DIVERSITÀ GENETICA NELLE RAZZE BOVINE LOCALI: UN APPROCCIO GENOMICO

Genetic diversity is a crucial factor for the adaptability and sustainability of livestock breeds, particularly local breeds that contribute to biodiversity and rural development. The study of genetic diversity in these populations is essential for developing effective breeding strategies that balance productivity with the preservation of unique genetic traits. This thesis explores the genetic diversity, inbreeding patterns, and population structure of local and beef cattle breeds through genomic and pedigree-based approaches, with a focus on the Alpine Grey breed, adapted to the harsh conditions of the Alpine regions, and five Italian beef breeds—Marchigiana, Chianina, Romagnola, Maremmana, and Podolica—each of which is adapted to distinct environments, ranging from the fertile lowlands to the more rugged and dry landscapes of central and southern Italy. The studies on inbreeding and genetic structure reveal distinct patterns in two cattle populations: Alpine Grey and five Italian beef breeds. In Alpine Grey cattle, a combination of pedigree and genomic data from 165,575 and 1,180 individuals, respectively, revealed a moderate correlation (0.20–0.54) between pedigree-based and genomic inbreeding coefficients. Runs of homozygosity (ROH) analysis showed that over 90% of ROH segments were shorter than 8 Mb, indicating the prevalence of ancient inbreeding. Two major ROH islands, identified on chromosomes 6 and 7, contained genes linked to immune response (HERC3, PYURF) and fertility (EIF4EBP3, SRA1). These results underscore the importance of precise genomic inbreeding analysis to monitor genetic health and maintain the adaptive traits of local breeds. Similarly, the genomic analysis of five Italian beef breeds, based on the genotypes of 14,799 individuals, revealed significant genetic differentiation, particularly in Chianina and Romagnola, which showed the most distinct clustering patterns in Principal Component Analysis (PCA) and Admixture analysis. Genomic inbreeding coefficients (FROH) ranged from 0.17 in Marchigiana to 0.15 in Romagnola. ROH islands identified on chromosomes 5 and 6 contained candidate genes such as FGF5, RAB21, KRT71, and DCAF16, which are associated with coat characteristics, growth, and environmental adaptation. These findings provide a comprehensive view of the genetic diversity and inbreeding patterns in these breeds, offering valuable insights for breeding strategies aimed at preserving genetic diversity while improving economically important traits. Lastly, in the study of Alpine Grey cattle’s genetic architecture, a Bayesian Genome-Wide Association Study (GWAS) on 21 morphological traits, based on phenotypic data from 36,309 animals and genomic data from 1,295 genotyped individuals, revealed moderate to high heritability estimates for key traits, such as stature (0.54) and udder depth (0.36). Significant correlations were observed within udder conformation traits, with genetic correlations as high as 0.95 between fore udder length and suspensory ligament. Key SNPs associated with body size, meat quality, and skeletal development were identified, including CACNA2D1 and HGF on chromosome 4 and MSC on chromosome 14. These findings contribute to understanding the genetic bases of morphological traits, facilitating the development of breeding programs that enhance productivity without compromising adaptability. Overall, this thesis contributes to confirming the critical role of genomic tools in understanding the genetic diversity and inbreeding dynamics of local and beef cattle breeds. Integrating genomic and pedigree-based approaches provides a deeper understanding of how historical and recent inbreeding events, selection, and population structure have shaped these breeds. These findings highlight the importance of continuing research on local cattle populations for biodiversity preservation, sustainable development, and resilience in the face of environmental challenges.