Pork is one of the most consumed meats in the world. Healthiness of pork is largely determined by the amount and type of fat. It is known that the amount of fat and its distribution between muscle and subcutaneous adipose tissue (SF) differs between breeds and individual animals within a breed, which implies genetic regulation of fat partitioning. The aim of this project was to investigate the molecular mechanisms regulating fat deposition in genetically diverse breeds and to identify DNA polymorphisms which might form the basis for the development of biomarkers for selective breeding towards desirable genotypes. An objective of the work presented here was to investigate whether breed-specific variations in fatty acid composition of muscle and SF are related to the breed-specific messenger RNA (mRNA) and protein expression of key lipogenic enzymes. The enzymes investigated were acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), stearoyl-CoA desaturase (SCD) and delta-6-desaturase (~ 6 D ) which cata lyse the biosynthesis of saturated (SFA), monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA) respectively. Significant between-breed differences in fatty acid composition were observed in SF of Large White x Pietrain (LWxP), Duroc x Pietrain (DxP) and Pielrain pigs. Sig nificant between-breed differences in fatty acid composition were also observed in muscle but not SF of Duroc 1 (D1), Duroc 1 x Duroc 2 (D1xD2, enhanced IMF), Duroc x Iberian (D1xl) and Large White x Landrace (LWxLr) pigs. A number of novel breed- and tissue-specific single nucleotide polymorph isms in the genes encoding for SeD, ~6D and ACC were identified in muscle and SF of pigs which differed in fatty acid compositions . Additionally, positive relationships were observed between n-6 PUFA content and 66D protein expression in SF of LWxP, DxP and Pietrain pigs, and between total MUFA and SCD mRNA expression in SF of D1 , D1xD2, Dxl and LWxLr pigs. An industrial placement undertaken as a part of this project identified the view of the Key Opinion Leaders regarding new and emerging approaches for modification of meat quality traits and increased public awareness about these approaches. Therefore, this resea rch has not only generated new knowledge, but also contributed to promoting science to the wider community and addressing the challenges of the international pig producing industry.

Effective methods for preventing cross-contamination of Salmonella and Y enterocolitica in pigs are necessary to maintain pork quality. However, control mechanisms to limit microbial contamination at farm level have received much less attention than later stages of pork processing. In addition, in Ireland, there is very little data relating to Y enterocolitica on farms. This means that further research is required to understand (and influence) the epidemiology of Salmonella and Y enterocolitica at farm level. This study investigated possible routes of cross contamination, from 'birth to carcass', examining samples drawn on-farm, during transport, lairage, slaughter and carcass production. The study established farm level prevalence's of 2.9% for Salmonella and 0.72% for Y enterocolitica. PFGE analysis of Salmonella identified transmission of strains from the farm into the abattoir, and confirmed lairage pens as major sources of cross-contamination. Bioserotyping identified pathogenic biotypes and 'non-pathogenic' 1A strains among isolated Y enterocolitica. Such analysis also associated 8 out of 10 regional cases of clinical human infection with biotype 1A. The study established that properly applied/monitored scald tank procedures can eliminate Y enterocolitica biotype lA, suggesting scalding as an effective control point during slaughter processes. Investigation of a farm based intervention, i.e. treatment of slurry with urea or ammonia, established this process significantly reduced bacterial numbers and increasing slurry fertiliser value.

Calpastatin is widely known as an endogenous specific inhibitor to the ubiquitously expressed calpain an enzyme responsible for proteolysis of myofibrillar proteins during post-mortem degradation of muscle. The presence of the calpastatin polypeptide in muscle indicates that the activity of calpain can be potentially down regulated which could result in meat toughness. Asssement of calpastatin activity in meat could be a predictive marker to meat tenderness and variation in the gene has the potential to become a candidate genetic marker which is associated with meat tenderness. The variability and inconsistency produced in meat tenderness post-mortem could be reduced if animals could be selected based on this potential genetic marker prior to slaughter which in turn will reduce the cost in meat processing and ultimately achieve the main objective of producing consistently tender meat. Previous studies have successfully sequenced bovine calpastatin cDNA and found that a series of promoters in the 5’ region are responsible for transcribing Type I, II and III mRNA for calpastatin. The presence and length of CA tandem repeat sequence 5’ to the transcription start site of Type I calpastatin mRNA is believed to play a significant role in regulating the transcriptional activity of this promoter. This thesis investigated the hypothesis that there was a relationship between length polymorphisms of CA repeat located 5’ to the promoter region of Type I bovine calpastatin which altered the level of calpastatin transcripts and ultimately influenced meat shear force value due to the variation in calpain inhibition. Apart from this, transcriptional activity of promoter for Type I, II, and Type III calpastatin were also assessed as well as their response towards agents involved in signalling cascade associated with the agents that stimulate hypertrophic growth. In order to investigate the CA tandem repeat polymorphisms, a PCR based cloning strategy was developed in this study which allowed amplification of this region. Cattle (n=6) of different breed and meat tenderness had their CA tandem repeat sequences amplified which were then cloned into a ZsGreen based reporter construct and transcriptional activity of the promoter were measured using fluorescence imager (Typhoon Trio). From the results, there was no direct correlation (R=0.28) found between the CA tandem repeat length and the shear force value of the meat. However, transcriptional activity for Type I promoter was significantly affected (P<0.05) by changing the length of CA tandem repeat (40-60bp). In general, the calpastatin promoters displayed negative response towards treatment with cAMP(P<0.05) and there were no significant changes to the promoter activity when it was treated with forskolin. Furthermore, a significant reduction in promoter activity (P<0.05) was observed from all calpastatin promoters with calcimycin treatment. The research shows that the type I calpastatin promoter has transcriptional activity and is regulated by secondary messengers which activate cAMP dependent kinases. Although altering the CA tandem repeat length alters promoter activity, there appears to be no simple relationship between its length and toughness, as determined by shear force. However the differential activity of the three calpastatin promoters indicates that there are potentially multiple mechanisms by which its activity can be regulated.