Innovative exploitation of pig genetic resources

This thesis is the results of a research activity performed during the Industrial Ph.D. program with the National Pig Breeders Association (ANAS). The first study takes advantage of already available knowledges related to molecular marker affecting coat color (MC1R gene) together with knowledge of genetic markers that control vertebrae number variability (NR6A1 p.P192L) in European domestic pigs and in Mora Romagnola breed. We investigated polymorphisms at these two genes to implements the use of these DNA markers and redefine the Mora Romagnola Herd Book breed standard. Furthermore, these DNA markers could be used for food traceability and authentication, improving economic sustainability of low-productivity breeds, whose products are often subject to frauds. The other two parts of the thesis take advantage from the morphological heterogeneity of Casertana breed to study phenotypic traits that cannot be genetically characterized using cosmopolitan pig breeds populations. In the second study of this thesis, we considered Casertana different ears conformation and phenotypic variability of other exterior traits (wattles and coat colours) to perform genome wide association study (GWAS) and a genome FST analyses. The study provides preliminary information about candidate genes involved in effecting monogenic traits not yet fixed in this population. In the third study, we considered the important variability of the tail shape in Casertana breed. We run a GWAS comparing the genome of curly-tailed and strait-tailed animals in order to identify genomic regions associated with the tail shape phenotype. Considering the potential relationship between tail shape and pig’s behavior and tail biting damages, the results of this study could help to develop further studies aimed at responding to animal welfare. This theme is a current topic in pig breeding, and it is considered also in ANAS new breeding programs for improve sustainability of Italian pig breeds for PDO and PGI productions.