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Peer-reviewedCC BY-NC-ND 4.0Poultry Science

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

  • Medhat S. Saleh1,2
  • Francesco Perini3
  • Antonio Camarda1
  • Stefano Bettini3
  • Cecilia Mugnai4
  • Vincenzo Landi1
  • Emiliano Lasagna3
4 affiliations
  1. 1Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, BA, 70010, Italy
  2. 2Department of Animal Production, Faculty of Agriculture, Benha University, Benha, 13736, Egypt
  3. 3Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, PG, 06121, Italy
  4. 4Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco, TO, 10095, Italy
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@article{saleh2026genomic,
  title = {{Genomic characterization and selection signals in Italian black Atriana chickens using high-density SNP array}},
  author = {Medhat S. Saleh and Francesco Perini and Antonio Camarda and Stefano Bettini and Cecilia Mugnai and Vincenzo Landi and Emiliano Lasagna},
  journal = {Poultry Science},
  year = {2026},
  month = oct,
  doi = {10.1016/j.psj.2026.108030},
  url = {https://doi.org/10.1016/j.psj.2026.108030},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Genomic characterization and selection signals in Italian black Atriana chickens using high-density SNP array
AU  - Medhat S. Saleh
AU  - Francesco Perini
AU  - Antonio Camarda
AU  - Stefano Bettini
AU  - Cecilia Mugnai
AU  - Vincenzo Landi
AU  - Emiliano Lasagna
PY  - 2026
DA  - 2026/10/23
JO  - Poultry Science
DO  - 10.1016/j.psj.2026.108030
UR  - https://doi.org/10.1016/j.psj.2026.108030
AB  - 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.
SN  - 0032-5791
SN  - 1525-3171
ER  -