was determined that about 36.1% (CSN2) to 55.1% (CSN1S2) of casein SNPs are shared between bezoars and domestic goats. Besides, more than 50% of the SNPs of the casein genes were shared by 2 or more domestic goat populations located on different continents, and 18 to 44% of the SNPs were shared by the four previously mentioned domestic populations. These results allow us to conclude that an important part of the diversity existing in the caprine casein genes emerged before the domestication of goats. Another objective of the Thesis consisted of characterizing copy number variation (CNV) in a population of 1036 MUG goats. Using the PennCNV and QuantiSNP software, we identified 4617 and 7750 autosomal CNVs, respectively, which were subsequently assembled into 486 CNV regions (CNVR). Genes located within CNV show an enrichment of functions related to olfactory transduction, ABC transporters and embryonic development. Interestingly, one of the CNVR identified in our study coincides with the position of the agouti signaling protein (ASIP) gene, which favors the synthesis of yellow/red pheomelanin. In several studies, increased copy number of the ASIP gene was associated with a white pigmentation in goats. However, when conducting a qPCR experiment with the objective of quantifying the number of copies of the ASIP gene in goat populations with different coat colors, we found that the ASIP CNV not only segregates in Saanen (white) goats, but also in MUG (black/brown) and Malagueñas goats (brown/blond). This result indicates the absence of a simple and linear relationship between the number of copies of the goat ASIP gene and the dilution of pigmentation. Finally, we have investigated the genomic architecture of coat color in MUG goats by combining different experimental techniques. This analysis revealed the existence of a close association between a missense mutation (c.801C>G, p.Cys267Trp) in the melanocortin receptor 1 (MC1R) gene and the black/brown color of MUG goats, which implies that the inheritance of pigmentation in this breed is monogenic.
Universitat Autònoma de Barcelona. Programa de Doctorat en Producció Animal

In dairy cows, the failure or unwillingness to eat sufficient in early lactation when yield is high leads to a state known as negative energy balance (NEB). In this state, cows mobilise body tissue mostly in the form of body lipid in order to make up the difference in energy available from feed ingested and that required to sustain obligatory requirements, such as maintenance, and milk production. A large NEB is an undesirable state since it is associated with increased disease and reduced fertility. Body lipid content can be predicted from visual assessment of the tailhead of cows using a system known as body condition scoring (BCS). Changes in this score over time can therefore be used to predict body lipid changes. I investigated the feasibility of automating the process of collecting condition score using a digital camera and laser lights. The correlation between CS and shape over the tail-head was 0.55 suggesting that it may be possible in future to include digital images in an automated and integrated dairy farm management system. Using random regression analysis, I analysed changes in milk production, feed intake, liveweight and BCS over one to three lactations and calculated energy balance from these daily predictions. These analyses showed that energy balance can be predicted from body measurements without the need to measure feed intake making it practical to use nationally. Using these techniques enabled the genetic analysis of large volumes of field data to predict daily breeding values for energy balance for 1250 progeny test sires. Substantial genetic variation was found in energy balance profiles. The mean total daughter body energy loss at day 305 of lactation was 779 MJ (SD=224 MJ), equivalent in energy terms to about 189 kg milk. Future selection indices may contain an adjustment for the amount of body energy used to support the milk production of a bulls' daughters leading to a more complete assessment of the utility of a bull. Analysis of data from the Langhill Dairy Research Centre demonstrated that there are differences in the way dairy cows of differing genetic merit for production mobilise body lipid to support lactation and that the amount of concentrate fed also affects the recovery of lost body lipid. Select cows contained about 3200 MJ less energy than control cows at the end of the third lactation and lose and gain body lipid in a cyclical way. Parameters of these curves may be used in future selection indices to allow selection o f genotypes that have profiles of body lipid loss and gain commensurate with high yields and long herd life. This may also be useful in future when selection indices contain more traits and farmers and advisors tailor their management to suit the type of cow. It may also provide guidance on how future selection indices should be developed to incorporate traits such as body lipid, traits that enable the robust cow to thrive over many high yielding lactations.

