Evaluation of Genetic Potential of Iranian Native Chicken Ecotypes; Insights for Conservation

ObjectiveDifferent climates and wide geographical area of Iran have caused considerable genetic diversity in Iranian chicken ecotypes. Artificial selection for genetic gain in economic traits leads to a reduction of genetic diversity in livestock and poultry breeds. On the other hand, by identifying the genetic potential of native ecotypes and managing breeding programs, it is possible to increase productivity in native chicken populations while maintaining genetic diversity. However, so far no genomic study has been performed to identify the genetic characteristics of native chickens. The aim of this study was to identify the genetic potential of Iranian native chicken ecotypes for appropriate targeting of breeding and genetic conservation programs. Materials and methodsIn this study, genomic data related to 51 native chicken ecotypes, 11 chickens of Arian line and 10 chickens of Leghorn breed were collected from the department of animal science at Shahid Bahonar University of Kerman. Mapping step against reference genome was done by BWA program. Identification of single nucleotide variants was performed by GTAK software. Phylogenetic analysis was investigated using the neighborhood joining method and Mega software. Fst and inbreeding coefficient among population were performed using Admixture and VCFtools programs. ResultsPercentage of alignment against the reference genome was reported between 83% and 95% for all samples and also 14.56 million single nucleotide variants were reported from the native and commercial chicken genomes. The results of phylogenetic tree analysis showed that almost all studied ecotypes were classified into separate groups. According to the reported results, it can be claimed that native chicken ecotypes are more genetically similar to the Arian line (compared to Leghorn breed). Findings obtained from admixture and Fst analysis also confirmed the results of phylogenetic analysis. For example, the highest Fst was estimated as 0.219 between Leghorn breed and Marandi ecotype. ConclusionsDue to the genetic similarity of most native chicken ecotypes and Arian line, breeding programs can be organized based on meat production traits. By targeting breeding programs, genetic resources can be improved to increase productivity while preserving the genetic diversity of native chicken ecotypes.