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
1403
9
1
gregorian
2024
12
1
15
4
online
1
fulltext
fa
شناسایی نشانه های انتخاب مثبت مرتبط با صفات مهم اقتصادی در بزهای نژاد بیتال
Identification of Positive Selection Signatures Associated with Important Economic Traits in Beetal Goats
ژنتیک و اصلاح نژاد دام
ژنتیک و اصلاح نژاد دام
پژوهشي
Research
<div style="text-align: justify;"><span style="line-height:2;"><span style="font-size:12px;"><span style="font-family:IRANsharp;"><span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA">چکیده </span><span lang="AR-SA"><span style="color:black">مبسوط</span></span><span dir="LTR"><span style="font-family:"Times New Roman",serif"></span></span></b></span></span><br>
<span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA">مقدمه و هدف</span></b><span lang="FA">:</span> <span lang="FA">شناسایی مناطق ژنومی که هدف انتخاب بوده</span><span dir="LTR">‎‎</span><span lang="FA">اند، یکی از راهکارهای اصلی تحقیقات زیستی است. به</span><span dir="LTR">‎</span><span lang="FA">عبارت دیگر اهلی</span><span dir="LTR">‎</span><span lang="FA">سازی و انتخاب به</span><span dir="LTR">‎</span><span lang="FA">شدت در خصوصیات ظاهری و رفتاری حیوانات اهلی امروز تغییر ایجاد کرده است. در این مسیر انتخاب</span><span dir="LTR">‎</span><span lang="FA">های انجام شده توسط انسان نشانه</span><span dir="LTR">‎</span><span lang="FA">های قابل شناسایی را در ژنوم بزهای امروزی به</span><span dir="LTR">‎</span><span lang="FA">جا گذاشته است که شناسایی این نشانه</span><span dir="LTR">‎</span><span lang="FA">ها می</span><span dir="LTR">‎</span><span lang="FA">تواند به اصلاح و بهبود ژنتیکی صفات مهم اقتصادی در این حیوانات کمک کند. طی دهه</span><span dir="LTR">‎</span><span lang="FA">های اخیر تمایل به شناسایی مناطق ژنومی که حاوی ژن</span><span dir="LTR">‎</span><span lang="FA">های کاندیدایی که هدف انتخاب بوده</span><span dir="LTR">‎</span><span lang="FA">اند رو</span><span dir="LTR">‎</span><span lang="FA">به افزایش بوده است. شناسایی نشانه</span><span dir="LTR">‎</span><span lang="FA">های انتخاب می</span><span dir="LTR">‎</span><span lang="FA">تواند دیدگاه</span><span dir="LTR">‎</span><span lang="FA">های ارزشمندی در مورد ژن</span><span dir="LTR">‎</span><span lang="FA">ها و یا مناطق ژنومی که تحت انتخاب مثبت بوده و یا هستند فراهم کند که به</span><span dir="LTR">‎</span><span lang="FA">نوبه خود منجر به درک بهتر ارتباط ژنوتیپ با فنوتیپ می</span><span dir="LTR">‎</span><span lang="FA">شود.</span> <span lang="FA">هدف از این مطالعه، شناسایی ژنهای کاندیدا و مناطق ژنومی تحت انتخاب مثبت در بزهای نژاد بیتال از طریق روشهای شناسایی ردپای انتخاب و هستی</span><span dir="LTR">‎</span><span lang="FA">شناسی ژن می</span><span dir="LTR">‎</span><span lang="FA">باشد.</span><span dir="LTR"><span style="font-family:"Times New Roman",serif"></span></span></span></span><br>
<span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA">مواد و روش</span><span dir="LTR">‎</span></b><b><span lang="FA">ها</span></b><span lang="FA">:</span> <span lang="FA">در این پژوهش اطلاعات ژنوتیپی مربوط به 631 رأس بزهای نژاد بیتال تعیین ژنوتیپ شده توسط آرایه</span><span dir="LTR">‎</span><span lang="FA">های </span><span dir="LTR">Caprine 50K</span> <span dir="LTR">BeadChip</span> شرکت ایلومینا استفاده شد. ابتدا جهت اطمینان از کیفیت داده<span dir="LTR">‎</span><span lang="FA">های تعیین ژنوتیپ، مراحل مختلف کنترل کیفیت روی داده</span><span dir="LTR">‎</span><span lang="FA">های اولیه تعیین ژنوتیپ شده قبل از آنالیزهای ژنومی انجام شد. برای فیلتراسیون داده</span><span dir="LTR">‎</span><span lang="FA">های ژنوتیپ شده، ابتدا نمونه</span><span dir="LTR">‎</span><span lang="FA">هایی که فراوانی نرخ تعیین ژنوتیپ آنها کمتر از</span> <span lang="FA">90% بود، شناسایی و حذف شد. در مرحله بعد نشانگرهایی که حداقل فراونی آللی در آنها کمتر از 5% بود حذف شدند. سپس نشانگرهایی که نرخ تعیین ژنوتیپ آنها در نمونه</span><span dir="LTR">‎</span><span lang="FA">ها کمتر از 95% بود شناسایی و حذف شدند. در نهایت برای </span><span dir="LTR">SNP</span><span lang="FA">های باقیمانده آنهایی که بر روی کروموزوم جنسی بودند و یا در تعادل هاردی-واینبرگ قرار نداشتند کنار گذاشته شدند.