تخمین اندازه موثر جمعیت با استفاده از داده‌های تراشه‌های SNP-CHIP 70K در اسب نژاد کرد
محورهای موضوعی : فصلنامه زیست شناسی جانوریبهاره صفایی 1 , حسین مرادی شهربابک 2
1 - دانشکده کشاورزی و منابع طبیعی دانشگاه تهران- کرج
2 - گروه علوم دامی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران
کلید واژه: اندازه موثر جمعیت, عدم تعادل لینکاژی, پلی‌مورفیسم تک نوکلئوتیدی, اسب کرد,
چکیده مقاله :
سال‌هاست نژادهای بومی بسیار مورد توجه قرار دارند و تلاش‌های زیادی برای حفظ این نژادها انجام می‌شود. مطالعه و ارزیابی ساختار جمعیت و تنوع یکی از راه‌های حفاظت از ذخایر ژنتیکی است. با توجه به اهمیت حفظ نژادهای مختلف اسب ایرانی ما نیز در این مطالعه به بررسی اندازه موثر جمعیت در اسب نژاد کرد پرداختیم. یکی از پارامترهای مهم برای بررسی ساختار جمعیت اندازه موثر جمعیت است. بدین منظور، عدم تعادل لینکاژی را با استفاده از اطلاعات نشانگرهای تک‌نوکلئوتیدی حاصل از تراشه‌های متراکم 70k در اسب نژاد کرد تخمین زدیم. در ابتدا بروی 65157SNP اولیه مراحل کنترل کیفیت داده‌ها توسط نرم‌افزار Plink (mind> 0.05، geno>0.05، MAF<0.01، hwe< 10-6) انجام گرفت و بدنبال آن تعدادی از داده‌ها حذف شدند و در نهایت تعداد 56012 SNP کروموزم‌های اتوزوم برای ادامه آنالیزها باقی ماندند. LDبا استفادها از آماره r2 تخمین زده شد و از این اطلاعات برای تخمین اندازه موثر جمعیت استفاده شد. r2 در فاصله‌ی 0 تا 5/2 kb بیشترین مقدار را داشت که با افزایش فاصله بین نشانگرها کاهش نشان داد. متوسط r2 در تمام کروموزوم‌ها 046/0 تخمین زده شد و محدوده‌ی آن از 041/0 تا 052/0 در بین کروموزوم‌ها تخمین زده شد. همچنین اندازه موثر در 4463 نسل قبل 6674 تخمین زده شد که در نسل حاضر نیز به 26 رسید.
Native breeds of each region should be given particular consideration, and we should put excessive effort in preserving these breeds. Studying and evaluating the population structure and diversity is a technique to protect the genetic reserves of indigenous breeds. In this study, regarding the importance of preserving diverse breeds of Iranian horses, we investigated the effective population size of Kurdish horses. One of the significant variables for examining the population structure is the effective population size. For this purpose, we estimated linkage disequilibrium using Single Nucleotide Polymorphism information obtained from 70k SNPchips in Kurdish horses. At first, data quality control procedures were performed on the initial 65157 SNPs by Plink software (mind>0.05، geno>0.05، MAF<0.01، hwe<10-6), and then some data were removed posteriorly, and ultimately the number of 56012 SNPs on autosomal chromosomes were left for further analyses. linkage disequilibrium was calculated using the r2 statistic, and we employed this information to estimate the effective population size. r2 had the highest value in the distance from 0 to 2.5 kb, which decreased with increasing distance between markers. The average r2 was estimated at 0.046 in all chromosomes, and ranged from 0.041 to 0.052 among chromosomes. Likewise, the effective population size was predicted to be 6674 in 4463 previous generations, which reached 26 in the current generation.
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