Genomic characterization and selection signals in Italian black Atriana chickens using high-density SNP array

The black Atriana (ATRI) is a local Italian chicken breed of historical and cultural importance. This study evaluated its genetic diversity and population structure and identified putative signatures of selection using runs of homozygosity (ROH) and the integrated haplotype score (iHS). Nineteen ATRI birds and 494 birds from 24 Mediterranean local breeds were genotyped with the Affymetrix Axiom 600 K Chicken Genotyping Array. After quality control, 505 birds and 495,454 autosomal SNPs were retained. In ATRI, observed heterozygosity, expected heterozygosity, and minor allele frequency averaged 0.345, 0.358, and 0.270, respectively. The inbreeding coefficients based on observed versus expected homozygosity and on ROH were 0.037 and 0.222, respectively. Principal component, NeighborNet, and ADMIXTURE analyses supported a distinguishable ATRI genomic profile while indicating affinities with several Mediterranean breeds. ROH and iHS analyses identified six candidate regions each, including two overlapping regions on chromosomes 2 and 14. These regions contained genes previously associated with growth, production, and environmental-response traits, including PTP4A3, TSNARE1, NDUFB6, WFIKKN1, and IFT140. Given the limited ATRI sample size, these candidate signals should be interpreted as exploratory and validated in larger independent populations. The findings provide baseline genomic information to support genetic monitoring and conservation planning for ATRI.