Master of Science
Department of Biological and Agricultural Engineering
Zifei Liu
This study reviewed state-of-the-art cattle enteric methane (CH4) emissions with three reported measuring units: g/head/d, g/kg DMI (dry matter intake), and %GEI (gross energy intake). Cattle emissions studies included in this meta-analysis were reported from 1995 to 2013. Fifty-five published studies were analyzed with specific objectives: (1) to gain basic information regarding magnitudes and distributions of enteric CH4 emission rates with various units, regions, cattle types and feed situations; (2) to identify and evaluate effects of influence factors or diet mitigation techniques on enteric CH4 emissions; and (3) to evaluate Intergovernmental Panel on Climate Change (IPCC) approaches to estimate enteric CH4 emissions. Emissions data (n=165) with the unit of g/head/d had large variances and non-normal distribution, and were not homogeneous across the studies. Emissions data (n=134) with the unit of g/kg DMI were not homogeneous across the studies, while emissions data (n=76) with the unit of %GEI had small variances and normal distribution, and were homogeneous across the studies. Therefore, data with the unit of %GEI may be better for meta-analysis compared to data with the units of g/head/d and g/kg DMI; however, the number of data with the unit of %GEI was small relative to the number of data with the units of g/head/d and g/kg DMI. Enteric CH4 emissions with the unit of g/head/d are significantly influenced by geographic region, cattle classification, sub-classification, humidity, temperature, body weight, and feed intake. Emissions and feed intake had a strong positive linear relationship with R2 of 0.75 (n=148). Emissions with the unit of g/kg DMI are significantly affected by humidity, body weight, and feed intake. The relationship between emissions and feed intake is positive. Emissions with the unit of %GEI are significantly associated with humidity, production stage, and body weight. IPCC Tier 1 and Tier 2 estimated emissions were approximate to most of the measured enteric CH4 emissions; however, the residuals were not normally distributed. Based on results from PRD method and paired t-tests, IPCC Tier 1 overestimated emissions in Asian studies, underestimated emissions in European studies for beef cattle, and underestimated emissions in Oceanian studies for dairy cattle. IPCC Tier 2 underestimated emissions in Asian studies for beef cattle. The underestimated emissions of IPCC Tier 2 in Asian studies might result from no consideration of effects from production stage and body weight.

Time budgets, avoidance distance scores-related behaviour and milk yield of pasture-based Jersey, Friesland and crossbred cows. by Madodana Sunson Dodzi The study was conducted at the University of Fort Hare farm to determine the time budgets, the avoidance-related behaviour variables and their relationship with milk yield in three pasturebased dairy genotypes: Jersey, Friesland and crossbreed. Twenty one clinically health dairy cows aged between 52 and 55 months, in mid lactation and comprising of seven cows from each genotype were used in the study. The time spent on different activities (grazing, lying down, standing and others) at pasture was recorded using stop watches across four seasons. The behavioural responses of the three genotypes to humans were determined by recording their avoidance distance scores (AD), exit speed (ES), pen scores (PS), pen behaviour scores (PBS), plat form scores (PLS) and the occurrence of kicking (KCK) and stepping (SPG) during milking on four consecutive days in four seasons. Time spent standing was higher (P < 0.05) for Friesland compared to Jersey and crossbred during the hot-wet season. In the cool-dry season the Jersey spent more time (P < 0.05) grazing than the other breeds. The Friesland and crossbred on the other hand devoted most of their time lying down compared to Jersey in the cool- dry season (P < 0.05). There were season differences in time spent on all activities (P < 0.05). Time spent on grazing was longest in post-rainy seasonal and lowest in hot- wet season (P < 0.05). The longest lying down period was observed in the hot-dry season and lowest in hot-wet season (P < 0.05). iii Daily milk yield Varied (P < 0.05) with genotype with the Friesland and Jersey producing higher yield than the crossbred. The highest amount was produced in hot-dry and the least in hot-wet season. Milk yield was positively correlated (P < 0.05) with lying down. Standing was negatively correlated with milk yield (P < 0.05). The Friesland had the highest avoidance distance scores (P < 0.05) and the Jersey had the lowest avoidance distance scores in all seasons. There was an association (P < 0.05) between genotype and exit speed scores, pen scores and stepping behaviour scores. The Friesland exhibited the highest exit speed scores than the other breeds. The Jersey had the lowest (P < 0.05) kicking behaviour scores. There was a relationship (r = 0.64) between avoidance distance scores and exit speed. Exit speed scores were correlated with pen score(r= 0.23). Milk yield was significant related (r= 0.17) to the occurrence of kicking behaviour. The genotypes showed different levels of sensitivity to season and milk yield was influenced by breed and season. It can be concluded that time budgets vary with season and farmers need to adopt measures that buffer the effect of season on welfare of dairy cows. It can also be concluded that avoidance distance scores differs according to genotype with Jersey being more confident to humans than other two breeds. It is therefore recommended that provision of shades or cooling mechanism should be adopted to buffer the effects of hot-wet season. Improving quality of feed during the cool-dry season may be critical for Jersey cows. Finally positive handling of the dairy cows is recommended in order to improve the welfare and milk yield of pasture based dairy cows.

