مقایسه ژنومی زنبورهای عسل نژاد ایتالیایی (Apis Mellifera Ligustica) و قفقازی (Apis Mellifera Caucasica) برای شناسایی نشانه‌های انتخاب

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه محقق اردبیلی، اردبیل، ایران.

2 گروه تحقیقات علوم دامی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان اردبیل، اردبیل، ایران.

3 گروه بیولوژی مولکولی، دانشگاه مجازی پاکستان، لاهور.

چکیده

هدف: زنبور عسل (Apis mellifera) یکی از مهمترین گونه‌های حشره از نظر اکولوژیکی و اقتصادی به شمار می‌رود. زنبور عسل یک الگوی ایده‌آل برای به کارگیری ژنومیک جمعیت برای درک نیروهای تکاملی شکل‌دهنده ژنوم حشرات اجتماعی ارائه ‌می‌دهد. مطالعه حاضر با هدف بررسی و شناسایی نشانه‌های انتخاب در سطح کل ژنوم، بین دو نژاد زنبور عسل ایتالیایی و قفقازی با توجه به اهمیت دو نژاد در زمینه تولیدات مرتبط با زنبور عسل در ایران و جهان انجام شد.
مواد و روش‌ها: به منظور انجام مطالعه کنونی، از داده‌های توالی‌یابی شده‌ کل ژنوم دو زیر گونه زنبور اروپایی موجود در پایگاه داده‌ای NCBI استفاده شد. پس از اعمال کنترل و پالایش کیفی توالی‌های دانلود شده، خوانش‌های با کیفیت بالا، توسط نرم‌افزار BWA به ژنوم مرجع زنبور عسل هم‌ردیف شدند. متعاقبا، پس از اعمال فیلترهای مختلف، SNPهای باکیفیت بالا توسط نرم‌افزار GATK استخراج شدند. در گام بعدی، با استفاده از روش‌های XP-EHH و Fst نسبت به شناسایی نشانه‌های انتخاب در زنبورهای عسل ایتالیایی نسبت به زنبورهای قفقازی اقدام گردید. همچنین به منظور بررسی ساختار ژنتیکی دو نژاد مورد مطالعه و بررسی اجمالی میزان آمیختگی و خلوص آنها، از برنامه ADMIXTURE استفاده شد.
نتایج: آنالیزهای صورت گرفته منجر به شناسایی 847 پنجره ژنومی (حاوی 244 ژن کد کننده پروتئین) توسط روش XP-EHH و 815 پنجره ژنومی (حاوی 439 ژن کد کننده پروتئین) توسط روش Fst شد. نتایج نشان دادند که تعداد 19 ژن توسط هر دو روش شناسایی شده‌اند که این ژن‌ها به عنوان نشانه‌های انتخاب نهایی مورد بررسی‌های بیشتری قرار گرفتند. از بین ژن‌های مذکور، LOC72499، LOC551114 و LOC411919 در ایمنی، LOC41390 در رفتارهای جستجوگری کارگران، LOC413200 در رشد و توسعه سلولی، LOC725885 در تمایز سلولی، رفتارهای پرستاری و جستجوگری زنبورها و رشد بال، LOC550886 در رفتارهای نظافتی، LOC410393 در سلامت روده‌ها و سم‌زدایی و LOC408718 نیز در رشد سلول‌های عصبی و تبدیل لارو به کارگر یا ملکه دخیل بودند. شناسایی نشانه‌های انتخاب می‌تواند به استراتژی‌های آمیخته‌گری، کنترل بیماری و مدیریت کلونی کمک ‌کند. علاوه بر این، اطلاعات ژنومی نژادها امکان پیش‌بینی رفتار آنها در برابر چالش‌های محیطی از جمله تغییرات اقلیمی را فراهم می‌آورد.
نتیجه‌گیری: از آنجایی که صفاتی مانند رفتار، جستجوگری غذا (شهد و گرده)، نظافت، دفاع از کلنی و ایمنی در زنبورهای عسل جزء مهمترین و اقتصادی‌ترین صفات به شمار می‌روند؛ لذا شناسایی ژنهایی مرتبط با این ویژگی‌ها در مطالعه کنونی، نشان از ظرفیت بالای داده‌های ژنومی برای شناخت هر چه بیشتر نژادهای مختلف زنبور عسل دارد.

کلیدواژه‌ها

عنوان مقاله [English]

Genomic comparison of Italian honeybees (Apis Mellifera Ligustica) and Caucasian honeybees (Apis Mellifera Caucasica) for identifying signatures of selection

نویسندگان [English]

  • Nemat Hedayat-Evrigh 1
  • Hadi Tavakoli 1
  • Reza Khalkhali-Evrigh 2
  • Reza Seyed Sharifi 1
  • Mirdarioush Shakoury 1
  • Kobra Pourasad 1
  • Tanveer Hussein 3
1 Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.
2 Animal Science Research Department, Ardabil Agricultural and Natural Resources Research and Education Center, AREEO, Ardabil, Iran.
3 Department of Molecular Biology, Virtual University of Pakistan, Lahore, Punjab, Pakistan.
چکیده [English]

The honeybee (Apis mellifera) is considered one of the most important insect species from an ecological and economic perspective. The honeybee provides an ideal model for utilizing population genomics to understand the evolutionary forces shaping the genomes of social insects. This study aimed to investigate and identify signatures of selection at the whole-genome level between the Italian and Caucasian honeybee breeds, considering the significance of these two breeds in honeybee-related production in Iran and globally.
Materials and Methods
The current study used whole-genome sequencing data of two subspecies of European honeybees available in the NCBI database. After applying quality control and filtration to the downloaded sequences, high-quality reads were aligned to the honeybee reference genome using BWA software. Subsequently, after applying various filters, high-quality SNPs were extracted using GATK software. In the next step, XP-EHH and Fst methods were employed to identify signatures of selection in the Italian honeybees compared to Caucasian bees. Additionally, to examine the genetic structure of the two studied breeds and to give a brief overview of their admixture and purity, the ADMIXTURE program was used.
Results
The analyses led to the identification of 847 genomic windows (containing 244 protein-coding genes) by the XP-EHH method, and 815 genomic windows (containing 439 protein-coding genes) by the Fst method. The results indicated that 19 genes were identified by both methods, and these genes were further investigated as final selection signatures. Among these genes, LOC72499, LOC551114, and LOC411919 were involved in immunity; LOC41390 in the foraging behaviors of workers; LOC413200 in cellular growth and development; LOC725885 in cellular differentiation, nursing, and foraging behaviors of bees as well as wing growth; LOC550886 in hygienic behaviors; LOC410393 in gut health and detoxification; and LOC408718 in growth of neural cells and the transformation of larvae into workers or queens. Identifying selection signatures can facilitate breeding strategies, disease management, and colony management. Furthermore, genomic information pertaining to various breeds enables the prediction of their behaviors in response to environmental challenges including climate changes.
Conclusion
Since traits such as behavior, foraging for food (nectar and pollen), cleanliness, colony defense, and immunity are among the most important and economically significant characteristics in honey bees, identifying the genes associated with these traits in the current study highlights the high potential of genomic data for better understanding the different breeds of honeybees.

کلیدواژه‌ها [English]

  • Whole-genome sequencing
  • Italian honeybee
  • Caucasian honeybee
  • Signature of selection

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مجله بیوتکنولوژی کشاورزی
دوره 17، شماره 3
شهریور 1404
صفحه 27-48

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