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Information Journal Paper

Title

Identification of genome diversity in marandi chicken using whole genome sequencing method

Pages

  161-176

Abstract

 Objective Evaluation and conservation of native chickens as future genomic resources are essential. In this study, genomic diversity of four Marandi breeds was investigated using whole genome sequencing technique. Materials and Methods Blood samples were taken from four chickens in East Azerbaijan province, Iran. whole genome sequencing (paired end sequencing) was done by Illumina Company (Hiseq 2500). Data quality control was performed by FastQC program. whole genome sequencing data were aligned with genome reference (Gallus_gallus-5. 0/galGal5) using MEM algorithm implemented in burrows wheeler aligner program (BWA). Single nucleotide polymorphisms (SNPs) and small insertions and deletions (Indels) were identified by the GATK program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversity of 4 chicken genomes was calculated with VCFtools. Results The short sequences were compared with the reference genome of over 99% and with the mean depth of 7X coverage. In this study, 8. 7 million SNPs and 9. 1 Indels were identified with the most counts of them in the intron and intergenic regions. The mean of observed and expected heterozygosity percentages for SNPs in four chicken genomes were 0. 33 and 0. 35, respectively. Conclusion Results from annotation showed that percentage of the silent SNPs (74. 64%) is higher than that the nonsynomous SNPs (missense and nonsense) in Marandi chicken genome. The results obtained from this research can be useful for Marandi chicken breeding and conservation programs.

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    APA: Copy

    Akbari, Rasol, Esmailizadeh, Ali, Amiri Ghanatsaman, Zeinab, & Ayatollahi Mehrgardi, Ahmad. (2020). Identification of genome diversity in marandi chicken using whole genome sequencing method. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, 12(1 ), 161-176. SID. https://sid.ir/paper/224527/en

    Vancouver: Copy

    Akbari Rasol, Esmailizadeh Ali, Amiri Ghanatsaman Zeinab, Ayatollahi Mehrgardi Ahmad. Identification of genome diversity in marandi chicken using whole genome sequencing method. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY[Internet]. 2020;12(1 ):161-176. Available from: https://sid.ir/paper/224527/en

    IEEE: Copy

    Rasol Akbari, Ali Esmailizadeh, Zeinab Amiri Ghanatsaman, and Ahmad Ayatollahi Mehrgardi, “Identification of genome diversity in marandi chicken using whole genome sequencing method,” JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, vol. 12, no. 1 , pp. 161–176, 2020, [Online]. Available: https://sid.ir/paper/224527/en

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