This thesis presents several Raman spectroscopic studies of bovine milk-derived products (skim and whole milk powder, anhydrous milk fat, processed cheese and soy cheese made from milk protein). Raman spectroscopy, unlike infrared spectroscopy (both mid- and near-infrared), has not been widely used as an analytical tool within the dairy industry. The purpose of this project was to assess the utility of Raman spectroscopy in several dairy industry relevant problems. FT-Raman spectroscopy coupled with partial least squares (PLS) reliably predicted the concentration of fat and protein within whole milk and protein within skim milk powders as evidenced by ratios of prediction to deviation in excess of three. It was shown that sample geometry did not significantly affect the calculated predictive models, thereby allowing the simplest, quickest method of sample presentation to be utilised without harming quantification model efficacy. The fat fraction of milk was further investigated, and it was shown that Raman spectra collected from anhydrous milk fat samples were a good basis for solid fat content (SFC) determination. Such spectra were collected when the samples were held at 40 �C, pretreated by baselining and area normalisation, and analysed using PLS with modified jack-knifing (PLS1-JK). Triacylglycerol class concentrations were also well predicted by PLS1-JK models developed from Raman spectroscopic data. Resonance enhancement of β-carotene within fat was shown to have little effect on the reliability of the optimal prediction model when compared to SFC Raman quantification. Raman microscopic mapping for heterogeneity description of processed cheese and soy cheese mimics was examined. The FT-Raman milk powder constituents study had shown fat and protein Raman spectra within complex dairy mixtures could be distinguished, hence this utility was applied to mapping of cheese systems. Univariate, principal components analysis and multivariate curve resolution methods of analyses were compared; as expected the more complex samples required multivariate methods of analyses. Raman microscopic mapping was not a time efficient method in comparison to the standard method of confocal laser scanning microscopy. However, Raman spectroscopic mapping is a more universal technique which allowed the presence of an unexpected localised constituent within the soy cheese mimics to be observed. It was proposed that this constituent was a crystalline form of a short saturated fatty acid.

This study illustrates the use of ACNielsen Homescan Panel (HSD) in three separate demand analyses of dairy products: (1) the effect of using cross-sectional data in a New Empirical Industrial Organization (NEIO) study of ice cream firm mergers in San Antonio; (2) the estimation of hedonic price models for fluid milk by quart, halfgallon and gallon container sizes; (3) the estimation of a demand system including white milk, flavored milk, carbonated soft drinks, bottled water, and fruit juice by various container sizes. In the NEIO study a standard LA/AIDS demand system was used to estimate elasticities evaluating seven simulated mergers of ice cream manufactures in San Antonio in 1999. Unlike previously published NEIO work, it is the first to use crosssectional data to address the issue associated with inventory effects. Using the method developed by Capps, Church and Love, none of the simulated price effects associated with the mergers was statistically different from zero at the 5% confidence level. In 1995 Nerlove proposed a quantity-dependent hedonic model as a viable alternative to the conventional price-dependent hedonic model as a means to ascertain consumer willingness to pay for the characteristics of a given good. We revisited Nerlove’s work validating his model using transactional data indigenous to the HSD. Hedonic models, both price-dependent and quantity-dependent, were estimated for the characteristics of fat content, container type, and brand designation for the container sizes of gallon, half- gallon, and quart. A rigorous explanation of the interpretation between the estimates derived from the two hedonic models was discussed. Using the Almost Ideal Demand System (AIDS), a matrix of own-price, crossprice, and expenditure elasticities was estimated involving various container sizes of white milk, flavored milk, carbonated soft drinks, bottled water, and fruit juices, using a cross-section of the 1999 HSD. We described price imputations and the handling of censored observations to develop the respective elasticities. These elasticities provided information about intra-product relationships (same product but different sizes), intrasize relationships (different products same container size), and inter-product relationships (different products and different sizes). This container size issue is unique in the extant literature associated with non-alcoholic beverage industry.