</span> <span lang="FA">پس از کنترل کیفیت داده</span><span dir="LTR">‎</span><span lang="FA">های اولیه تعیین ژنوتیپ شده با استفاده از نرم</span><span dir="LTR">‎</span><span lang="FA">افزار </span><span dir="LTR">PLINK</span><span lang="FA"> (</span><span dir="LTR">v1.90; http://pngu.mgh.harvard.edu/purcell/plink</span><span lang="FA">) نهایتاً 36861 نشانگر </span><span dir="LTR">SNP</span><span lang="FA"> و 594 رأس دام وارد آنالیزهای بعدی شدند. برای شناسایی نشانه</span><span dir="LTR">‎</span><span lang="FA">های انتخاب از روش مبتنی بر عدم تعادل پیوستگی ژنی و آزمون نمره هاپلوتیپ تمایز یافته (</span><span dir="LTR">iHS</span><span lang="FA">) با استفاده از بسته نرم</span><span dir="LTR">‎</span><span lang="FA">افزاری </span><span dir="LTR">REHH</span> در نرم<span dir="LTR">‎</span><span lang="FA">افزار </span><span dir="LTR">R</span><span lang="FA"> انجام شد. ژنهای کاندید با استفاده از </span><span dir="LTR">SNP</span><span lang="FA">هایی که در بازهی 1% بالای </span><span dir="LTR">iHS</span> واقع <span lang="FA">شده بودند، با استفاده از نرمافزار</span><span dir="LTR">PLINK </span><span lang="FA"> و توسط لیست ژنی شرکت ایلومینا در محیط </span><span dir="LTR">R</span> شناسایی شدند. همچنین، برای بررسی وجود <span dir="LTR">QTL‎</span><span lang="FA">های مرتبط با صفات مربوط به صفات مهم اقتصادی در مناطق شناسایی شده معنیدار، از آخرین نسخهی منتشر شده پایگاه </span><span dir="LTR">genome </span> <span dir="LTR">Animal</span><span lang="FA"> استفاده شد. به</span><span dir="LTR">‎</span><span lang="FA">منظور شناسایی مراحل بیولوژی ژن</span><span dir="LTR">‎</span><span lang="FA">های شناسایی شده از آنالیز هستی</span><span dir="LTR">‎</span><span lang="FA">شناسی استفاده شد. برای تجزیه و تحلیل هستی</span><span dir="LTR">‎</span><span lang="FA">شناسی ژن</span><span dir="LTR">‎</span><span lang="FA">های شناسایی شده از پایگاه برخط </span><span dir="LTR">DAVID</span><span lang="FA"> (</span><span dir="LTR">http://david.abcc.ncifcrf.gov</span><span lang="FA">) استفاده گردید.</span> <span lang="AR-SA">همچنین </span><span lang="FA">برای تفسیر بهتر عملکرد ژن</span><span dir="LTR">‎</span><span lang="FA">های به</span><span dir="LTR">‎</span><span lang="FA">دست آمده از پایگاه</span><span dir="LTR">‎</span><span lang="FA">های اطلاعاتی آنلاین</span><span dir="LTR">GeneCards </span> <span dir="LTR">http://www.genecards.org)</span><span lang="FA">) و </span><span dir="LTR">(http://www.uniprot.org) UniProtKB</span><span lang="FA"> استفاده شد.</span></span></span><br>
<span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA">یافته</span><span dir="LTR">‎</span></b><b><span lang="FA">ها</span></b><span lang="FA">: از مجموع 53347 نشانگر </span><span dir="LTR">SNP</span><span lang="FA"> به</span><span dir="LTR">‎</span><span lang="FA">کار رفته در این تحقیق، 36861 نشانگر توانستند مراحل مختلف کنترل کیفیت را بگذرانند. به</span><span dir="LTR">‎</span><span lang="FA">طور کلی 3963 نشانگر به</span><span dir="LTR">‎</span><span lang="FA">دلیل حداقل فراوانی آللی کمتر از 05/0، 1342 نشانگر به</span><span dir="LTR">‎</span><span lang="FA">دلیل نرخ تعیین ژنوتیپ کمتر از 95% در هر نمونه، 9761 نشانگر به</span><span dir="LTR">‎</span><span lang="FA">دلیل عدم تعادل هاردی واینبرگ و 1420 نشانگر با موقعیت ناشناخته و همچنین 37 نمونه به</span><span dir="LTR">‎</span><span lang="FA">دلیل فراوانی تعیین ژنوتیپ کمتر از 90% حذف شدند.