نوع مقاله : مقاله پژوهشی
نویسندگان
1 دانش آموخته کارشناسی ارشد.گروه علوم دامی، دانشگاه اراک، اراک، ایران
2 استادیار. گروه علوم دامی. دانشکده کشاورزی و محیط زیست. دانشگاه اراک. ایران.
3 استادیار. گروه علوم دامی. دانشکده کشاورزی، دانشگاه هرات، هرات، افغانستان
چکیده
هدف از این تحقیق شناسایی تنوع تعداد کپی (CNV) در سطح ژنوم یکی از نژادهای گوسفند کشور افغانستان به نام نژاد عربی و بررسی ارتباط مناطق ژنومی حامل این نوع تنوع، با مسیرهای بیولوژیکی مختلف بود. برای این منظور 15 نمونه حیوان با سن های مختلف از محیط پرورش این دام ها در استان هرات افغانستان جمع آوری و سپس با استفاده از آرایه هایIllumina Ovine 50kSNP تعیین ژنوتیپ شدند. پس از اجرای مراحل مختلف کنترل کیفیت داده ها، شناسایی تنوع CNV در سطح ژنوم این حیوانات با استفاده از مدل Hidden Markov نرم افزار PennCNV (نسخه 1/0/3) انجام شد. نتایج حاصل نشان داد که تمام حیوانات مورد مطالعه دارای تغییر در تعداد کپی در سطح ژنوم بودند. در مجموع، 306 تنوع CNV در تمام کروموزوم های اتوزومی شناسایی شد. کل طول توالی این مناطق ژنومی معادل 128 مگاجفت باز و متوسط CNV به ازای هر گوسفند 20/4 مگا جفت باز بودند. پس از ادغام مناطق همپوشان در مجموع 286 ناحیه CNVR شناسایی شد. این مناطق ژنومی به منظور بررسی مسیرهای متابولیکی مرتبط با آن ها مورد ارزیابی های بیوانفورماتیکی قرار گرفت. نتایج مطالعه هستی شناسی، نشان داد که بسیاری از این مناطق با مسیرهای بیولوژیکی مختلفی مانند باروری و عملکرد تولیدمثلی، خصوصیات لاشه و وزن بدن، توسعه سیستم ایمنی و سیستم اسکلتی-ماهیچه ای در ارتباط هستند.
کلیدواژه‌ها
عنوان مقاله [English]
Genomic detection of copy number variations (CNVs) in Arabic sheep breed of Afghanistan using Ovine 50k SNPChip array
نویسندگان [English]
- Roqiah Mahmodi 1
- Mohammad Hossein Moradi 2
- Amir Hossein KhaltAbadi Farahani 2
- Mohammad Osman Karimi 3
1 Department of Animal Science, Arak Univeristy, Arak, Iran
2 Department of Animal Science, Arak University, Arak, Iran
3 Herat University, Herat, Afghanistan
چکیده [English]
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.
کلیدواژه‌ها [English]
- Afghan sheep
- Copy Number Variation (CNV)
- Gene ontology analysis
- Genetic variation
- Genome detection
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