The dairy industry today is beginning to dedicate more focus on the growth of the calf from birth to first breeding to better improve the milk production as well as the overall performance of the individual cows. While the development of the rumen is one of the most vital contributors to the performance of the calf, it remains unknown what molecular mechanisms are responsible for the development of the rumen, and more specifically the proliferation of rumen epithelial cells. The objectives of this study were to investigate the existing data on rumen development through meta-analysis and to explore the effects of sodium butyrate and lipopolysaccharide (LPS) on rumen development in calves through experiment. In the first study a meta-analysis was performed to summarize the literature on calf performance and derive equations that relate rumen (e.g., rumen pH, reticulorumen weight, papillae area) and non-rumen factors (e.g., feed composition, form of feed, housing) to animal performance (e.g., intake of milk replacer (MR), starter, and forage; average daily gain (ADG); and feed efficiency). We looked at four different relationships to further investigate the connections between rumen, non-rumen, and performance factors. In the first and second relationships of interest, the effect of dietary and environmental variables on rumen variables and performance variables were examined, respectively. The third relationship of interest was how rumen variables influenced performance variables. The final relationship of interest was investigating the additive effects of the rumen, dietary, and environmental variables on the performance variables. Forward selection, multiple regression was used to derive equations to select variables that explained variation in the response variable in each model. Results showed that the variation in calf ADG was explained by daily forage intake, calves that were weaned, total starter intake, and total MR intake (concordance correlation coefficient (CCC) = 0.976). The variation in feed to gain ratio was explained by the weight of the ruminal contents, daily forage, MR, and starter intakes, percent of starter in the diet, and total starter intake (CCC = 0.992). The variation in daily forage intake was explained by the percent of the diet that was starter or MR (CCC = 0.998). The variation in daily starter intake was explained by the percent of acid detergent fiber in the starter, a pelleted starter (versus a texturized), diets including starter and forage (versus a milk replacer only diet), and the percent of the diet that was MR (CCC = 0.998). The variation in daily MR intake was explained by the percent of the diet that was starter, final body weight, ruminal propionate concentration, and daily starter intake (CCC = 0.918). Based on these analyses, although dietary and environmental factors are closely associated with calf performance, ruminal factors such as volatile fatty acid (VFA) concentration and ruminal contents appear to have additional, additive influences on calf performance. In the second study, 24 Holstein bull calves were challenged with oral doses of LPS and sodium butyrate. The hypothesis here was that LPS and sodium butyrate would instigate rumen cell proliferation independently and additively. Calves were assigned to one of four treatments: control (CON; n=5), butyrate (BUTY; n=5), LPS only (LPS-O) (n=6), or LPS plus butyrate (LPSB; n=6). All treatments were administered orally twice daily consisting of either: 0.9% saline (CON); 11 mM sodium butyrate (BUTY); LPS ranging from 2.5 to 40 µg/kg metabolic body weight (BW0.75, LPS), or both butyrate and LPS (LPSB). Calves were fed milk replacer (22% CP, 20% fat, as-fed) and starter (20% CP, 3% fat, as-fed) based on metabolic BW, or about 12% BW of MR and 3% BW of starter. Feed intake, fecal and respiratory scores, and rectal temperature were recorded daily. Calf BW, hip height, jugular blood samples, and rumen content samples (via oroesophageal tube) were collected weekly. Calves were weaned at 6 wk of age and euthanized at 8 wk of age, whereupon ruminal weights and ruminal samples for papillae area and epithelial thickness were collected. Blood and rumen samples were analyzed for concentrations of beta-hydroxybutyrate, glucose, LPS-binding protein, and VFA. Data were analyzed as a 2x2 factorial with the repeated effect of week. Three non-orthogonal contrasts (CON versus the average of all other treatments; LPS-O versus LPSB, and LPSB versus BUTY) were investigated. Feed intake, health measures, and blood metabolites did not differ by treatment. Calf BW increased by week (P < 0.0001). Irrespective of week, LPS calves weighed more and had higher ADG than BUTY calves (P = 0.020). Irrespective of week, withers height was greater in LPS compared to CON (P = 0.006). Rumen pH and rumen VFA concentrations did not differ by treatment but did decrease and increase, respectively, with week in conjunction with increased starter intake. Total empty forestomach (P = 0.014) and reticulorumen weights (P = 0.012) were greater in LPSB compared to BUTY. Overall, LPS and sodium butyrate appeared to have synergistically affected some, but not all rumen measurements without affecting calf growth, intake, or health. Results from the meta-analysis emphasize the importance of continuing to focus on the solid feed intake of the calf from birth through weaning. Implications from the LPS study are imperative to other dairy scientists who will attempt to further study the effects of LPS on the rumen.
Master of Science in Life Sciences
Dairy calves are born with an under-developed stomach. The stomach has four compartments: the rumen, reticulum, omasum, and abomasum. The rumen is the largest component where finger-like projections called papillae grow to absorb nutrients for the calf. It is vital to the calf that the rumen develops not only the papillae to absorb nutrients but also to foster a microbe-rich environment so the microbes can act as a defense mechanism for the calf to aid in fighting disease. While it is known that things like solid feed support the development of the rumen, the mechanism behind how that is happening still remains unclear in the literature. The objective of this study was first to better understand the relationships that exist in the literature between dietary, environmental, and ruminal factors, and second to investigate the claim that certain components of the bacteria in the rumen are stimulating rumen development independently and additively with sodium butyrate. In order to investigate the relationships amongst the dietary, environmental, and ruminal parameters, a computer program called R Studio was used to analyze over 30 different models that extracted data from a database that included a collection of 36 studies from the literature. This is also known as a meta-analysis. The associations of interest that we found were: average daily gain (ADG) of the calf was associated with daily forage intake, calves that were weaned, total starter intake, and total MR intake. Feed efficiency of the calf was associated with the weight of the ruminal contents, daily forage, milk replacer (MR), and starter intakes, percent of the diet composed of starter, and total starter intake. Daily forage intake was associated with the percent of the diet that was starter or MR. Daily starter intake was associated with acid detergent fiber in the starter, a pelleted starter (versus a texturized starter), diets including starter and forage (versus a MR only diet), and the percent of the diet that was MR. Daily MR intake was associated with the percentage of the diet that was starter, final body weight (BW), ruminal propionate concentration, and daily starter intake. These relationships emphasized that although dietary and environmental factors are more closely associated with calf performance, ruminal factors such as rumen contents and volatile fatty acid concentrations appear to have additional, additive influences on calf performance. The second part of the study objective was to explore an idea that, to our knowledge, has not been published in the literature. In the second study, 24 dairy calves were challenged with oral doses of a gram-negative bacteria lipopolysaccharide (LPS), and a short-chain fatty acid sodium butyrate. The hypothesis in this study was that the LPS and sodium butyrate would trigger metabolic pathways on the rumen cell membranes to a greater extent together, versus independently, to increase the amount of cells growing. Calves were assigned to one of four treatments: control (CON), butyrate (BUTY), LPS only (LPS-O), or LPS plus butyrate (LPSB). To study this effect, each treatment group was administered their respective treatment orally as a liquid twice daily. To measure the results, the following data was collected: feed intake, fecal and respiratory scores, rectal temperature BW, hip and withers height, blood samples, rumen content and pH samples, papillae area, epithelial thickness, and organ weights. Blood and rumen samples were analyzed for blood metabolites and volatile fatty acids concentrations respectively. Data were analyzed and results showed no difference amongst feed intake, health measures, rumen pH, rumen VFA concentration, and blood metabolites by treatment. Calves on the LPS treatment weighed more and had higher ADG than BUTY treatment calves. Withers height was higher in the LPS group when compared to CON. Stomach weights were higher in the LPSB group when compared to the BUTY group.

