Genomic diversity, population structure and runs of homozygosity in Spanish native chicken breeds assessed with...

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_ROH) ranged from 0.027 in the CES breed to 0.147 in the ACA and RVxx breeds. The results showed the existence of different levels of genetic diversity in local Spanish breeds. These findings will help in performing conservation strategies for native Spanish breeds and promote the utilization of these genetic resources.