Raziskovalni projekti

Krškopolje pig (KKP) is the only Slovenian autochthonous pig breed, which gains importance due to sustainability goals (preservation of biodiversity, efficient use of resources, and meat quality). The project performed an in-depth genetic and metabolic characterization of KKP under controlled conditions and compared it with modern lean hybrids (MP). The project had two main objectives. Within the first, we investigated the genetic structure of the KKP breed and its relationship with the phenotype. We genotyped 618 KKP with SNP-chip, and conducted whole-genome sequencing on 142 representative animals. We found relatively high genetic diversity but small effective population size, indicating a risk of decreasing variability. A high frequency of the undesirable RYR1 mutation was observed, and the effects of this and other genes (e.g., PRKAG3 and MC4R) on various traits were examined. The estimated heritability of intramuscular fat (IMF, 0.39), together with genetic correlations, suggests that selection for higher IMF could improve meat quality. Using GWAS and selection signature analysis, we identified genomic regions and candidate genes linked to leanness, fatness, and meat quality. Genetically, KKP clusters close to Schwäbisch-Hällisches and Landrace breeds. In the PDK4 gene promoter, we discovered an SNP (rs335510174) that likely affects gene expression. In the second part, we addressed metabolic and transcriptomic characterization and the influence of diet. KKP and MP were reared under identical conditions with standard or reduced-protein feed. Using the InraPorc model, we assessed the breed’s nutritional requirements. At slaughter, carcass measurements and histomorphological, biochemical, and transcriptomic analyses of adipose and muscle tissue were performed. Results show that reducing dietary protein decreases growth and muscle development in MP, but has no significant effect in KKP, demonstrating good adaptability and potential for further protein reduction in KKP feed. Compared to MP, KKP show slower growth, lower leanness, higher fatness (greater backfat thickness, IMF, lipogenic activity, larger adipocytes), and more oxidative muscle metabolism. KKP meat has higher pH, darker colour, higher saturated fatty acids, and more muscle pigment. Transcriptomic analysis revealed more differentially expressed genes in KKP adipose tissue compared to MP (e.g., genes for collagen metabolism, cholesterol metabolism, extracellular matrix modulation, and inflammation). We confirmed higher expression of key genes involved in lipogenesis (ACACA, FASN, SCD) and adipogenesis (PPARG). In muscle, a larger number of differentially expressed genes reflected differences in growth rate, glycolysis, and signalling pathways. Overall, the results provide deeper insight into genotype–phenotype relationships in fat-type pig breeds, support better utilisation of KKP potential, and contribute to understanding fat and muscle metabolism.