Identification of single nucleotide polymorphism in Iranian Helmeted Guineafowl ‎ecotypes to study the phylogenetic relationships and inbreeding ‎

Document Type : Research Paper


1 M.Sc. Graduate,, Department of Animal Science, Faculty of Agriculture, Shahid ‎Bahonar University of Kerman, Kerman, Iran

2 Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, ‎Kerman, Iran

3 Associate Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of ‎Kerman, Kerman, Iran

4 Ph.D. Graduate, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

5 Ph.D. Graduate, Institute of Biotechnology, Shiraz University, Shiraz, Iran‎


The Helmeted Guineafowls were originated from West Africa and spread widely across the world, due to their ability to adapt to different environmental conditions. The main goal of this investigation was to identify the single nucleotide variations (SNVs) in order to explain the genetic structure of Helmeted Guineafowl in Iran. The whole genome of six Guineafowl ecotypes (18 samples) including Tabriz (blue and grey), Rasht, Tabriz (white), Rasht×Tabriz cross, Shiraz and Lar were sequenced. Paired-end libraries with 125 bp of Guineafowl samples were sequenced by whole genome Illumina platform. The phylogenetic tree analysis based on the maximum likelihood and neighbor joining was constructed. Runs of homozygosity (ROHs) were detected across all individual genomes by PLINK software. In the current study, around 14.48 million SNVs were detected. To evaluate the phylogenic relationships among all Guineafowl ecotypes, we applied two different phylogenic methods based on neighbor-joining and maximum-likelihood methods. Similar results were reported by these methods, all Helmeted Guineafowl ecotypes were classified separately except Shiraz and Lar ecotypes, which showed the most amount of genetic similarities. The results of runs of homozygosity (ROH) analysis indicated that the highest level of inbreeding at all levels of ROH were observed in the white Tabriz ecotype, in contrast Tabriz (blue and grey) ecotype showed the lowest level of inbreeding at all levels of ROH. These findings can provide new insight into genetic structure of Helmeted Guineafowl ecotypes in order to develop the breeding programs.


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