The principle aims of the work presented in this thesis were to further investigate the porcine acute phase proteins (APP) and determine the factors influencing the baseline concentrations of haptoglobin (Hp), C-reactive protein (CRP), Pig major acute phase protein (Pig-MAP) and transthyretin (TTR). The APP are used as markers of inflammation and sub-clinical disease and are considered potential biomarkers for pig health and welfare. They have also been identified as a possible means of breeding for disease resistance, however little is known about the genetics of the porcine APP. This study investigated associations between the APP genes and baseline concentrations and the heritability of those concentrations. An enzyme linked immunosorbent assay (ELISA) was developed for the measurement of porcine CRP, in-house methods were used for the determination of Hp and TTR and a commercial assay was used in the measurement of Pig-MAP. A population of pure line high health boars (n=~345) from 7 lines was used in the initial study each of which had an archived DNA sample and serum samples available for use. Baseline herd concentrations of the 4 APP were determined and correlations between Hp and CRP, Hp and Pig-Map and CRP and Pig-MAP were identified. Significant differences were found between the 7 breeding lines in CRP, Pig-MAP and TTR concentrations, indicating that selective breeding for performance traits may also have affected innate immune traits such as APP concentrations. Single nucleotide polymoiphisms (SNP) were identified in the 4 APP genes and 17 were genotyped across the boar population with line differences apparent in their allele frequencies for CRP, Pig-MAP and TTR. Statistical analysis showed that there were significant associations between 3 of the SNP located in the Hp gene and Hp baseline concentrations (p<0.01); all 3 SNP were also in high linkage disequilibrium. The association indicates that Hp is under genetic control and would also be better suited to use as a biomarker due to the lack of line effects in the boars. A heritability study was earned out utilising a mixed sex population of 297 animals (120 male, 177 female) comprising 7 breeding lines located on 2 farms. Initial analysis identified significant differences between male and females in Hp concentration, between pig lines in Hp, CRP and TTR and between the 2 farm units for CRP concentrations. This study showed that the baseline concentrations of the 4 APP could be affected by a variety of factors such as sex, commercial line and individual farm units and this must be taken into account if they are to be used as biomarkers. Heritability was estimated at 0.15, 0.13, 0.12 and 0.07 for Hp, CRP, Pig-MAP and TTR, respectively. All 4 APP show low heritability in serum concentration, this may prove problematic if they are utilised as a breeding trait. Overall, the findings from this study indicate that baseline concentrations of porcine Hp, CRP, Pig-MAP and TTR are influenced by various factors including sex, breeding line, and farm unit and this must be taken into account before they are utilised as biomarkers. They are traits of low heritability but the evidence suggests there may be a genetic component to their regulation thus requiring further investigation
