شناسایی جایگاه‌های ژنومی مرتبط با چندقلوزایی تحت انتخاب بین نژادهای گوسفندان بومی ایران و گوسفند نژاد رومانوف با عملکرد تولیدمثلی بالا

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی، دانشگاه تهران، کرج. ایران

2 گروه علوم دامی دانشکده کشاورزی دانشگاه تهران. کرج. ایران

3 گروه علوم دامی، دانشکده کشاورزی ، دانشگاه تهران، کرج. ایران

4 گروه علوم دامی دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران.

چکیده

به منظور شناسایی ژن‌های مرتبط با عملکرد تولیدمثلی تحت انتخاب بین نژادهای گوسفندان بومی ایران  و نژاد رومانوف روسی از اطلاعات ژنومی 233 رأس گوسفند استفاده شد. داده‌های مربوط به گوسفندان نژاد رومانوف از پایگاه اطلاعاتی iSheep و اطلاعات ژنومی گوسفندان ایرانی از پایگاه اطلاعاتی به آدرس https://disk.yandex.ru/d/3N2wEv0-9_NL0w، تهیه شدند. کنترل کیفی و غربالگری داده‌ها، آنالیز شاخص تمایز ژنتیکی(FST)  و آنالیز مولفه‌های اصلی (PCA) جهت تعیین گروه‌های ژنتیکی با استفاده از نرم افزار PLINK1.9، صورت گرفت. متعاقب غربالگری نهایی صورت گرفته، اطلاعات ژنومی تعداد 488752 نشانگر SNP مشترک مربوط به کروموزوم‌های بدنی تعداد 79 رأس از نژاد رومانوف در مقابل تعداد 120 رأس مربوط به 9 نژاد از جمعیت‌های دامی ایرانی برای جستجوی نشانه‌های انتخاب، مورد استفاده قرار گرفت. از برآوردگر نااریب FST (θ) و آماره‌ی XPEHH جهت کاوش نشانه‌های انتخاب مورد استفاده قرار گرفتند. استخراج ژن‌های مرتبط با مناطق ژنومی تحت انتخاب توسط پایگاه اطلاعاتی آنلاین BIOMART با انطباق روی ژنوم گوسفند (Oar_v3.1)  انجام شد. تعداد 489 ژن مرتبط با مناطق ژنومی تحت انتخاب (معادل 1/0 درصد کل نشانگرهای مورد مطالعه) شناسایی شدند. بررسی مناطق ژنومی تحت انتخاب نشان داد، از میان 489 ژن شناسایی شده مرتبط با تفاوت‌های موجود بین دو گروه مورد مطالعه، تعداد 7 ژن درگیر در مسیرهای بیولوژیکی مرتبط با سنتز استروئید و استروئیدوژنز تخمدان بودند که به‌عنوان موارد تحت انتخاب مرتبط با صفت چندقلوزایی، شناسایی شدند. شناسایی این مسیرهای بیولوژیکی و تلفیق آن با سایر اطلاعات مرتبط با صفت چندقلوزایی می‌تواند در طراحی برنامه‌های اصلاح نژادی جهت بهبود عملکرد تولیدمثلی، موثر باشد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Identification of genomic regions related to litter size involving divergent selection in Iranian indigenous and high reproductive Romanov sheep breeds

نویسندگان [English]

  • parviz Azizi 1
  • Mohammad Moradi Shahrbabak 2
  • Hossein Moradi Shahrbabak 3
  • Mahdi Mokhber 4
1 Department of Animal Science, Faculty of Agriculture, Universityof Tehran, Karaj. Iran.
2 Department of Animal Science, Faculty of Agriculture, University of Tehran. Karaj. Iran
3 Department of Animal Science, Faculty of Agriculture, Universityof Tehran, Karaj. Iran.
4 Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia. Iran.
چکیده [English]

In order to identify genes related to reproductive performance under divergent selection in Iranian indigenous and high reproductive performance Romanov sheep breeds, the genomic data of 233 sheep were used. The genomeic data of Romanov sheep were obtained from the iSheep database and the genomic data of Iranian sheep was achieved from the database at https://disk.yandex.ru/d/3N2wEv0-9_NL0w. Data filtering and quality control, genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. Following the final filtering, the genomic information of 488,752 common SNPs from autosomal chromosomes of 79 Romanov heads compared to 120 heads of nine Iranian indigenous sheep breeds to screening signature of selection. The ubiased FST (θ) estimator and XPEHH statistic were used to explore the signs of selection. The genes related to selected genomic regions were extracted using the BIOMART online database corresponding to areas in the sheep genome assembly (Oar 3.1). A total of 489 genes associated with the selected genomic regions (consisting of 0.1% of the studied markers) were identified. Investigation of the genomic regions under selection showed that out of all the identified genes related to the difference between the two studied groups, 7 genes were involved in biological pathways related to steroid synthesis and ovarian steroidogenesis that may be associated with litter size. Identifying this pathway and other complementary studies about genes involved in reproduction could be effective in designing breeding programs to improve reproductive performance.

کلیدواژه‌ها [English]

  • Selective Sweep
  • Genomic array
  • Litter Size
  • Iranian native sheep
  • Romanov

Extended Abstract

Introduction

Around 12,000 BP, sheep (Ovis aries) were among the first animals domesticated by humans during the Neolithic Revolution. Iran has a good genetic diversity by having more than 30 breeds of sheep. Heep production plays a significant role in providing animal protein. These breeds are bred for meat and to a limited extent milk with thick wool, but are hardy and resilient in harsh environments. By development of molecular genetics, identification of selection signatures which reflects natural or artificial selection has become possible, and numerous methods have been developed in this regards. Using selection signature methods, we aimed to uncover adaptive selection signals, profile production types, and elucidate gene functions within selection patterns related to reproduction and litter size in sheep.

 

Materials and Methods

In order to identify genes related to reproductive performance with divergent selection between Iranian indigenous sheep breeds and high reproductive performance Romanov sheep breed, the genomic data of 233 sheep were used. The genomic data of Romanov sheep were obtained from the iSheep database and the genome of Iranian sheep was retrieved from the database at https://disk.yandex.ru/d/3N2wEv0-9_NL0w. Data filtering and quality control, genetic differentiation index analysis (FST) and principal component analysis (PCA) were performed to determine genetic groups using PLINK 1.9 software. . Following the final filtering, the genomic information of 488,752 common SNPs from autosomal chromosomes of 79 Romanov heads compared to 120 heads of nine Iranian indigenous sheep breeds to screening signature of selection. The unbiased FST (θ) estimator and XPEHH statistic were used to explore the signs of selection. The genes related to the selected genomic regions were extracted using the BIOMART online database corresponding to areas in the sheep genome assembly (Oar 3.1).

 

Results and discussion

A total of 489 genes associated with the selected genomic regions (consisting of 0.1% of studied markers) were identified. Investigation of the genomic regions under selection showed that out of all identified genes related to the difference between the two studied groups, 7 genes were involved in biological pathways related to steroid synthesis and ovarian steroidogenesis that may be associated with litter size.

 

Conclusion

 Identifying this pathway and other complementary studies about genes involved in reproduction could be effective in designing breeding programs to improve reproductive performance.

 

Author Contributions

Parviz Azizi: Investigation, Preparation, Writing original draft of the Manuscript,

Methodology Data curation, Software and Analysis.

Mohammad Moradi Shahrbabak: Conceptualization, Validation, Review and Editing the

manuscript, Project administration and Supervision.

Hossain Moradi Shahrbabak: Conceptualization, Validation, Review and Editing the

manuscript, Project administration and Supervision.

Mehdi Mokhber: Validation, Review and Editing the

Manuscript,

All authors contributed equally to the conceptualization of the article and writing of the

original and subsequent drafts.

 

Data Availability Statement

Data were obtained from iSheep data base

 

Acknowledgements

The authors would like to thank all participants of the present study.

 

Ethical considerations

The study was approved by the Ethics Committee of the University of Tehran (Ethical code:

IR.7108004/6/52). The authors avoided data fabrication, falsification, plagiarism, and

misconduct.

 

 

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علوم دامی ایران
دوره 56، شماره 1
فروردین 1404
صفحه 1-18

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  • تاریخ دریافت: 12 دی 1402
  • تاریخ بازنگری: 22 اردیبهشت 1403
  • تاریخ پذیرش: 22 اردیبهشت 1403

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