Investigation of structure and genetic diversity of three native chicken ecotypes with common ancestor and commercial lines using whole genome sequencing data

The genetic resources of domestic chickens include a wide range of breeds and populations which vary greatly in body size, skin color, body weight, egg, and meat production. In the current study, to study phylogenetic relationships, genetic diversity, and inbreeding, whole-genome sequencing data of 54 chickens of a common ancestor (Red Junglefowl), native ecotypes, and commercial lines were applied. An average of 98 million short reads were processed using bioinformatics software and single-nucleotide polymorphisms (SNP) were called. The genetic structure of the populations was studied using Admixture, SNPhylo software and SNPRelate package. Plink software was used to perform quality control and to calculate inbreeding. Genetic diversity in the populations was estimated using VCFtools software. The results showed that the lowest genetic distance with the common ancestor was related to Lari ecotype and the highest and lowest common SNP with Red Junglefowl was related to Arian broiler line and Leghorn laying line, respectively. Inbreeding in commercial lines (Arian and Leghorn) was more than native ecotypes. Compared to the common ancestor, higher genetic diversity was observed in native ecotypes (Lari, Khazak and Marandi, respectively) than in commercial lines. Our results indicated the importance of using markers across the genome to increase awareness of potentially harmful homozygosity and to prevent the loss of genetic diversity of native ecotypes. Genetic diversity in native ecotypes can only be maintained through organized breeding programs.