Conservation Status of Two Italian Local Poultry Breeds: Faraona Camosciata and Oca Padovana

The present study aimed to assess the conservation status and characterize the phenotypic and genomic diversity of two endangered Italian poultry genetic resources to guide their conservation plans. Blood samples and morphometric data were collected on 50 Faraona Camosciata (FAC, Numida meleagris) and 50 Oca Padovana (OPD, Anser anser) adult animals. Genomes were profiled by low coverage whole genome sequencing. Observed and expected heterozygosity, genomic inbreeding, population structure, runs of homozygosity (ROH), ROH islands, and Gene Ontology enrichment were evaluated. Morphometric measures revealed significant sexual dimorphism within both breeds. FAC females exceeded males for several traits, and OPD males exceeded females for most features. Both breeds had very low heterozygosity and high inbreeding, consistent with their small effective sizes. The ROH length spectra indicated distinct histories: FAC was enriched in numerous short tracts under 2 Mb, compatible with older, diffuse autozygosity, and OPD carried a higher burden of long tracts between 4 and 16 Mb, consistent with more recent common ancestry. Recurrent ROH islands were detected in both breeds. In FAC, islands were enriched for hydrolase and catabolic functions, and organelle related components, including genes such as RAD54L, SEC63, and POMGNT1. In OPD, islands emphasized kinase regulation, ion channel and contractile complexes, and endocrine metabolism, featuring IGF2, INS, TH, and GJA1 genes. Results provide a baseline for genetic management that prioritizes avoidance of matings among relatives, rotation of animals across centers, balanced contributions, and monitoring through genetic methods, while underscoring the importance of improved genome annotation for these non-model species.