Samuele Bovo

Metabolomics is a powerful phenomics approach for investigating the molecular mechanisms linking genotype to phenotype and identifying biologically informative traits for precision livestock breeding. However, the genetic architecture of the plasma metabolome remains incompletely characterised in pigs. Here, we investigated the genetic determinism of plasma metabolites in 268 Italian Duroc pigs using untargeted high-throughput metabolomics and genome-wide association analyses. Plasma metabolomic analysis identified 580 quality-controlled metabolites, which were integrated with genotypes from a panel of approximately 60,000 single nucleotide polymorphisms. Heritability estimates indicated moderate genetic contribution on the plasma metabolome, with ~ 46% of metabolites showing heritability greater than 0.20. Overall, 89 metabolite quantitative trait loci (mQTL) regions were identified, involving 156 metabolites and metabolite ratios. Most associations were related to lipid and amino acid metabolism, and several loci harboured biologically plausible candidate genes involved in transport, enzymatic activity, and metabolic regulation. Several mQTL exhibited pleiotropic effects, some metabolites showed evidence of polygenic control, and conditional and ratio-based analyses uncovered additional associations not detected by single-metabolite analyses alone. These findings improve the biological interpretation of metabolic pathways underlying economically relevant traits and support the integration of metabolomics and genomics for precision breeding, feeding, and management strategies in pigs.

Honey is primarily composed of sugars, along with various secondary components, including environmental DNA (eDNA) derived from all organisms directly or indirectly involved in its production process. Specifically, DNA of plant origin is mainly found in the pollen collected by honey bees from the same flowers where they collected nectar. The European chestnut ( Castanea sativa , Miller) is highly valued in beekeeping for its abundant nectar production. In this study, we gathered insights on the genetic variability of C. sativa by analyzing DNA extracted from 21 chestnut monofloral honey samples produced in four regions in Northern Italy. The DNA was amplified using six C. sativa microsatellite markers commonly used for genotyping chestnut tree genetic resources. All eDNA‐derived samples successfully amplified the microsatellite loci, showing a high level of genetic variability, with a total of 35 different alleles, averaging 23.95 ± 2.09 alleles per honey sample. Some unexpected and rare C. sativa alleles were also identified in several honey samples. Genetic diversity of C. sativa was evaluated using honey‐derived microsatellite fingerprints by categorizing honey samples based on their production region and comparing their profiles using the fixation index F _ST . The highest F _ST value was observed between honey samples from Emilia‐Romagna and Trentino‐Alto Adige regions, while the lowest F _ST value was between Veneto and Trentino‐Alto Adige samples. Cluster analysis and Principal Component Analysis using microsatellite data indicated distinct geographically defined groups corresponding to the honey production regions. The findings suggest that honey eDNA can be utilized to assess the genetic variability of chestnut accessions, aiding in determining the geographical origin of chestnut honey samples, thus indirectly supporting their geographic authentication.

Early genetic studies have suggested that body size in rabbits can be considered a quantitative trait. Several rabbit breeds can be distinguished based on body size, including a few dwarf breeds differentiated by other morphological characteristics. While a large deletion in the HMGA2 gene is a major locus associated with dwarfism in Netherland Dwarf rabbits, it may not fully explain the reduced body size in this breed or other dwarf breeds. In this study, we compared the genomes of two dwarf rabbit breeds (Dwarf Lop and Netherland Dwarf) with those of non‐dwarf rabbits by analysing whole‐genome sequencing data obtained using a DNA‐pool sequencing approach. We applied the fixation index (F_ST) and pooled heterozygosity (H_P) statistics to identify signatures of selection related to small body size by contrasting dwarf with non‐dwarf breeds and comparing dwarf breeds. We identified several genomic regions that contain genes previously linked to body dimensions in various species, including LCORL‐NCAPG, COL2A1, GHRHR and CENPE. Functional enrichment analysis of genes within the top differentiated regions revealed biological terms related to skeletal development, further supporting the biological relevance of these loci. Additionally, the use of the latest version of the reference rabbit genome enabled the identification of a genomic region containing FGFR3, a gene linked to achondroplasia. Some genomic regions showed differentiation between the two dwarf breeds, suggesting that their small body size may, in part, arise through different genetic mechanisms. Overall, these findings support a polygenic architecture underlying small size in rabbits, influenced by a few major loci.