Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array

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Mahmodi Roqiah; Moradi Mohammad Hossein; KHALTABADI FARAHANI AMIR HOSSEIN; Karimi Mohammad Osman

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Journal: Journal of Animal Production Year:2020 | Volume:22 | Issue:4 Page(s): 501-513

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Title

Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array

Author(s)

Mahmodi Roqiah | Moradi Mohammad Hossein | KHALTABADI FARAHANI AMIR HOSSEIN | Karimi Mohammad Osman | Issue Writer Certificate

Keywords

Afghan sheepQ1

Copy Number Variation (CNV)Q1

Gene ontology (GO) analysisQ2

Genetic variationQ1

Genomic detectionQ1

Abstract

The aim of this study was to identify the genome-wide copy number variations (CNV) in one of the sheep breeds in Afghanistan named Arabic breed, and to study the associations between these regions containing this kind of diversity with different biological pathways. For this purpose, 15 animal samples from different ages were collected from their natural rearing environment in Herat province of Afghanistan and then were genotyped using Illumina Ovine 50kSNP array. After various steps of the data quality control, the genome-wide detection of CNVs was carried out using Hidden Markov Model in PennCNV (version 1. 0. 3) software. The results showed that all animals used in this study have CNVs in their genome. In total, 306 CNVs were observed for autosomal chromosomes. The total genomic length of CNVs was 128 Mbp and the average CNV numbers per animal was 20. 4. After merging overlapped regions, a total of 286 CNVR regions were identified. These genomic regions were then further evaluated using bioinformatics tools for identifying the metabolic pathways associated with them. The results of gene ontology study indicated that many of these regions are associated with different metabolic pathways such as fertility and reproductive performance, body weight and carcass characteristics, immune system development, and skeletal-muscular system.

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APA: Copy

Mahmodi, Roqiah, Moradi, Mohammad Hossein, KHALTABADI FARAHANI, AMIR HOSSEIN, & Karimi, Mohammad Osman. (2020). Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), 22(4 ), 501-513. SID. https://sid.ir/paper/388847/en

Vancouver: Copy

Mahmodi Roqiah, Moradi Mohammad Hossein, KHALTABADI FARAHANI AMIR HOSSEIN, Karimi Mohammad Osman. Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE)[Internet]. 2020;22(4 ):501-513. Available from: https://sid.ir/paper/388847/en

IEEE: Copy

Roqiah Mahmodi, Mohammad Hossein Moradi, AMIR HOSSEIN KHALTABADI FARAHANI, and Mohammad Osman Karimi, “Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array,” JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), vol. 22, no. 4 , pp. 501–513, 2020, [Online]. Available: https://sid.ir/paper/388847/en

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