</span> <span lang="FA">نتایج این پژوهش منجر به شناسایی ده منطقه ژنومی روی کروموزوم</span><span dir="LTR">‎</span><span lang="FA">های 4، 6، 7، 11 (دو منطقه)، 13، 14، 15، 17 و 18 با بالاترین ارزش آزمون آماره </span><span dir="LTR">iHS</span><span lang="FA"> شد. ژن</span><span dir="LTR">‎</span><span lang="FA">های شناسایی شده در مناطق مورد انتخاب با اندازه بدن (</span><i><span dir="LTR">SPP1, TNPO2</span></i><span lang="FA">)، متابولیسم چربی (</span><i><span dir="LTR">SDCBP</span></i><span lang="FA">)، رشد و توسعه استخوان (</span><i><span dir="LTR">IBSP, MEPE</span></i><span lang="FA">) و متابولیسم انرژی<br>
(</span><i><span dir="LTR">TRPC3, UCP2, FBP1</span></i><span lang="FA">) مرتبط بودند. برخی از این ژن</span><span dir="LTR">‎</span><span lang="FA">ها در مناطق تحت انتخاب با مطالعات قبلی هم</span><span dir="LTR">‎</span><span lang="FA">خوانی داشتند. بررسی </span><span dir="LTR">QTL</span><span lang="FA">های گزارش شده در مناطق انتخابی و اورتولوگوس گاوی در مناطق شناسایی شده، </span><span dir="LTR">QTL</span><span lang="FA">های مرتبط با میانگین خوراک مصرفی، وزن لاشه و اندازه بدن قرار داشتند. از بین مسیرهای زیستی شناسایی شده، مسیرهای </span><span dir="LTR">skeletal system development</span><span lang="FA"> و </span><span dir="LTR">calcium channel complex</span><span lang="FA"> و مسیرهای </span><span dir="LTR">KEGG</span><span lang="FA"> شامل </span><span dir="LTR">Glucagon signaling pathway</span><span lang="FA"> و </span><span dir="LTR">AMPK signaling pathway</span><span lang="FA"> نقش مهمی در تنظیم یون کلسیم، متابولیسم مواد غذایی، هموستازی گلوکز و رشد و توسعه عضلات اسکلتی داشتند.</span> <span lang="FA"><span style="font-family:"2 Mitra""></span></span></span></span><br>
<span style="direction:rtl"><span style="unicode-bidi:embed"><b><span lang="FA">نتیجه</span><span dir="LTR">‎</span></b><b><span lang="FA">گیری</span></b><span lang="FA">: در هر صورت، ژن</span><span dir="LTR">‎</span><span lang="FA">های متعددی که در نواحی شناسایی شده بر اساس عملکرد می</span><span dir="LTR">‎</span><span lang="FA">توانند به</span><span dir="LTR">‎</span><span lang="FA">عنوان کاندیداهای تحت انتخاب مطرح باشند. برخی از این ژن</span><span dir="LTR">‎</span><span lang="FA">ها در مناطق تحت انتخاب با مطالعات قبلی هم</span><span dir="LTR">‎</span><span lang="FA">خوانی داشتند و بیشتر در مسیرهای بیولوژیکی مرتبط با رشد، وزن بدن، فرآیندهای متابولیکی،</span> <span lang="FA">صفات تیپ نقش دارند. همچنین، بررسی </span><span dir="LTR">QTL‎</span><span lang="FA">های موجود در مناطق تحت انتخاب نشان داد که این </span><span dir="LTR">QTL‎</span><span lang="FA">ها با بعضی صفات اقتصادی مهم از قبیل وزن بدن، عمق بدن، وزن و ترکیبات لاشه ارتباط دارند. در هر حال نیاز به بررسی</span><span dir="LTR">‎</span><span lang="FA">های پیوستگی و عملکردی بیشتری جهت شناسایی عملکرد ژن</span><span dir="LTR">‎</span><span lang="FA">ها می</span><span dir="LTR">‎</span><span lang="FA">باشد. همچنین بررسی بیشتر </span><span dir="LTR">QTL‎</span><span lang="FA">های مرتبط با مناطق ژنومی انتخاب شده از مطالعات جستجوی نشانه</span><span dir="LTR">‎</span><span lang="FA">های انتخاب و مطالعات پیوستگی ضروری است.</span> <span lang="FA">نتایج این تحقیق می</span><span dir="LTR">‎</span><span lang="FA">تواند در درک ساز و کار ژنتیکی کنترل کننده صفات رشد مورد استفاده قرار گیرد و با توجه به تأیید مناطق قبلی پویش ژنومی و شناسایی مناطق ژنومی جدید، استفاده از یافته</span><span dir="LTR">‎</span><span lang="FA">های این پژوهش می</span><span dir="LTR">‎</span><span lang="FA">تواند در انتخاب ژنتیکی بز از طریق افزایش وزن بدن مفید واقع شود.</span></span></span></span></span><br>
</span></div>
