Genetic insights for sustainable livestock farming through bioinformatic analysis of SNP data

The thesis thoughtfully examines how genetics is essential for developing sustainable livestock production methods. The research contributes to a deep understanding of how genetic factors interact with various farming environments to support ecological, economic, and social sustainability by using cutting-edge bioinformatic approaches to unravel the genomic details. The introductory chapters create a thorough framework and explain the fundamentals of sustainability, particularly in the context of agriculture and animal husbandry. The manuscript examines the transition from conventional genetics to modern genomics via the perspective of animal breeding and genetics, highlighting the significance of Single Nucleotide Polymorphisms (SNPs) and their molecular implications in determining key traits. The core of the thesis consists of three comprehensive case studies on Pagliarola sheep, Holstein-Friesian cattle, and Comisana sheep, each of which sheds light on a distinct breed. A comprehensive examination of the critically endangered Pagliarola sheep breed reveals a wealth of information on genetic diversity, population dynamics, and historical introgression incidents. Genotyping 24 individuals from the residual Pagliarola population, we compared its genetic architecture with 21 Italian local breeds. The population genetically divides into two groups both of which appear to be neighboring Italian Merino-derived breeds. The fixation index (FST) outlier analysis identified key differentiating genes between Pagliarola and Merino-derived Italian breeds, solidifying its genetic uniqueness. This exploration not only aids in the conservation of a valuable genetic resource but also underscores the role of endemic breeds in mitigating climate challenges and preserving local agricultural heritage. The thesis shifts its attention to the transboundary Holstein-Friesian cattle breed and explores the complex genetic discrepancies that exist among the North American and Italian populations as a result of various breeding goals and geographic factors. In order to analyze the genetic makeup of the Italian Holstein (itHOL), Parmigiano Reggiano Holstein (prHOL), and North American Holstein (naHOL) populations of Holstein-Friesian cattle. Different genetic profiles are discovered for each subpopulation by multidimensional scaling and ADMIXTURE studies. Additionally, investigations of selection signatures with both haplotype and single marker oriented analyses find significant SNPs close to genes linked to fertility, illness resistance, and milk quality. Notably, convergent signals are present in genes related to milk composition and production, such as the VPS8 gene. This genetic understanding highlights the alignment of specialist breeding techniques and local sustainability objectives in the context of Parmigiano Reggiano cheese production. Finally we investigated the genetic foundations of parasite resistance in Comisana sheep breed by developing a model for determining resistance breeding values through the combination of phenotypic and SNP data. Starting from FEC we calculated estimated breeding values (EBVs) for GIN resistance. The most and least genetically resistant sheep to GINs were found using the extreme ends of EBVs and compared through a case-control genome-wide association study (case-control GWAS). We found 18 significant Single Nucleotide Polymorphisms (SNPs) connected to 13 genes covering 12 chromosomes. Some of these genes contribute to adaptation processes and production features, and others have an impact on the physiology and pathophysiology of the digestive system. 11 important pathways that control immune response, drug metabolism, detoxification, and other metabolic activities were identified by enrichment analysis of these genes. These findings not only support environmentally friendly farming practices by reducing pharmacological treatments but also support economic sustainability by lowering production losses and veterinary costs. The thesis in its entirety represents an innovative effort to use genetic knowledge for ethical cattle farming. The research highlights the potential for customized breeding techniques that correspond with environmental needs and production requirements by revealing the complex genetic tapestry of these various breeds. These results shed light on a strategy for balancing ecological resilience and contemporary agricultural methods, guiding further study and pointing the way to concrete initiatives for a more sustainable livestock sector.