Genomic diversity, population structure and runs of homozygosity in Spanish native chicken breeds assessed with high-density SNP data.

M S Saleh, A Martínez, A Torres, M F Baquero, G Rusco, A Pons, A Canales, V Landi

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Article in Poultry science, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

M S SalehDepartment of Veterinary Medicine, University of Bari Aldo Moro, Strada Provinciale per Casamassima km 3, 70010 Valenzano (Bari), Italy; Department of Animal Production, Faculty of Agriculture, Benha University, 13736 Benha, Egypt.

A MartínezDepartment of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain.

A TorresAnimal Foodstuff Production Unit, Canary Agrarian Research Institute, Aptdo. No. 60, 38200 La Laguna, Tenerife, Spain.

M F BaqueroAnimal Foodstuff Production Unit, Canary Agrarian Research Institute, Aptdo. No. 60, 38200 La Laguna, Tenerife, Spain.

G RuscoDepartment of Veterinary Medicine, University of Bari Aldo Moro, Strada Provinciale per Casamassima km 3, 70010 Valenzano (Bari), Italy.

A PonsInstitute of Agri-Food and Fisheries Research and Training of the Balearic Islands (IRFAP), Balearic Islands, Spain.

A CanalesDepartment of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain.

V LandiDepartment of Veterinary Medicine, University of Bari Aldo Moro, Strada Provinciale per Casamassima km 3, 70010 Valenzano (Bari), Italy. Electronic address: vincenzo.landi@uniba.it.

Funding

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6 · The paper itself

Abstract

The local genetic resources of Spanish chickens constitute important components of biodiversity. Therefore, this study aimed to investigate the genetic diversity, population structure, runs of homozygosity (ROH) and inbreeding levels in Spanish local breeds. A total of 114 samples from three varieties of Andaluza Azul (AAZ), Andaluza Azul Británica (ABR) and Andaluza Azul Ceniza (ACA); Canaria (CAN); Combatiente Español (CES); Mallorquina (MLL) and Utrerana Franciscana (UF) Spanish breeds were genotyped using the Axiom 600k Chicken Genotyping Array. These genotype data were merged with 40 genotypes for the Spanish Prat (PTxx) and Red Villafranquina (RVxx) breeds from the Synergistic Plant and Animal Breeding (SYNBREED) project. The principal component analysis (PCA) results separated the Spanish local breeds into two clusters. The admixture results are consistent with the PCA results. At K2, the MLL and AAZ breeds showed clear genetic identity. The genetic differentiation results are consistent with the PCA plot, with Fst values ranging from 0.0027 (AAZ and ABR) to 0.259 (MLL and ABR). The values of observed and expected heterozygosity and minor allele frequency ranged from 0.185 to 0.353, 0.211 to 0.363 and 0.159 to 0.275, respectively, in the Spanish breeds. The average number of ROH ranged from 20.83 to 102.33 and the average length of ROH ranged from 1086 to 3310 Kb. The inbreeding coefficient based on ROH (F

Indexed as

ChickensGenetic VariationPolymorphism, Single NucleotideAnimalsBreedingGenotypeHomozygoteInbreedingSpainGenetic diversityPopulation structureRun of homozygositySNP arraySpanish native chicken

Identifiers

PMID42190477

DOI10.1016/j.psj.2026.107080

PMCPMC13223837

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LicenceCC BY-NC-ND

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