Research on Animal Production
پژوهشهاي توليدات دامي
Res Anim Prod
Agriculture
http://rap.sanru.ac.ir
1
admin
2251-8622
2676-461X
8
10.61186/rap
14
8888
13
fa
jalali
1402
7
1
gregorian
2023
10
1
14
3
online
1
fulltext
fa
شناسایی و طبقهبندی واریانتهای ژنومی گاومیشهای رودخانهای خوزستان با استفاده از فناوری توالییابی
Identification and Classification of Genome Variants of Khuzestan River Buffalos Using Sequencing Technology
ژنتیک و اصلاح نژاد دام
ژنتیک و اصلاح نژاد دام
پژوهشي
Research
<div style="text-align: justify;"><span style="font-family:IRANsharp;"><span style="line-height:2;"><span style="font-size:11pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA" style="font-size:10.0pt">چکیده<b> </b>مبسوط</span></b></span></span></span><br>
<span style="font-size:11pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA" style="font-size:10.0pt">مقدمه و هدف: </span></b><span lang="FA" style="font-size:10.0pt">توسعه سریع فناوریهای توالییابی کل ژنوم و ابزارهای بیوانفورماتیک، نقطه شروعی برای کشف تنوع ژنتیکی گستره در سطح کل ژنوم موجودات را فراهم میکند. گاومیش از جمله حیوانات اهلی مهم در سطح جهانی است که ارزش اقتصادی زیادی برای جوامع انسانی دارد که برای تولید محصولاتی مثل شیر، گوشت، چرم و نیز به</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">عنوان نیروی کار از آن</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">ها استفاده می</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">شود. گاومیش</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">های نژاد خوزستانی یکی از مهمترین نژاد گاومیش در ایران هستند که در غرب و جنوب</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">غربی ایران پراکنده شده</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">اند. بیشترین جمعیت این نژاد در استان خوزستان وجود دارد که با شرایط جغرافیایی این منطقه کاملاً سازگار شده</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">اند. در این مطالعه، شناسایی تنوع ژنتیکی در سطح کل ژنوم گاومیش</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">های نژاد خوزستانی با استفاده از تکنیک توالی</span><span dir="LTR" lang="FA" style="font-size:8.0pt">‎</span><span lang="FA" style="font-size:10.0pt">یابی انجام گرفت. </span></span></span></span><br>
<span style="font-size:11pt"><span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA" style="font-size:10.0pt"><span style="color:black">مواد و روش</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span></b><b><span lang="FA" style="font-size:10.0pt"><span style="color:black">ها</span></span></b><span lang="FA" style="font-size:10.0pt"><span style="color:black">: کنترل کیفیت خوانش</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">های توالی</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">یابی شده با استفاده از پارامترهای مرتبط با کیفیت به</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">وسیله</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">ی نرم</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">افزار </span></span><span dir="LTR" lang="EN-GB" style="font-size:8.0pt"><span style="color:black">FastQC (v0.12.1)</span></span> <span lang="FA" style="font-size:10.0pt"><span style="color:black">انجام شد. ارزیابی خوانش</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">های قطعات توالی</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">یابی نشان داد که همه</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">ی نمونه</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="FA" style="font-size:10.0pt"><span style="color:black">ها از کیفیت بالایی برخوردار بودند. </span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">برای هم ردیفی داده</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">ها با ژنوم مرجع از بسته نرم</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">افزاری </span></span><span dir="LTR" style="font-size:8.0pt"><span style="color:black"> BWA-MEM</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">استفاده شد. در ادامه واریانت</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">های</span></span> <span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">ژنومیک با</span></span> <span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">استفاده</span></span> <span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">از نرم</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">افزار </span></span><span dir="LTR" style="font-size:8.0pt"><span style="color:black">Freebay</span></span><span dir="LTR" lang="EN-GB" style="font-size:8.0pt"><span style="color:black">es</span></span> <span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">به</span></span><span dir="LTR" lang="FA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">دست</span></span> <span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">آمد</span></span><span dir="LTR" style="font-size:8.0pt"><span style="color:black">.</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black"> سپس، فیلتراسیون نهایی روی فایل واریانت</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">ها انجام گرفت. این فیلتراسیون به</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">منظور افزایش کیفیت آنالیز و حذف واریانت</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">های با کیفیت پایین انجام گرفت. </span></span></span></span></span><br>
