مقایسه روش های مختلف لایه بندی جمعیتی گاوهای سرابی و نجدی با استفاده از نشانگرهای ژنتیکی متراکم

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشگاه زابل، دانشکده کشاورزی، زابل -ایران

2 استاد دانشکده کشاورزی دانشگاه زابل

3 گروه علوم دامی ، دانشکده کشاورزیف دانشگاه زابل، زابل، ایران

4 هیئت علمی گروه اصلاح دام دانشگاه تهران

چکیده

هدف: تاکنون از روش­های مختلفی برای بررسی ساختار جمعیتی با استفاده از نشانگرهای موجود درکل ژنوم (چند شکلی­های تک­نوکلئوتیدی (SNP)) استفاده شده است که هر کدام نقاط ضعف و قوتی دارند. در پژوهش حاضر از خوشه­بندی شبکه­ای بدون نظارت یا SPC که روشی مبتنی بر داده­کاوی است، برای بررسی ساختار جمعیت گاوهای سرابی و نجدی استفاده شد.
مواد و روش­ها: جمعیت مورد مطالعه 424 رأس گاو شامل 213 رأس گاو نجدی و 211 رأس گاو سرابی بود که باChip 40 K v 2 Illumina Bead برای نشانگرهای تک­نوکلئوتیدی تعیین توالی شدند. برای تجزیه ساختار جمعیت از بسته­ی نرم­افزاری (SPIN) SORTING POINTS INTO NEIGHBORHOOD  استفاده شد. بعد از ویرایش داده­ها، 27859 نشانگر اتوزومی تجزیه و تحلیل شدند.
نتایج: خوشه­بندی بر اساس شباهت­ها و تفاوت­های نوکلئوتیدها، منجر به طبقه­بندی دو جمعیت پایه و نه زیر جمعیت شد.
نتیجه­گیری: در مقایسه با سایر روش­های موجود برای لایه­بندی جمعیت، در حال حاضر روش SPIN با توجه به عدم نیاز به فرض­های پیشین، کارایی مناسبی جهت تجزیه و تحلیل ساختار جوامع دارد.

کلیدواژه‌ها


عنوان مقاله [English]

Comparison of the diffrent clustering methods for population structure of Sarabi and Nadjdi cows by using dense genetic markers

نویسندگان [English]

  • Ahad Khasali aghtaei 1
  • Mehdi Vafaye Valleh 2
  • Gholam Reza Dashab 3
  • Hossein Moradi Shahrbabak 4
1 Zabol university,Agri facualty,zabol, iran
2 Department of Animal Science, Faculty of Agriculture, University of Zabol, Zabol, Iran
3 Department of Animal Science.Faculty of Agriculture, University of Zabol,Zabol,Iran
4 Department of Animal Science Faculty of Agricultural Science and Engineering College of Agriculture and Natural Resources University of Tehran
چکیده [English]

Objective
So far, various methods have been used to investigate the structure of the population using the markers available in the whole genome (single-nucleotide polymorphism (SNP)), each of which has Weakness and strength. In the present study, an unsupervised network clustering (SPC), a data-mining method, was used to survey the population structure of the Sarabi and Najdi cows.
Materials and methods
The study population 424 cattle consisted of 213sarabi cattle and 211 Najdi cattle, sequenced with Illumina Bead Chip 40 K v 2 for single nucleotide markers. SORTING POINTS INTO NEIGHBORHOOD(SPIN) was used to analyze population structure. After editing data, 27859 autosomal markers were analyzed.
Results
Clustering results based on the similarities and differences between nucleotides led to the classification of two base populations and nine clusters.
Conclusions
Comparison the number of samples and other existing methods for population layering, the use of the SPIN method with high computational efficiency and the needn`t for prior assumptions makes it possible to analyze the structure of populations.
 
Citation: Khasaliaghtaei A, Vafaye Valleh M, Dashab GR, Moradi Shahrbabak H (2019) Comparison of the Different Clustering Methods for Population Structure of Sarabi and Nadjdi Cows by Using Dense Genetic Markers. Agricultural Biotechnology Journal 11 (1), 25-54. 
 
Agricultural Biotechnology Journal 11 (1), 25-54.
DOI: 10.22103/jab.2019.13193.1098
Received:  January 16, 2019; Accepted: April 28, 2019
© Faculty of Agriculture, Shahid Bahonar University of Kerman-Iranian Biotechnology Society

کلیدواژه‌ها [English]

  • Single-nucleotide polymorphism
  • Unsupervised network clustering
  • Data mining
  • Demographic structure
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