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The aim of this thesis is to explore some of the quantitative genetic aspects of resistance to gastrointestinal nematode parasites in small ruminants. The focus is on animals in temperate areas such as Northern Europe and consequently on the parasite species which poses the main production losses in this area, Teladorsagia circumcincta. Most of the published genetic parameter estimates in the literature for resistance to nematode parasites are for sheep, while there is a distinct lack of estimates for goats. A genetic analyses of parasitological and production data from a cashmere goat population (kids) was performed. The data were collected over a time span of four years from a farm in Scotland. The heritability of the indicator trait of resistance faecal egg count (Fec) was estimated to be 0.17 while that of the mean of several measurements was 0.32. The heritability of fibre traits was in excess of 0.5, while the heritability of live weight was 0.22. The genetic correlations between Fec and the production traits were slightly positive but not significantly different from zero. The phenotypic correlations were very close to zero. Fec data collected over four years from a commercial flock of Scottish Blackface in Scotland were analyzed using random regressions analyses to estimate the genetic and phenotypic parameters of the flock and how they change over time. The random regression model gave at least as good description of the data as univariate models fitted at individual time points. The added benefit of random regression analysis was that it allowed heritabilities and correlations to be interpolated for time points when data were not available, thereby enabling sampling time strategies to be determined. Genetic correlations between samples taken from 14 to 24 weeks of age were all greater than 0.8. The distribution of Fec in sheep has been found to generally fit the negative binomial distribution, with a small proportion of animals shedding most of the parasites. This fact could be utilised for separating or culling the most parasitised animals, as an immediate control measure. By means of computer simulation, a scenario of exploiting this particular distribution of Fec combined with selection over ten years in a closed flock was examined, in silico. Different management scenarios and different culling/separation scenarios were explored. The impact on lamb performance after ten years of separating the worst animals based on Fec did not exceed a 4% improvement in live weight in any scenario. The effect of culling was higher but there is a trade off by the fact that there is a profit loss due to the loss of animals. Thus there is relatively low merit in using, additionally to selection, separation/culling to help control the impact of nematode parasites. Protein supplementation has been proposed as a means of helping to reduce the impact of gastrointestinal parasites. The interaction of genotype and nutrition and the effect of different levels of protein supplementation on estimated genetic and phenotypic parameters for a flock of lambs were examined using computer simulation, for artificial and natural challenge scenarios. In the artificial challenge scenario the correlations between Fec and production traits became stronger as dietary protein level was reduced and the parasitic challenge was increased. There was little discernible pattern for natural challenge. It may be concluded that the predicted genotype x environment interaction is of little practical significance with respect to challenge level and dietary protein content. These results contribute to our understanding of the genetics properties of the resistance to gastrointestinal nematodes of small ruminants. They will allow more effective design of breeding strategies for nematode resistance in small ruminants. In particular, this thesis has demonstrated that breeding schemes for improving nematode resistance in small ruminants are predicted to be robust with respect to a) age of sampling b) nutritional regime (protein) and c) management (culling or separation).