<span style="direction: rtl;"><span style="unicode-bidi: embed;"><b style="font-size: 11pt;"><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">یافته</span></span><span dir="LTR" lang="AR-SA" style="font-size:8.0pt"><span style="color:black">‎</span></span></b><b style="font-size: 11pt;"><span lang="AR-SA" style="font-size:10.0pt"><span style="color:black">ها: </span></span></b><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">درصد</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">همردیفی</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">برای</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">همه</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">ی</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">نمونه</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">ها</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">بالاتر از 97/44 درصد و میزان</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">همپوشانی</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">در</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">نمونه</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">های</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">توالی</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">یابی</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">شده</span></span> <span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">بین 4/3x</span></span><span lang="FA" style=""><span style="color: black;"><span style="font-size: 10pt;"> تا 12/9x</span></span></span><span style="font-size: 11pt;"> </span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">بود که نشان دهنده</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">ی کیفیت مناسب خوانش</span></span><span dir="LTR" lang="AR-SA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="AR-SA" style="font-size: 10pt;"><span style="color:black">ها است. همچنین، در این مطالعه تعداد 76.676.529 میلیون واریانت شناسایی شده است که </span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">به</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">طور نسبتاً مساوی در بین کروموزوم</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">های گاومیش</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">های خوزستانی توزیع شده بودند. بیشترین و کمترین تعداد واریانت</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">ها به</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">ترتیب روی کروموزوم شماره 1 و 28 مشاهده شد. در این مطالعه، تعداد جهش</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">های جابه</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">جایی<sup> </sup>و معکوس شناسایی شده در سطح ژنوم به</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">ترتیب برابر با 298.193.017 و 135.694.466 و نسبت جهش</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">های جابه</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">جایی به معکوس به</span></span><span dir="LTR" lang="FA" style="font-size: 8pt;"><span style="color:black">‎</span></span><span lang="FA" style="font-size: 10pt;"><span style="color:black">میزان</span></span> <span lang="FA" style="font-size: 10pt;"><span style="color:black">2/1989 </span></span><span dir="LTR" style="font-size: 8pt;"><span style="color:black">(Ts/Tv)</span></span><span style="font-size: 10pt;"><span style="color:black"> برآورد شد. </span></span></span></span><br>
<b><span dir="RTL" lang="FA" style="font-size:10.0pt"><span style="color:black">نتیجهگیری: </span></span></b><span dir="RTL" lang="FA" style="font-size:10.0pt"><span style="color:black">وجود تنوع ژنتیکی در جمعیت گاومیشهای بومی ایران، پارامترهای باارزشی هستند که با مطالعه آنها میتوان پتانسیل ژنتیکی صفات اقتصادی در این جمعیتها را بهمنظور طراحی برنامههای مناسب اصلاح نژادی مورد ارزیابی قرار داد.</span></span></span></span></div>
<span style="font-size:11pt"><span style="text-justify:kashida"><span style="text-kashida:0%"><span style="line-height:80%"><span style="direction:rtl"><span style="unicode-bidi:embed"><span sans-serif="" style="font-family:Calibri,"><span lang="FA" style="font-size:10.0pt"><span style="line-height:80%"><span 2="" mitra="" style="font-family:"><span style="color:black"></span></span></span></span></span></span></span></span></span></span></span>