The dairy industry is one of the most important and influential agricultural sector in New Zealand. Ensuring and enhancing the industry's productivity and efficiency represent a fundamental issue in New Zealand economic growth. September 2007, the NZ Labour Government proposed an Emission Trading Scheme as a way to comply with its Kyoto obligation, and it is the first country in the world that brings agricultural sector in. Given the emission intensive nature of dairy production, the industry is facing substantial increases in production costs and reduction in payout. The efficiency performance of dairy farming might also be affected as a result of changing farming practices. The overall objective of the thesis is to analyze the efficiency performance of NZ dairy farming, with implications regarding the climate change issue. Stochastic frontier analysis is applied to a panel of NZ dairy farms in 1998/99-2006/07. The structures of the existing production technology, technological change over time, and difference between South Island and North Island dairy farming are investigated within this stochastic frontier framework. An input efficiency measure is defined and evaluated at the expected cost minimizing input bundle. If the efficiency performance for emission intensive inputs could be improved, dairy farms will decrease their emissions without loss of production or additional costs. This input efficiency measure therefore allows for the combination of a farm's environmental pressure with its economic performance. Finally, the likely impacts of the ETS on dairy industry are discussed through an analysis regarding the point of obligation issue, and an illustration of changing farming practices when fertilizer price goes up as a result of emission charges.

This study examined The Margin Protection Program for Dairy’s impact on the “effective margins” or margins realized by dairy producers in various regions. Each selected margin and percentage of production history offered by the national policy was analyzed in a forecasting, national and regional manner. Couplet margins were simulated for fifteen regions from 2017 through 2020. Five scenarios were analyzed for the change in MPP’s effects under a 15%, 10%, and 5% drop in the price of milk as well as a 50% increase in the price of corn and a scenario where milk decreases 15% while corn prices simultaneously increases 25%. The results demonstrate that more than half of the regions have higher probabilities of triggering indemnities at every coverage level when compared to the US, MPP margin. Margins change in response to the policy effects, where lower coverage levels experience margin increase, and higher coverage levels experience margin decrease. In the US, MPP margin, risk reduction is observed at every coverage level. The program was found to decrease risk at most coverage levels, where higher shocks to the margin increased the protection offered by the program’s effects.

Vermont is a largely rural and homogenous New England state not often thought of as a destination for Latino migrant farm laborers, but in recent years dairy farms have begun hiring Latino workers; there are now an estimated 1200 in the state, although the exact number is unknown (Baker, 2013). As the dairy industry is the largest contributor to sales from agriculture for the state, these farmworkers play an essential role in Vermont’s economy (U.S. Department of Agriculture, 2014b). These migrant dairy farmworkers hail primarily from Mexico, with a small fraction from Central America, and lack sufficient documentation to work and live legally in the U.S. Myriad stressors are inherent to both dairy farm labor and living as an illegal immigrant. In a state like Vermont so near the Canadian border, where federal immigration officials have jurisdiction, there is an additional layer of risk. This thesis explores the social, political, geographic, and economic context of Vermont as it relates to the experiences of stress for Latino migrant dairy farmworkers in the state. In addition to reviewing the literature to better understand of the context for stress and stressors affecting migrant farmworkers the U.S., this thesis uses information from a survey administered to Latino migrant dairy farmworkers in Vermont. This thesis utilizes the Migrant Farmworker Stress Inventory (MFWSI), a survey instrument designed to assess the types and severities of stressors inherent to migrant farmwork. This survey is supplemented by questions targeting Vermont-specific stressors for migrant farmworkers. Demographic characteristics reveal Vermont’s Latino migrant farmworkers to be mostly Spanish-speaking males from Mexico or Guatemala in their late 20s, and although over half the population are married/in a partnership and have children, less than half those farmworkers live with their partners or kids. Among these farmworkers, 36% exhibit “caseness,” for stress, i.e. degree of stress correlated with poor mental or physical health outcomes defined as a score of ≥80 on the MFWSI. The mean stress score for this population is 74.55, above the average for studies in the literature using the MFWSI. Significant stressors from this study include those related to social isolation, language barriers, and migration and legal insecurity. Factors contributing significantly to overall stress or more extreme levels of specific stressors include: living closer to the Canadian border, getting surveyed in cold months, being Guatemalan, being in a marriage or partnership, having contact with health clinics, getting paid lower wages, working longer hours, not having family or partners on the farm, having a previous farm injury, having a Driver’s Privilege Card, and not having contact with various organizations that help migrant farmworkers in Vermont. Exploratory questions reveal that keeping busy and socializing are the main ways farmworkers reduce stress in their lives, but that having a work permit/legal status, or being able to be with family would most reduce their stress. This thesis concludes with suggestions for increasing support for organizations that provide essential services to migrant farmworkers, like health services, ESL and education, and advocacy for improved labor conditions. Continued research should use the insights gleaned from this thesis to explore further strategies for coping with the stressors prevalent amongst Vermont’s Latino migrant dairy farmworkers.

A study of the reproductive performance of 179 dairy cows during the period from December 1978 through March 1984 was conducted at the Western Kentucky University Farm, Bowling Green, Kentucky. The climatic data showed seasonal variation in temperature as follows: winter 3.10C, spring 15.7°C, summer 23.8°C, and fall 12.0°C. The seasonal humidity was similar for winter (81.2%), spring (83.4%), and fall (85.3%); but for summer it was considerably higher (89.4%). The conception rate varied through all the months but was lowest during the summer months. Seasonal data for conception rate were obtained and the results were as follows: winter 54.1%, spring 46.4%, summer 15.6% and fall 39.0%. Low fertility during summer months was associated with high air temperatures and high relative humidities. The coefficient of correlation for temperature vs. conception was low (-0.15) because there was low fertility in some winter months and in some summer months. The coefficient of correlation for humidity vs. conception was high (-0.65), and the coefficient of determination was 42%. A completely randomized design and analysis were used, resulting in significant differences among seasonal fertility rates but no significant differences among months within seasons. Significant differences were found for the following comparisons: winter vs. spring, summer, and fall; spring vs. winter, summer, and fall; and summer vs. spring, fall, and winter. The total services involved were 546, and the total conceptions obtained were 155--resulting in a service per conception ratio of 3.52. The average number of days open was 177 (79 cows). The average number of days in the calving interval was 457 (63 cows).

I sistemi di valutazione genetica nel mondo sono in rapido sviluppo. Attualmente, i programmi di selezione “tradizionale” basati su fenotipi e rapporti di parentela tra gli animali vengono integrati, e nel futuro potrebbero essere sostituiti, dalle informazioni molecolari. In questo periodo di transizione, questa tesi riguarda ricerche su entrambi i tipi di valutazioni: dall’accertamento sull’accuratezza degli indici genetici internazionali (tradizionali), allo studio di metodi statistici utilizzati per integrare informazioni genomiche nella selezione (selezione genomica). Tre capitoli valutano gli approcci per stimare i valori genetici dai dati genomici riducendo il numero di variabili indipendenti. In modo particolare, la correzione di Bonferroni e il test di permutazioni con regressione a marcatori singoli (Capitolo III), analisi delle componenti principali con BLUP (Capitolo IV) e indice Fst tra razze con BayesA (Capitolo VI). Inoltre, il Capitolo V analizza l’accuratezza dei valori genomici con BLUP, BayesA e Bayesian LASSO includendo tutte le variabili disponibili. I risultati di questa tesi indicano che il progresso genetico atteso dall’analisi dei dati simulati può effettivamente essere ottenuto, anche se ulteriori ricerche sono necessarie per ottimizzare l’utilizzo delle informazioni molecolari in modo da ottimizzare i risultati per tutti i caratteri sotto selezione.
Genetic evaluation systems are in rapid development worldwide. In most countries, “traditional” breeding programs based on phenotypes and relationships between animals are currently being integrated and in the future might be replaced by the introduction of molecular information. This thesis stands in this transition period, therefore it covers research on both types of genetic evaluations: from the assessment of the accuracy of (traditional) international genetic evaluations to the study of statistical methods used to integrate genomic information into breeding (genomic selection). Three chapters investigate and evaluate approaches for the estimation of genetic values from genomic data reducing the number of independent variables. In particular, Bonferroni correction and Permutation test combined with single marker regression (Chapter III), principal component analysis combined with BLUP (Chapter IV) and Fst across breeds combined with BayesA (Chapter VI). In addition, Chapter V analyzes the accuracy of direct genomic values with BLUP, BayesA and Bayesian LASSO including all available variables. The results of this thesis indicate that the genetic gains expected from the analysis of simulated data can be obtained on real data. Still, further research is needed to optimize the use of genome-wide information and obtain the best possible estimates for all traits under selection.

Thesis (Ph.D.) -- University of Western Sydney, Hawkesbury, 1998.
"A thesis presented to the University of Western Sydney for the degree of Doctor of Philosophy, September, 1998" Bibliography: leaves 193 - 219.

Dairy production systems are an important global contributor to anthropogenic greenhouse gas (GHG) emissions including methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2). Due to the role GHG play in climate change, it is important to investigate ways to minimise their global warming potential (GWP) and to maximise the efficiency of dairy production systems. Finding a balance between improving productivity and suppressing the range and quantity of GHG produced in dairy production is crucial in order to maintain sustainability in the future. The Langhill herd is part of a long term genetic x feeding systems study, representative of a range of dairy production systems which may be found in the UK. Two feeding regimes (low forage (LF) and high forage (HF)) were applied to each of two genetic lines (control (C) and select (S) genetic merit for milk fat plus protein) giving four contrasting dairy production systems (LFC, LFS, HFC, HFS). Biological efficiency (production and energetic) and environmental efficiency (GWP) were assessed by way of life cycle analysis (LCA), accounting for dairy system inputs and outputs from off-farm production of imported feeds and fertilisers to raw milk leaving the farm gate over a period of seven years. Calculations were conducted using the Intergovernmental Panel on Climate Change (IPCC) methods, with system specific data implemented where possible. Select genetic line under low forage regime (LFS) had the highest gross production and energetic efficiencies (p<0.001). In LFS, milk yields were 56% higher per cow than the lowest ranked HFC system, representing a difference of around 3500kg per cow. Milk solids yield per kg dry matter intake was 18% higher in LFS compared to HFC. High forage with control genetic line required 17% more net energy intake than LFS to produce each kg of milk solids. LFS allocated the highest proportion of net energy to lactating after accounting for body maintenance (p<0.001). Rate of change in efficiency throughout lactation varied significantly (p<0.001) amongst systems, with loss of efficiency minimised in LFS and greatest in HFC. However, LFS involuntary culling rate was significantly higher than other systems (p<0.001). LFS was the most environmentally efficient system and HFC the least (p<0.001), both per unit productivity and per unit total land use. Implementing low forage regime with select genetic line lowered GWP per kg energy corrected milk (ECM) by 24% compared to HFC (p<0.001). GWP of LFC was around 8% lower per kg ECM than HFS (p<0.001). Methane from enteric fermentation contributed the greatest proportion of overall GWP (46-49%) in all systems. However, key factors in the differences amongst systems were higher off-farm CO2 equivalent emissions under low forage, and higher on-farm N2O emissions under high forage regime. HFC produced 91% more nitrous oxide per kg ECM from animal manures compared to LFS, and 65% more N2O from applied manufactured fertilisers (p<0.001). Conversely GWP associated with off-farm production of imported feeds in LFS was 11% higher than in HFC (p<0.001). In low forage systems high gross emissions were offset by high productivity but this was not the case for the high forage systems. Cows of high genetic merit managed under a Low Forage feeding regime had improved production, energetic and environmental efficiencies. However, issues with animal health and fertility raise questions about long term sustainability of the LFS dairy production system, emphasising the importance of examining trade offs between systems.

ABSTRACT Water and Air Quality Performance of a Reciprocating Biofilter Treating Dairy Wastewater Seppi Matthew Henneman Agricultural non-point source pollution is the leading water quality problem in surface water and the second leading problem in ground water in the US. Among the contaminants, nutrients (such as nitrogen, phosphorus, potassium) can be transported from agricultural fields when cropland is not managed properly. In California, dairy manure application to cropland has become tightly regulated with the goal of decreasing such nutrient pollution. Dairies unable to balance their manure nutrient supply with cropland application area may benefit from a nitrogen removal technology. One such technology is the reciprocating biofilter, known as the ReCip® technology. A pilot-scale ReCip® unit was installed at the Cal Poly dairy to evaluate its treatment efficacy, in particular for nitrogen removal, when treating wastewater from flush dairies. This pilot-scale system was the first application of the ReCip® technology to dairy wastewater, and recently it was found to be effective for removal of ammonium, total nitrogen, and biochemical oxygen demand (BOD). In the ReCip®, wastewater is repeatedly pumped back and forth between two gravel-filled basins. This reciprocation creates two treatment environments: an aerobic environment, which promotes reactions such as nitrification and BOD oxidation, and an anoxic/anaerobic environment, which promotes reactions such as denitrification of nitrate into nitrogen gas and methanogenesis. At Cal Poly, the ReCip® treated storage lagoon water, and ReCip® effluent containing nitrate was returned to the lagoon, possibly contributing to odor control. Emission of air pollutants is a concern about dairy waste in general (volatile organic compounds, hydrogen sulfide, methane, etc.) and for nitrification-denitrification systems in particular (nitrous oxide). In the present work, the first detailed air emission study was conducted on ReCip®. Emissions of air pollutants were measured with flux chambers during different seasons, and, simultaneously, the water quality within the pore volume of the gravel beds was measured to explore whether pore water quality correlated to air emissions. These air emissions studies were performed within a yearlong study of overall ReCip® treatment performance. Water quality constituents measured were pH, alkalinity, temperature, dissolved oxygen (DO), total ammonia nitrogen (TAN), soluble nitrogen, soluble non-purgeable organic carbon, nitrite, and nitrate. During the submerged phase of the reciprocation cycle, pore water DO generally declined from 1-2 mg/L to <0.1 mg/L, while TAN declined and nitrate accumulated, although total nitrogen also declined due to denitrification. The extent of denitrification was correlated to influent BOD loading. The average removals by the ReCip® were 93% TAN, 61% CBOD5, 74% TKN, and 57% TSS. A simple CBOD5 removal model was developed that described and predicted CBOD5 ­removal in the system. Key air pollutants emitted by the ReCip® and their annual mean concentrations were nitrous oxide (0.74 ppm), ammonia (0.15 ppm), and methane (3.85 ppm). The air emission potential of the lagoon water influent was compared to that of the ReCip® effluent. The decreases in emission potential were 82% for ammonia, 93% for methane, and 99% for hydrogen sulfide. The average masses emitted (g emitted/kg loaded into system) by the ReCip® were 1.7 g N2O/kg N, 0.15 g NH3/kg N, 2.1 g CH4/kg CBOD5, 1.0 g ethanol/kg CBOD5,and 0.004 g H2S/kg CBOD5.

