تجزیه تنوع ژنتیکی و ساختار جمعیت ژنوتیپ‌های گندم دوروم(Triticum turgidum L.) با استفاده از نشانگرهای SilicoDArT تولید شده از DArTseq در سطح کل ژنوم

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری ژنتیک و به‌نژادی گیاهی، گروه زراعت و اصلاح نباتات، واحد سنندج، دانشگاه آزاد اسلامی، سنندج، ایران

2 گروه زراعت، اصلاح نباتات و بیوتکنولوژی، دانشکده کشاورزی و منابع طبیعی، واحد سنندج، دانشگاه آزاد اسلامی، سنندج، ایران.

3 گروه بیوتکنولوژی و به نژادی گیاهی، واحد کرمانشاه، دانشگاه آزاد اسلامی، کرمانشاه، ایران

4 گروه زراعت و اصلاح نباتات، دانشگاه آزاد اسلامی واحد سنندج، سنندج، ایران

5 عضو هیأت علمی مرکز تحقیقات کشاورزی دیم سرارود کرمانشاه

چکیده

هدف: گندم دوروم (Triticum turgidum L.) با متوسط تولید سالانه 40 میلیون تن، دهمین غله‌ی بسیار مهم و متداولی است که در سراسر جهان کشت می‌گردد. لذا هدف از این مطالعه تجزیه تنوع ژنتیکی و ساختار جمعیت ژنوتیپ‌‌های گندم دوروم برای آگاهی و استفاده از آن در مطالعات ژنومیک آینده با استفاده از نشانگرهای SilicoDArT تولید شده از DarTseq بود. مواد و روش‌ها: DNA مربوط به 94 ژنوتیپ گندم دوروم به روش CTAB از برگ‌های تازه استخراج شد. کیفیت و کمیت DNA استخراج شده با استفاده از دستگاه اسپکتروفتومتر اندازه گیری و غلظت DNA نمونه‌ها به میزان 50 نانوگرم در میکرولیتر تصحیح گردید. نمونه‌های DNA درDiversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) برای تجزیه ژنوتیپی DArTseq با استفاده از پلاتفرم تجزیه ژنوتیپی بوسیله تعیین توالی (GBS) پردازش شدند. تجزیه تنوع ژنتیکی و ساختار جمعیت بر روی 7882 نشانگر باقیمانده با استفاده از نرم افزارهایPower Markerv.3.25 ، DARwinver5.0، STRUCTURE 2.1.، GenAlex v. 6.41و Rv3.2.3 انجام گرفت. نتایج: مقدار محتوی اطلاعات چندشکلی (PIC) نشانگرهای SilicoDArT از 023/0 تا 499/0 با میانگین 38/0 متغیر بود. متوسط تکرارپذیری و میزان قرائت توالی‌ها در تمام گروه‌های لینکاژی به ترتیب بالای 98/0 و 92/0 بود. تعداد نشانگرهای SilicoDArT نقشه‌یابی شده از 300 نشانگر در گروه لینکاژی (Chr1A) تا 853 نشانگر در گروه لینکاژی (Chr7B) متفاوت بود. اندازه کروموزوم تحت پوشش نشانگرهایSilicoDArT از kbp1/829200 در گروه لینکاژی (Chr3B) تا kbp 79/589293 در گروه لینکاژی(Chr1A) متغیر بود. نتایج تجزیه کلاستر به روش اتصال- همسایگی (NJ)، ساختار جمعیت و تابع تشخیص مؤلفه‌های اصلی همخوانی بالایی با هم داشتند و بطور واضح ژنوتیپ‌های مورد بررسی را در چهار گروه مجزا قرار دادند. بیشترین میزان تنوع ژنتیکی مربوط به تنوع درون جمعیتی بود. نتیجه‌گیری: تعداد نسبتاَ بالای زیرجمعیت‌ها و وجود تنوع ژنتیکی بالا در میان و درون جمعیت‌ها از ویژگی‌های مجموعه ژنوتیپ‌های گندم دوروم مورد مطالعه در این تحقیق بود. لذا با توجه به اتلاف 84% تنوع ژنتیکی گندم دوروم طی فرآیندهای اولیه اهلی سازی، این جمعیت‌ها می‌توانند به عنوان یک منبع ارزشمند در تحقیقات بنیادی و کاربردی در پروژه‌های به‌نژادی مورد استفاده قرار گیرد.

کلیدواژه‌ها

عنوان مقاله [English]

Genetic diversity and population structure analysis of Durum wheat (Triticum turgidum L.) genotypes using whole genome DArTseq-generated SilicoDArT markers

نویسندگان [English]

  • Peyman Ebrahimi 1
  • Ezzat Karami 2
  • Alireza Etminan 3
  • Reza Talebi 4
  • Reza Mohammadi 5
1 PhD Student in Plant Genetics and Breeding, Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
2 Department of Agronomy, Plant Breeding and Biotechnology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.
3 Department of Plant breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
4 Department of Agronomy & Plant Breeding, College of AgricultureIslamic Azad University, Sanandaj BranchSanandajIran
5 Faculty member of Sararud Dryland Agricultural Research Center, Kermanshah
چکیده [English]

Objective Durum wheat (Triticum turgidum) with an average annual production of 40 million tons, is the tenth most important and common crop grown worldwide. The aim of this study was to analysis the genetic diversity and population structure of durum wheat genotypes for knowledge and apply in future genomic studies using SilicoDArT markers generated by DarTseq. Materials and Methods The DNA of 94 durum wheat genotypes were extracted by CTAB method from fresh leaves. The quality and quantity of extracted DNA were measured using spectrophotometer and adjusted to 50 ng / μl. The DNA samples were processed at Diversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) for DArTseq analyses using genotyping by sequencing Platform. Genetic diversity and population structure analysis were performed on the remaining 7882 markers using: Power Markerv.3.25, DARwinver 5.0, STRUCTURE2.1., GenAlexv. 6.41 and Rv3.2.3 software. Results The amount of polymorphic information content (PIC) of SilicoDArT markers ranged from 0.023 to 0.499 with an average of 0.38. The mean reproducibility and call rate of sequences in all linkage groups were above 0.98 and 0.92, respectively. The number of mapped SilicoDArT markers varied from 300 markers in the linkage group (Chr1A) to 853 markers in the linkage group (Chr7B). Chromosome size covered by SilicoDArT markers ranged from 829200 kbp in the linkage group (Chr3B) to 589293.786 kbp in the linkage group (Chr1A). The results of cluster analysis by Neighbor-Joining (NJ) method, population structure and discriminant analysis of principal components were highly consistent with each other and clearly divided the studied genotypes into four distinct groups. Genetic diversity among populations was primarily within the population (76.36 vs. 23.64%). Conclusions The relatively high number of subpopulations and the presence of high genetic diversity among and within populations were the characteristics of studied durum wheat genotypes in this study. Therefore, considering the loss of 84% genetic diversity of durum wheat during the early domestication processes, these populations can be used as a valuable resource in basic and applied research in breeding projects.

کلیدواژه‌ها [English]

  • Durum wheat
  • Linkage group
  • Marker
  • Polymorphism
  • Population

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مجله بیوتکنولوژی کشاورزی
دوره 13، شماره 3
مهر 1400
صفحه 43-68

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