کاربرد مکان‌یابی ارتباطی و عدم تعادل پیوستگی در مطالعات ژنومی گیاهی با تاکید بر ژنوم غلات

نوع مقاله : مروری

نویسندگان

1 استاد گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران.

2 دانشجوی پسا دکتری، گروه به‌نژادی و بیوتکنولوژی گیاهی، دانشکده کشاورزی، دانشگاه تبریز، تبریز، ایران.

3 گروه کشاورزی و علوم محیطی، دانشگاه میلان، میلان، ایتالیا.

چکیده

آگاهی از تنوع ژنتیکی و درک صفات پیچیده ژنتیکی در گونه­های زراعی نقش مهمی در بهره­برداری از منابع ژنتیکی داشته و باعث سازگاری، توسعه و گسترش کشت ارقام زراعی به ویژه غلات در مناطق مختلف جغرافیایی می­گردد. در این راستا، شناسایی و استفاده از نشانگرهای آگاهی بخش مرتبط با صفات کمی جهت استفاده در برنامه­های به­نژادی و انتخاب به کمک نشانگر از اهمیت زیادی برخوردار می­باشد. یکی از کاربردهای اصلی نشانگرها تهیه نقشه‌های مولکولی ژنوم و آنالیز پیوستگی جمعیت‌های نقشه‌یابی است. در مطالعات پیوستگی و انتخاب ژنومی تعیین میزان و گستره عدم تعادل پیوستگی (LD) در تشخیص تعداد نشانگر مورد نیاز و اندازه نمونه، اهمیت به­سزایی دارد. علاوه بر این، گزینش به­منظور افزایش فراوانی موتاسیون­های جدیدی که فقط در برخی از زیر جمعیت­ها سودمند هستند، باعث باقی گذاشتن علائمی در سطح ژنوم می­شود. اغلب این مناطق با ژن­ها و QTLهای مرتبط با صفات مهم اقتصادی در ارتباط هستند. دسترسی به فناوری­های نسل جدید توالی­یابی، حجم بالای داده­های فنوتیپی و تنوع زیاد ابزارهای آماری موجب شده است که مطالعات مکان­یابی ارتباطی مبتنی بر عدم تعادل پیوستگی در گیاهان بتواند موفقیت­های فراوانی را در شناسایی مکان­های ژنی کنترل کننده صفات کمی به همراه داشته باشد. نقشه­یابی ارتباطی مبتنی بر عدم تعادل پیوستگی می­تواند وضوح نقشه ژنتیکی را با توجه به ارائه مخزن ژنی گسترده­تر و وقایع نوترکیبی افزایش دهد. برخلاف نقشه­یابی پیوستگی، روش مکان­یابی ارتباطی با بهره­گیری از تنوع موجود در جمعیت­های طبیعی و لحاظ کردن تمامی وقایعی که در طول تکامل افراد رخ داده است، ارتباط بین تنوع فنوتیپی و چند شکلی موجود در ژنوم را شناسایی می­کند و روشی امیدوار کننده برای غلبه بر محدودیت­های نقشه­یابی پیوستگی است. علی­رغم اینکه نقشه­یابی ارتباطی از توان آماری بالایی برخوردار است اما کاربرد این روش در جمعیت­های دارای ساختار، در گونه­های با میزان کم عدم تعادل پیوستگی و در صفاتی که توسط آلل­های نادر کنترل می­شود، بسیار پیچیده و گاهی ناممکن است. LD پایه و اساس نقشه­یابی در سطح ژنوم (GWAS) است، که تحت تاثیر عوامل متعددی از جمله رانش ژنتیکی، ساختار جمعیت و گزینش طبیعی است. از عوامل محدود کننده فوق، ساختار جمعیت به عنوان یکی از عوامل اصلی اعتبارسنجی نتایج GWAS شناخته می­شود. بنابراین آگاهی در مورد الگوی عدم تعادل پیوستگی به منظور مطالعات بیشتر GWAS و گزینش ژنومی اهمیت بسزایی دارد. معیار تعیین کننده موفقیت استفاده از مطالعات GWAS و گزینش ژنومی (GS) به مقدار LD بین نشانگرها و جایگاه­های ژنومی مسبب صفات کمی در طول کل ژنوم بستگی دارد. با توجه به اهمیت روش عدم تعادل پیوستگی در مطالعات نقشه­یابی صفات کمی، در این مقاله سعی شده است تا به عمده­ترین ابعاد عدم تعادل پیوستگی، نحوه کاربرد آن در جمعیت، محدودیت­های آن و استفاده از آن در به­نژادی گیاهی به ویژه غلات پرداخته شود. همچنین، در این مقاله برخی از اطلاعات مربوط به نرم­افزارهای آماری مورد استفاده در عدم تعادل پیوستگی ارایه می­شود و در نهایت چالش­ها و چشم­اندازهای استفاده از این رویکرد بحث خواهد شد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Application of association mapping and linkage disequilibrium in plant genomic studies with emphasis on cereal genome

نویسندگان [English]

  • Babak Abdollahi Mandolakani 1
  • Hossein Abbasi Holasou 2
  • Salar Shaaf 3
1 Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
2 Post-doctoral student, Department of Plant Breeding and Biotechnology, Faculty of Agricultural Sciences, Tabriz University, Tabriz, Iran.
3 Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy.
چکیده [English]

Knowledge of genetic diversity and understanding the genetic architecture of complex traits in crop species can play a key role in exploiting genetic diversity and lead to crop cultivation's adaptation, development and expansion in different geographical environments. In this regard, identifying and utilizing informative markers related to quantitative traits is a prerequisite for application in breeding programs and marker-assisted selection (MAS). One of the major uses of these markers is the construction of genome-wide molecular maps and genetic analysis. In genome-wide association study (GWAS) and genomic selection (GS), determining of extent and level of linkage disequilibrium (LD) is critical in sample size and marker density. Moreover, selection for increasing frequency in new mutations advantageous only in a subset of populations leaves some signatures in the genome. Locations of selection signatures are often correlated with genes and QTLs affecting economically important traits. Access to next-generation sequencing technologies, high phenotypic data and a variety of sophisticated statistical tools have enabled LD-based association mapping studies in plants to identify gene loci controlling quantitative traits successfully. Alternatively, the LD-based association mapping (AM) approach can enhance the genetic map resolution to a greater extent due to the representation of a more comprehensive gene pool and more recombination events in history. Association mapping has emerged as a tool to resolve complex trait variation down to the sequence level by exploiting evolutionary recombination events at the population level. Genetic diversity, LD extent in genome and intra-population relationship, determine quality of mapping, marker diversity, statistical methods and power of mapping. LD in population is the foundation of GWAS, whereas it is always affected by genetic drift, population stratification and natural selection. Of the above threats, population stratification is recognized as a major one to the validity of GWAS results. Therefore, knowledge concerning the pattern of LD is essential for performing GWAS and GS. As one of the most important measures in population genetics, LD is the basis of effective population size estimation, genomic selection, GWAS study and QTL mapping. Due to the importance of LD method in mapping studies of the quantitative traits, in this review, we will present LD, its application in population, current status, limitations, and its use in plant breeding, especially in cereals. Finally, this study provides some information about commonly used statistical software and packages in the calculation of LD, and the challenges and perspectives of this approach have been discussed in this study as well.

کلیدواژه‌ها [English]

  • Cereal
  • Mixed Linear Model
  • Population Structure
  • Marker-Trait Association
  • Association mapping

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