Genetic characterisation of Germanata Veneta and Mignon local duck breeds (Anas platyrhynchos) using whole-genome sequencing

This study investigated the genetic diversity and conservation status of two endangered Italian duck breeds: Germanata Veneta (GER, n = 50) and Mignon (MIG, n = 50). The DNA was extracted from blood and analysed through whole-genome sequencing. The single nucleotide polymorphism (SNP) calling allowed the identification of 186,287 shared SNPs which were used to estimate expected and observed heterozygosity, and inbreeding coefficients based on homozygosity (FHOM) and on runs of homozygosity. Both breeds showed low genetic variability and high inbreeding (GER: FHOM = 0.305 ± 0.184; MIG: FHOM = 0.369 ± 0.163). Multidimensional scaling revealed substructure within MIG, supported by phylogenetic and admixture analyses. Runs of homozygosity islands in GER were located on chromosomes 1, 2, 10, 11 and 21, with 524 SNPs enriched in immune response genes. In MIG, runs of homozygosity islands mapped to several chromosomes and included 614 SNPs related to muscle and cytoskeletal functions. Genes associated with small body size (e.g. SHOX, IGF2R and PRKG2) were found in MIG. A genome-wide association study comparing GER and MIG identified major genetic differences on chromosomes 2, 3, 5 and 13, including genes related to fatty acid metabolism (HADHA and HADHB) and dwarfism (POC1A). The results revealed low variability and high inbreeding, providing data to inform conservation programs aimed at mitigating the risk of genetic erosion. Low genetic diversity and high inbreeding were observed in both Germanata Veneta (GER) and Mignon (MIG) duck breeds.ROH islands in GER were enriched in immune-related genes, while those in MIG were associated with muscle function and body size.GWAS identified genetic differences linked to fatty acid metabolism and dwarfism, particularly on chromosomes 3 and 13. Low genetic diversity and high inbreeding were observed in both Germanata Veneta (GER) and Mignon (MIG) duck breeds. ROH islands in GER were enriched in immune-related genes, while those in MIG were associated with muscle function and body size. GWAS identified genetic differences linked to fatty acid metabolism and dwarfism, particularly on chromosomes 3 and 13.