Fasciola hepatica is a trematode parasite with wide geographical and host ranges, primarily affecting ruminants in the United Kingdom. Infection of host animals leads to significant economic losses in production, with reduced weight gains and milk quality and quantity. Clinical disease, known as fasciolosis, is expensive to treat and causes significant morbidity and mortality. More than three quarters of dairy herds surveyed in England and Wales have been exposed to this parasite, and the number of diagnoses of fasciolosis, made by the Animal Health Veterinary Laboratories Agency, has increased dramatically in the last fifteen years. Experimental studies have demonstrated failure to diagnose bovine tuberculosis (BTB) when co-infection with F. hepatica is present. In Chapter 2, we demonstrate a novel method for estimating the prevalence of BTB in England and Wales and show that, in light of the imperfect diagnostic test for BTB, the prevalence may be significantly higher than currently reported. In Chapter 3, a logistic regression model for the presence or absence of BTB on farms in England and Wales is designed, based upon those previously published. The addition of a variable to describe the burden of F. hepatica found in the locality of each farm significantly increases the predictive power of the model and may help to explain the under-diagnosis of BTB suggested in Chapter 2. A significant, negative association is demonstrated between F. hepatica exposure and the BTB status of the farm. The difference between the model predictions for BTB status made with F. hepatica exposure as tested and the predictions made assuming F. hepatica exposure is negative is then calculated to provide an estimate of the missing BTB diagnoses due to co-infection. We show this under-ascertainment to be over one third of cases. The significant, negative association between F. hepatica exposure and BTB diagnosis described at the herd level in Chapter 3, is then tested on an animal level. In Chapter 4, milk samples from individual animals testing negative and inconclusive, or negative and positive to the BTB test are assessed using the anti-F. hepatica antibody ELISA and an exposure value obtained. Significantly higher exposure to F. hepatica was not found in either pairing of BTB outcome-cattle and potential reasons for this are discussed. Chapter 5 investigates the association between F. hepatica exposure and other infectious diseases such as Bovine Viral Diarrhoea virus (BVDv), Leptospira spp, Infectious Bovine Rhinotracheitis, Johnes Disease and Neospora caninum. A random effects model is constructed using information collected about animal and farm parameters, to predict F. hepatica exposure. Vaccination against BVDv and Leptospira spp are shown to be significantly associated, the former being positively and the latter being negatively correlated. Johnes Disease prevalence is negatively associated with F. hepatica exposure and Salmonella Dublin prevalence is positively associated. Farm management and husbandry variables were also found to be significantly associated with F. hepatica exposure. In total, this thesis adds to the growing realisation that co-infection with this pathogen can have significant repercussions on the diagnostic ability of the BTB test and on the health and welfare of the national herd.

Bovine viral diarrhoea (BVD) is a highly significant endemic disease of cattle caused by bovine viral diarrhoea virus (BVDV). Infections with BVDV cause substantial economic losses brought about by its effects on reproduction and exacerbation of concurrent bacterial or viral infections. Since this disease was first described in 1946, diagnostic tools and disease control strategies have evolved considerably. Within Europe, an increasing number of countries have been implementing successful systematic control programmes, highlighting the feasibility and benefits of BVDV control. With its focus on the Northern Ireland industry, this thesis aims to identify and address important knowledge gaps in relation to BVD control in order to implement a systematic disease control programme. Diagnostic tools were reviewed by comparing and validating reverse transcription polymerase chain reaction (RT-PCR) methods, evaluating the testing of serum pools for antibody and by comparing commercial enzyme-linked immunosorbent assay (ELlSA) kits. A non-random survey for antibodies and virus indicated widespread seropositivity to BVDV and bovine herpesvirus type 1 in bulk tank milk samples from 181 dairy herds based across the country. It was followed by a cross-sectional study of dairy and suckler herds, including a risk factor analysis, which looked for evidence of viral circulation in the young stock cohort. It found an overall true seroprevalence of 58.7% (95% Cl: [54.7-62.70/0]). Finally, a genetic typing study in bovine samples collected between 1999 and 2011 did not detect any evidence of BVDV-2 or border disease virus. The analysis indicated that the predominant subtype circulating in Northern Ireland is BVDV-1a and described for the first time the detection of BVDV-1b. Results obtained have been employed to inform decisions on the most appropriate BVD control programme for Northern Ireland, to generate data on available diagnostic investigation tools and to provide a benchmark to assess the success of such a programme.

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With the removal of milk quotas in Ireland in 2015, for the first time in 30 years, Irish dairy farmers will be able to increase milk production without the necessity to purchase additional milk quota rights. The aim is to increase milk production by 50% by 2020 compared to the 2007 - 2009 average. Increasing milk volume will challenge both farmers and processors alike. Ireland's milk production is characterised by a spring-calving system, to coincide with grass growth. Ireland ability to produce milk cheaply from grazed grass is considered as the main competitive advantage of Irish dairy farming compared to their European counterparts. In the spring and autumn, grass quantity, and/or quality, can be limiting, resulting in the requirement to supplement the diet with concentrates and forages. With the increase in milk production expected in the coming years, there will be increased demand for feed and supplementation in the Irish grass-based system. These supplementary feeds will have different effects on nitrogen utilisation efficiency, which can affect milk protein fractions and nitrogen excretion, which is important from an environmental perspective. Maximising the efficiency with which milk is processed into high-value dairy products is a clear objective for milk processing plants in Ireland. There is limited information on the effect that dairy cow diet has on milk protein components and milk processability. The objective of this thesis is to increase the knowledge that is available on the effect of supplementing spring-calving grazing dairy cows during times of limited grass availability and/or sub-optimal quality on milk production, nutrient use efficiency and milk processability.

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