Estimation of Effective Population Size and Genomic Inbreeding Coefficients in Baluchi Sheep Using Genome-Wide Single Nucleotide Polymorphisms (SNPs)
محورهای موضوعی : Camel
م. پسندیده
1
(Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran)
م. قلی زاده
2
(Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran)
ق. رحیمی میانجی
3
(Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran)
کلید واژه: Baluchi sheep, effective population size, genome wide evaluation, inbreeding coeffi-cients,
چکیده مقاله :
The aim of this study was to estimate the effective population size (Ne) and genomic inbreeding coefficients in 96 Baluchi sheep genotyped using Illumina OvineSNP50 BeadChip. Using NEESTIMATOR software, the estimation of contemporary Ne based on heterozygote-excess and linkage disequilibrium (LD) methods was obtained 15 and 25, respectively. The historical Ne estimated with SNeP software showed a fast decreasing trend over the last 1000 generations. The Ne estimate for the previous 4 generations was ranged from 48 to 75. Three estimates of inbreeding coefficients including genomic relationship matrix (FGRM), excess of homozygosity (FHOM) and correlation between uniting gametes (FUNI) were calculated using GCTA software. The values of FGRM, FHOM and FUNI were calculated the same at -0.017. The average expected and observed heterozygosity using PLINK software were calculated as 0.374 and 0.383, respectively. Our results showed a considerable genetic variation in Baluchi sheep, however the low values of Ne emphasize that measures should be taken to avoid a further reduction in the effective population size. The results of this study provide guidance for future sheep breeding to increase the conservation activities of the native sheep breeds.
هدف از این مطالعه، بررسی اندازه مؤثر جمعیت و میزان همخونی ژنومی در 96 رأس گوسفند بلوچی با استفاده از اطلاعات نشانگرهای SNP موجود در سراسر ژنوم حاصل از تراشه متراکم است. با استفاده از نرم ­افزار NEESTIMATOR، اندازه مؤثر کنونی جمعیت براساس روش­ های هتروزیگوسیتی اضافی و LD به ترتیب 15 و 25 تخمین زده شدند. نتایج به دست آمده از اندازه مؤثر تاریخی جمعیت با استفاده از نرم­افزار SNeP، نشان دهنده یک روند کاهشی سریع در طول 1000 نسل گذشته بود. اندازه Ne در چهار نسل قبل در دامنه 75-48 رأس بود. ضریب همخونی با استفاده از سه روش ماتریس روابط خویشاوندی (FGRM)، میزان هموزیگوسیتی (FHOM)و همبستگیگامت­ها (FUNI)با استفاده از نرم­افزارGCTA محاسبه شدند. مقادیر FGRM، FHOM وFUNI به­طور مشابه برابر با 0.017- محاسبه شدند. میانگین هتروزیگوسیتی مورد انتظار و مشاهده شده با استفاده از نرم­افزارPLINK به ترتیب 0.374 و 0.383 برآورد شدند. نتایج این تحقیق نشان داد که تنوع ژنتیکی مناسبی در نژاد بلوچی وجود دارد اما مقادیر پایین Ne بیانگر اجرای اقدامات ویژه ­ای برای جلوگیری از کاهش شدیدتر اندازه مؤثر جمعیت در این نژاد است. بنابراین طراحی برنامه­ های مناسب برای حفاظت از حیوانات خالص این نژاد ضروری است.
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