$ beta$-Galactosidase (E.C. 3.2.1.23) or lactase was produced by the growth of a selected Bacillus subtilis strain (KL88) which was adapted to grow at 10$ sp circ$C. The growth and enzyme production were maximal at 2% (w/v) lactose supplemented with 0.2% (w/v) yeast extract. A Fast Protein Liquid Chromatography system (FPLC) was used for $ beta$-galactosidase purification. The enzyme was purified to 44-fold over the crude extract with a recovery of $ sim$54%. Native-PAGE and SDS-PAGE using "PhastSystem" showed the presence of two isoenzymes having molecular weights of 88 and 170 kD. The purified enzyme showed high activity at low temperatures (10$ sp circ$C) and recorded an optimum pH of 7.0. The K$ sb{ rm m}$ values were found to be 2.21 mM and 28.08 mM for o-nitrophenyl-$ beta$-D-galactopyranoside (ONPG) and lactose, respectively.
$ beta$-Galactosidase from psychrotrophic Bacillus subtilis was specific to the $ beta$-D-glycosidic linkage normally present in lactose.
To investigate the possibility of producing proteinase-free $ beta$-galactosidase from this psychrotrophic microorganism, FPLC was used for the rapid separation of $ beta$-galactosidase.

This dissertation investigates the dairy farming industry in the Northeastern United States and, in particular, the key drivers of economic viability and competitive advantage for small and midscale commercial dairy producers. The research approach employed was a literature review combined with primary case study observation and data collection. Historical perspective has been presented to provide an overarching contextual framework for this study. Four dairy farms were purposefully selected for case study research because they represented various aspects of a pre-defined set of variables and because they demonstrated relevant similarities as well as significant differences in terms of alternative business strategy. The classical business opportunity analytical process has been customized for practical use application by small and midscale dairy farmers. This tailored process has been validated using research findings; it offers a fresh way of identifying a strategic approach in pursuit of economic viability and competitive advantage that best fits an operation's unique set of characteristics. This process is intended for practical use application on a broader scale by dairy farmers in the Northeast to facilitate their understanding of challenging industry dynamics, of emergent market opportunity and inherent potency, and of both internal and external hurdles to be overcome. Finally, recommendations for next steps have been presented.

Dairy farms can apply anaerobic digestion (AD) as a manure management system, while producing renewable energy. Ultimately, this can reduce greenhouse gas (GHG) emissions. There is much research work that has quantified the changes in emissions due to AD. However, important methodologies such as the Intergovernmental Panel on Climate Change (IPCC) Guidelines, rely only on a small sample of the accumulated scientific findings in the field. This thesis improves the robustness of these methodologies by applying data-driven techniques to estimate values of the energy output of AD systems and their consequent effect in GHG emissions. For this purpose, meta-analyses techniques are applied to mathematically combine metrics from 155 non-standardised research publications (i.e. with different boundaries, scopes and functional units). As a first step, a novel database is created by systematically searching for relevant articles and assessing them against defined criteria. The database is divided in two parts. Given that the offset of GHGs is highly dependent on the energy output of AD system, empirical methane yields (i.e. key metric of AD performance) are collected in Part I of the database. GHG released from different farm activities are input to Part II of the database. To quantify the change in emissions from these activities, standard baseline and AD scenarios are defined. The second step of the meta-analysis consists of applying uni- and multi-variate tests to the database. For Part I, methane yields are analysed in terms of type of digesters. From the batch digesters, new maximum methane yields are proposed based on the combined results of 42 peer reviewed articles. These results offer better estimates than default values of methane yields from the 2007 Guidelines of the IPCC, which only consider two studies. For continuously stirred tank digesters and semi-continuous digesters lower methane yields are revealed. Multi-variate analysis of methane yields together with operating conditions and manure composition, enable the identification of clusters. These groups of variables can be useful to build potential AD scenarios in dairy farms. For Part II of the database, relative changes in emissions between the activities in the standardised baseline and AD scenarios, are examined. It is found, through meta-analysis, that replacing raw manure by anaerobically-treated manure (i.e. digestate) in storage tanks and for field- application, mitigates baseline emissions by 38.7% and 6.9%, respectively. These relative changes can be used to estimate emissions from digestate, being more specific and evidence-based than the current methodology from the IPCC. In addition, relative changes found for offset of fossil fuels by biogas generated in the AD scenarios indicate a reduction of baseline emissions by 9.0%. Only methane leaks from digesters significantly increase the baseline emissions (by 7.4%). Finally, results found by meta-analyses of methane yields and changes in emissions are applied to four dairy farm case studies. The work presented in the case studies demonstrates the benefits of enhancing the robustness of methods to estimate the effect of AD on GHG emissions from dairy farms.