<div style="text-align: justify;"><span style="font-size:14px;"><span style="font-family:Times New Roman;"><span style="line-height:2;"><b><span style="color:black">Extended Abstract</span></b><br>
<b><span style="color:black">Background:</span></b> The identification of selection targeted genomic regions is one of the main aims of biological research. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic animals. The selection of animals by humans has left detectable signatures on the genome of modern cattle. The identification of these signals can help us to improve the genetic characteristics of economically important traits in cattle. The interest in the detection of genes or genomic regions that are targeted by selection has been growing over the last decade. Identifying the signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. This study aimed to identify effective genes and genomic regions on positive signatures of selection in Beetal goats using selection signature and gene ontology methods.<br>
<b><span style="color:black">Methods:</span></b> <span style="color:black">In this study, data from 631 Beetal goats genotyped using the Caprine 50 K Bead Chip were used to identify genomic regions under selection associated with important traits in Beetal goats. Quality control measures were performed in Plink by setting an animal call rate of 0.90, SNP call rate of 0.95, and SNPs with minor allele frequencies (MAF) lower than 0.05 or that do not conform to the Hardy–Weinberg expectation (p-value ≤ 0.000001) and unknown positions. After quality control of the initial data using Plink software (v1.90; http://pngu.mgh.harvard.edu/purcell/plink), 36,861 SNP markers in 594 animals of cattle were finally entered for further analysis.</span> <span style="color:black">To identify the signatures of selection, the statistical method iHS was used under REHH software packages. Candidate genes were identified by SNPs located at 1% upper the range of iHS using Plink v1.9 software and the gene list of Illumina in R. Additionally, the latest published version of Animal Genome Database was used for defining QTLs associated with economically important traits in identified locations.</span> <span style="color:black">In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes belonging to a functional class can be considered a group of genes that have some specific and common characteristics.</span> <span style="color:black">GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.</span> <span style="color:black">Moreover, gene ontology analysis for identified genes was performed using the DAVID online database.</span></span></span></span><br>
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<span style="line-height:2;"> </span></v:textbox><span style="line-height:2;"> </span><w:wrap anchorx="margin"><span style="line-height:2;"> </span></w:wrap></v:shape><v:shape href="https://creativecommons.org/licenses/by-nc/2.0/" id="Picture_x0020_17" o:button="t" style="position:absolute; left:0; text-align:left; margin-top:230px; width:63.85pt; height:23.6pt; z-index:251663360" type="#_x0000_t75"><span style="line-height:2;"> </span><v:fill o:detectmouseclick="t"><span style="line-height:2;"> </span></v:fill></v:shape></span><span style="line-height:2;"><b><span style="color:black">Results: </span></b><span style="color:black">After quality control filters, 36,861 SNPs were left while 9761 SNPs were removed due to Hardy-Weinberg Equilibrium, 1342 SNPs were removed due to unknown positions, 3963 were removed due to a minor allele threshold, and 1342 were removed due to missing genotypes. Besides 37 individuals were removed after quality control measures. Using the iHS approach, 10 genomic regions were identified on chromosomes 4, 6, 7, 11 (two regions per chromosome), 13, 14, 15, 17, and 18. Some of the genes located in identified regions under selection were associated with body size (SPP1, SCN9A, and TNPO2), fat metabolism (SDCBP), skeletal development (IBSP and MEPE), and energy metabolism (UCP2, TRPC3, and FBP1). Some of the genes under selection were found to be consistent with some previous studies.</span> <span style="color:black">Results of the gene ontology analysis identified two biological pathways, namely skeletal system development and a calcium channel complex, with two important KEGG pathways, including the glucagon signaling pathway and the AMPK signaling pathway, which play an important role in glucose metabolism, homeostasis, and skeletal system development. </span><br>
<b><span style="color:black">Conclusion:</span></b> <span style="color:black">Overall, various genes found within these regions can be considered the candidates under selection based on function. Most of the genes under selection were found to be consistent </span></span><span style="line-height:90%"><v:shape filled="f" id="Text_x0020_Box_x0020_12" o:gfxdata="UEsDBBQABgAIAAAAIQC75UiUBQEAAB4CAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbKSRvU7DMBSF
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" stroked="f" style="position:absolute; left:0; text-align:left; margin-top:-39px; width:446.4pt; height:20.7pt; z-index:251677696; v-text-anchor:top" type="#_x0000_t202"><span style="line-height:2;"> </span><v:textbox><span style="line-height:2;"> </span></v:textbox><span style="line-height:2;"> </span><w:wrap anchorx="margin"><span style="line-height:2;"> </span></w:wrap></v:shape></span><span style="line-height:2;"><span style="color:black">with some previous studies and to be involved in several processes, such as growth, body weight, metabolic pathways, and domestication-related changes, including system development and immune systems. Furthermore, a survey on extracted QTLs showed that these QTLs were involved in some important economic traits in goats, such as feed conversion ratio, subcutaneous fat, Marbling score, meat tenderness, body weight, average daily gain, conformation traits, the length of productive life, carcass traits, and composition carcass traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes and surveys on QTLs related to selected regions. However, will be necessary to carry out more association and functional</span> <span style="color:black">studies to demonstrate the implication of genes obtained from association analyses. Using these findings can accelerate genetic progress in breeding programs and can be used to understand the genetic mechanism controlling this trait.</span> <span style="color:black">The results of our research can be used to understand the genetic mechanism controlling growth traits. Since this study supported previous results from the genome scan of production traits and revealed additional regions, using these findings could potentially be useful for genetic selection in goats for a better body weight.</span></span></span></span><br>
</div>
آماره iHS, بز, پویش ژنومی, رد پای انتخاب, وزن بدن
Body weight, iHS statistics, Genomic scan, Goat, selective sweeps
83
92
http://rap.sanru.ac.ir/browse.php?a_code=A-10-928-6&slc_lang=fa&sid=1
Hossein
Mohammadi
حسین
محمدی
h-mohammadi64@araku.ac.ir
100319475328460023874
100319475328460023874
Yes
Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک، اراک، ایران
Abouzar
Najafi
ابوذر
نجفی
abozar.najafi@ut.ac.ir
100319475328460023875
100319475328460023875
No
Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, Iran
گروه علوم دام و طیور، پردیس ابوریحان، دانشگاه تهران، پاکدشت، ایران