<div style="text-align: justify;"><span style="font-family:Times New Roman;"><span style="font-size:11pt"><span style="line-height:90%"><b><span style="font-size:10.0pt"><span style="line-height:90%">Extended Abstract</span></span></b></span></span><br>
<span style="font-size:11pt"><span style="line-height:90%"><b><span style="font-size:10.0pt"><span style="line-height:90%">Introduction and Objective: </span></span></b><span lang="EN-GB" style="font-size:10.0pt"><span style="line-height:90%">The rapid development of sequencing technologies and bioinformatic tools has made it possible to sequence the entire genome of many species, providing a starting point for exploring the genome-wide genetic diversity of organisms. The buffalo is one of the most important domesticated animals in the world and has great economic value for humans, being used for milk, meat, leather and most importantly as labor. Khuzestani buffalo are among the most important buffalo in Iran. These animals are scattered in western and southwestern Iran. The largest population of this breed is in the Khuzestan province and they are fully adapted to the geographical features of this region</span></span></span></span><br>
<span style="font-size:11pt"><span style="line-height:90%"><b><span style="font-size:10.0pt"><span style="line-height:90%">Material and Methods: </span></span></b><span lang="EN-GB" style="font-size:10.0pt"><span style="line-height:90%">In this study, whole genome sequencing of the Khuzestan buffalo was performed in paired-end format using Illumina technology. Quality control of the readings obtained met all quality parameters and processing of the readings showed that all samples were of high quality. The BWA-MEM software package was then used to match the data to the reference genome. Genome variants were obtained with the Freebayes software. The final filtering of the variant file then took place. This filtering serves to increase the quality of the analysis and to sort out inferior variants</span></span><span style="font-size:10.0pt"><span style="background:white"><span style="line-height:90%"><span style="color:#3b3b3b">.</span></span></span></span><span lang="EN-GB" style="font-size:10.0pt"><span style="line-height:90%"><span style="font-family:"Times New Roman",serif"></span></span></span></span></span><br>
<span style="font-size:11pt"><span style="line-height:90%"><b><span style="font-size:10.0pt"><span style="line-height:90%">Results: </span></span></b><span lang="EN-GB" style="font-size:10.0pt"><span style="line-height:90%">The alignment percentage for all samples was over 97.44% and also the coverage in the sequenced samples ranged from x 4.3 to x 9.12, indicating reasonable quality of the reads. Also, in this study we identified 76,676,529 million variants fairly evenly distributed on the chromosomes of the Khuzestan buffalo. The highest and the lowest number of variants were observed on chromosome 1 chromosome 28, repectively. In this study, the total number of translocation and inversion mutations in the genome level was 298,193,017 and 135,694,466, respectively. In addition, the ratio of transitions to transversion was estimated at 2.1989 (Ts/Tv).</span></span></span></span><br>
<span style="font-size:11pt"><span style="line-height:90%"><b><span style="font-size:10.0pt"><span style="line-height:90%">Conclusion:</span></span></b><span lang="EN-GB" style="font-size:10.0pt"><span style="line-height:90%"> The presence of genetic diversity in the native population of Iranian buffalos are valuable parameters that can be studied to evaluate the genetic potential of economic traits in these populations in order to design suitable breeding programs.</span></span></span></span></span></div>
توالییابی کل ژنوم, خوزستانی, گاومیش, واریانت
Buffalo, Khuzestan, Variant, Whole genome sequencing
98
104
http://rap.sanru.ac.ir/browse.php?a_code=A-10-1798-1&slc_lang=fa&sid=1
Seyed Milad
Hosseini
سید میلاد
حسینی
milad.hosseiny88@gmail.com
100319475328460021128
0009-0009-6997-7219
Yes
Agriculture and Natural Resources Campus, University of Tehran, Karaj, Iran
پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران
Hossein
Moradi Shahrbabak
حسین
مرادی شهربابک
hmoradis@ut.ac.ir
100319475328460021129
100319475328460021129
No
Animal Science Department, Agriculture and Natural Resources Campus, University of Tehran, Karaj, Iran
گروه علوم دامی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران
Mohammad
Moradi Shahrbabak
محمد
مرادی شهربابک
moradim@ut.ac.ir
100319475328460021130
100319475328460021130
No
Animal Science Department, Agriculture and Natural Resources Campus, University of Tehran, Karaj, Iran
گروه علوم دامی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران