شناسایی نشانگرهای تک نوکلئوتیدی مؤثر بر صفات مهم گوسفندان بومی ایران با استفاده از ردپای انتخاب

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکترا، گروه علوم دامی دانشکده کشاورزی دانشگاه فردوسی مشهد

2 استاد، گروه علوم دامی، دانشکده کشاورزی؛ دانشگاه فردوسی مشهد

3 استادیار، محقق دانشگاه کشاورزی سوئد (SLU)

4 دانشیار، گروه علوم دامی دانشکده کشاورزی دانشگاه فردوسی مشهد

چکیده

سابقه و هدف: شناسایی تعداد فراوان نشانگرهای ژنومی توالی یابی شده در ژنوم حیوانات اهلی ما را قادر به مطالعه ساختار ژنومی آنها می کند. معمولا برای توالی یابی نشانگرهای ژنومی حیوانات اهلی از نمونه‌های جمع‌آوری شده از نقاط مختلف دنیا استفاده می شود. شناسایی نشانگرهای ژنومی اختصاصی حیوانات بومی هر منطقه جغرافیایی می‌تواند منجر به بهبود اطلاعات مربوط به ساختار ژنومی آن گونه شود. تا به حال، برای جمعیت گوسفندان بومی ایران نشانگرهای ژنومی اختصاصی شناسایی نشده‌است. هدف این پژوهش شناسایی واریانت‌های ژنتیکی موثر بر صفات مهم اقتصادی و فیزیولوژیکی گوسفندان اهلی و وحشی ایران و پیشنهاد آنها به عنوان نشانگر اختصاصی از طریق ردپای انتخاب بود.
مواد و روش: برای شناسایی واریانت‌های ژنتیکی نواحی تحت انتخاب گوسفندان اهلی و وحشی، ابتدا اطلاعات توالی یابی کل ژنوم 20 گوسفند اهلی (Ovis aries) و 14 گوسفند وحشی (Ovis orientalis) از پروژه Next Gene گرفته شدند. سپس واریانت‌های ژنتیکی کنترل کیفیت شده و واریانت‌های ژنتیکی نواحی تحت انتخاب با استفاده از روش‌های آماری iHS و XP-EHH شناسایی شدند. برای این واریانت‌ها واریانس ژنوتیپی برآورد شد. علاوه بر آن، واریانس ژنوتیپی نشانگرهای ژنومی شناخته شده در گوسفندان نژادهای مرینوس، سافوک، تکسل و افشاری جهت مقایسه با گوسفندان بومی ایران، نیز برآورد شدند. آستانه انتخاب واریانت‌های ژنومی برای ضرایب iHS و XP-EHH در گوسفندان اهلی کران 999/0 و در گوسفندان وحشی کران 999/0 و 001/0 در نظر گرفته‌شد. نهایتا از بین واریانت‌های شناسایی‌شده، آنهایی که واریانس ژنوتیپی بیشتر از 25/0 داشتند، به عنوان نشانگر اختصاصی این گونه‌ها پیشنهاد شدند.
یافته ها: در این پژوهش 170 واریانت ژنومی با ضرایب iHS و XP-EHH بالاتر از 83/3 و 44/3 در گوسفندان اهلی و 150 واریانت ژنومی با ضرایب iHS بالاتر از 05/3 و XP-EHH پایین تر از43/4- در گوسفندان وحشی شناسایی و انتخاب شدند. واریانس ژنوتیپی واریانت‌های ژنومی شناسایی شده، در دامنه 27/0 تا 50/0 بود. واریانس ژنوتیپی نشانگرهای ژنومی شناخته شده در نژادهای مرینوس، سافوک و تکسل و نژاد بومی افشاری به صورت میانگین در دامنه 02/0 تا 50/0 برآورد شدند. این مقایسه بیانگر تاثیر قابل‌توجه واریانت-های شناسایی شده در گوسفندان بومی ایران است. بسیاری از این واریانت‌ها در نواحی ژنتیکی مرتبط با صفات اقتصادی گوسفند نظیر صفات لاشه، شیر و پشم قرار داشتند. علاوه بر این، هستی شناسایی ژن‌های شناسایی شده مرتبط با واریانت‌های ژنومی پیشنهادی نشان داد، این واریانت‌ها در مجاورت نواحی ژنی مرتبط با فرآیندهای متابولیکی صفات تولیدی و تولیدمثلی هستند.
نتیجه‌گیری: مطالعه حاضر نشان داد که تعداد قابل توجهی نشانگر معنی‌دار مرتبط با صفات مهم اقتصادی و فیزیولوژیکی در گوسفندان اهلی و وحشی ایران وجود دارد که در آرایه‌های تجاری موجود در بازار در نظر گرفته نشده‌است. تشخیص نشانگرهای جدید می تواند به بهبود اطلاعات ما در خصوص ساختار ژنومی گوسفندان بومی ایران کمک کند. همچنین، این نتایج در کنار مطالعات مشابه می‌تواند به طور موثری در تولید آرایه‌های تجاری برای گوسفند ایرانی مورد استفاده قرار گیرد.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Identification of SNP markers related to important traits for Iranian native sheep using selection signature

نویسندگان [English]

  • Maryam Moghadam 1
  • Saeed Zerehdaran 2
  • Mohammad Hossein Banabazi 3
  • Ali Javadmanesh 4
1 Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad
2 Animal Science department, Faculty of Agriculture, Ferdowsi University of Mashhad
3 Researcher Sveriges lantbruksuniversitet (SLU) Swedish University of Agricultural Sciences
4 Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad
چکیده [English]

Background and objective
Identification of several genomic markers sequenced in farm animal enable us to study the structure of their genome. Samples from different parts of the world are usually used for sequencing genomic markers. Information on the sequence of specific markers of domestic animals of each geographical area will improve our knowledge about their genomic structure. The sequence of specific genome markers for Iranian native sheep were not yet identified. Present study aims to identify single-nucleotide polymorphism (SNPs) influencing important economic and physiological traits of Iranian domestic and wild sheep as candidate markers using selection signature.
Materials and methods
In order to identify significant genetic variants under selection in domestic and wild sheep, the whole genome sequence of 20 domestic (Ovis aries) and 14 wild sheep (Ovis orientalis) obtained from the Next Gene project was used. After doing quality control, variant under selection were detected using statistical methods consisting iHS and XP-EHH. Genetic variance for identified variants were estimated. The genetic variance of known variants in Merino, Suffolk, texel and Afshari were also estimated. The threshold for selecting variants based on iHS and XP-EHH methods were considerd to be 99.9% in domestic sheep and 99.9% and 0.001% in wild sheep, respectively. Finally, variants with genetic variances higher than 0.25, were identified and suggested as candidate markers.
Results
In present study, 170 genomic variants with iHS and XP-EHH values higher than 3.83 and 3.44 in domestic sheep and 150 genomic variants with iHS values higher than 3.05 and XP-EHH values lower than -4.43 in wild sheep were identified and suggested as candidate markers. Genetic variance of these variants were 0.27 to 0.50 and the genetic variance of known variants in Merino, Suffolk, Texel and Afshari were from 0.02 to 0.50. This comparison shows the importance of identified variants in Iranian domestic and wild sheep. Most of identified variants in domestic and wild sheep associated with economically important traits including carcass, milk and wool related traits. The ontology of genes related to identified variants showed that these variants are located near genes related to metabolic process of production and reproduction traits
Conclusion
Present results showed that there are many significant genetic variants associated with economic traits in domestic and wild Iranian sheep which are not included in the commercial sheep arrays available in the market. Identification of new SNPs related to economic traits in domestic and wild sheep may help to improve the studies related to genomic structure of Iranian sheep. These results together with similar studies could be efficiently used for producing SNP arrays designed for Iranian native sheep.

کلیدواژه‌ها [English]

  • Genome sequencing
  • Genomic marker
  • Selection signature
  • Sheep array
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