فراتحلیل QTLهای مرتبط با فتوسنتز، شناسایی ژن‌های کاندیدا و مسیرهای عملکردی در برنج

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه زراعت و اصلاح نباتات، دانشکده علوم کشاورزی دانشگاه گیلان. رشت، ایران.

2 پژوهشکده آبزی پروری آب‌های داخلی، موسسه تحقیقات علوم شیلاتی کشور، سازمان تحقیقات، آموزش و ترویج کشاورزی، بندرانزلی، ایران.

3 گروه بیوتکنولوژی کشاورزی، دانشکده علوم کشاورزی دانشگاه گیلان. رشت، ایران.

10.22126/cbb.2026.13994.1148

چکیده

مقدمه: توسعه‌ی راهکارهای بهبود صفات عملکردی در محصولات استراتژیک مانند برنج، نیازمند شناسایی دقیق جایگاه‌های ژنتیکی مرتبط است. اگرچه پژوهش‌های متعددی در زمینه  QTLهای فتوسنتزی برنج انجام شده، اما به دلیل تفاوت در شرایط آزمایشگاهی و والدین، یکپارچه‌سازی نتایج جهت بهره‌برداری کاربردی همچنان یک چالش است. فراتحلیل داده‌های موجود و دستیابی به جایگاه‌های مشترک روی ژنوم یا متاQTL (Meta-QTL: MQTL)، راهکاری کارآمد برای عبور از محدودیت‌های مطالعات انفرادی و شناسایی نواحی ژنتیکی با ثبات بالا محسوب می‌شود.
مواد و روش‌ها: در این تحقیق، ابتدا مطالعات مربوط به QTLهای مرتبط با صفات فتوسنتزی در برنج گردآوری و بررسی شدند. از میان ۲۷ مطالعه شناسایی‌شده، در نهایت ۱۷ مطالعه شامل ۱۲۹ QTL واجد شرایط برای انجام فراتحلیل انتخاب شد. سپس نقشه توافقی تهیه و بر اساس دستورالعمل نرم‌افزار BioMercator، نواحی MQTL بر حسب سانتی‌مورگان تعیین شدند. در ادامه، ژن‌ها و نشانگرهای مجاور نواحی متاQTL شناسایی شدند و در نهایت، مسیرهای عملکردی ژن‌های کاندید با استفاده از پایگاه‌های داده و ابزارهای بیوانفورماتیکی مرتبط مورد بررسی قرار گرفتند.
یافته‌ها: براساس نتایج در کل ۳۲ متاQTL شناسایی شدند؛ کروموزوم‌های ۱ و ۳ با پنج ناحیه‌ی متا بیشترین و کروموزوم ۹ با دو ناحیه‌ی متا کمترین تعداد متاQTL را داشتند. همچنین در کروموزوم‌های ۷، ۸، ۱۰ و ۱۱ هیچ ناحیه‌ی متایی شناسایی نشد. با استفاده از ابزارهای آنلاین، ژن‌های موجود در این نواحی متاQTL مورد شناسایی قرار گرفته و به‌عنوان ژن‌های کاندید معرفی شدند. در مجموع ۱۳۱ شناسه‌ی ژنی در ۲۹ متاQTL یافت شد؛ بیش‌ترین تعداد ژن‌ها مربوط به MQTL6.3 با ۵۹ شناسه بود. در مقابل، متاQTL های 1.2، 3.2 و 4.3 هرکدام تنها یک شناسه‌ی ژنی داشتند و در MQTL12.3 و MQTL3.1 هیچ ژنی شناسایی نشد. از جمله‌ی ژن‌های مهم شناسایی‌شده می‌توان به OsCML19، OsSTA36، OsRDCP4، OsPP2C60، OsSEQ18، OsZIP54 و OsUCL18 اشاره کرد. تحلیل هستی‌شناسی و مسیرهای عملکردی این ژن‌ها نشان داد که تنش‌هایی مانند سرما، گرما و شوری، باعث تغییراتی در فتوسنتز و میزان کلروفیل می‌شود که در این وضعیت مسیرهای زیستی نظیر تاخوردگی پروتئین‌ها، متابولیسم ترکیبات دیواره سلولی، پاسخ به هیدروژن پراکسید و رشد ریشه به‌طور چشمگیری فعال می‌شوند. همچنین فعالیت‌های مولکولی همچون اتصال عوامل رونویسی، عملکرد نیترات ردوکتاز و ترکیب یون مولیبدن با کوفاکتور آن، تغییر بیان معناداری نشان می‌دهند.
نتیجه‌گیری: اگرچه مکان‌یابی QTL در مطالعات موردی با چالش‌هایی همچون اثرات محیطی، تفاوت والدین، زمینه ژنتیکی و نقشه کروموزومی مواجه است، فراتحلیل QTL در تحقیق حاضر با ترسیم نقشه جامع کروموزومی، امکان بررسی همزمان مجموعه QTLهای جمع‌آوری شده را فراهم آورد و متاQTLهای معنی‌دار شناسایی شد. بررسی نواحی ژنومی این متاQTLها منجر به ردیابی ژن‌های کلیدی دخیل در پاسخ به تنش، مسیرهای فعال‌شده در شرایط تنش و محصولات پروتئینی حاصل از آنها انجامید و در نهایت مسیرهای مهم بیولوژیکی و عملکردی در سطح سلولی و مولکولی شناسایی شدند. این یافته‌ها می‌توانند درک سازوکارهای مولکولی فتوسنتز را بهبود بخشیده و زمینه‌ساز به‌نژادی مؤثر گیاهان باشند. با این حال، نتایج فراتحلیل به کیفیت و تنوع مطالعات اولیه (نوع جمعیت، تراکم نشانگر، روش آماری، محیط و مرحله رشد) وابسته است. در این پژوهش، به‌دلیل تعداد محدود مطالعات مرتبط با صفات فتوسنتزی، همه داده‌ها بدون در نظر گرفتن تنوع محیطی و رشدی وارد شدند؛ بنابراین متاQTLها و ژن‌های کاندید معرفی‌شده نیازمند اعتبارسنجی در جمعیت‌ها و محیط‌های مستقل، از طریق نقشه‌یابی دقیق، تحلیل بیان و روش‌های مولکولی هستند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Meta-QTL analysis of photosynthesis-related traits, identification of candidate genes and functional pathways in rice

نویسندگان [English]

  • Shayan Kazemi Lifshagerd 1
  • Atefeh Sabouri 1
  • Zahra Pezeshkian 2
  • Mehdi Sohani 3
1 Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Iran.
2 Inland Water Aquaculture Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bandar Anzali, Iran.
3 Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Iran.
چکیده [English]

Introduction: Improving yield-related traits in major crops such as rice requires accurate identification of the genomic regions controlling these traits. Although many studies have reported QTLs for photosynthesis-related traits in rice, differences in mapping populations and experimental conditions have made it difficult to combine their results for practical applications. Meta-analysis provides an effective approach to integrate QTL data from different studies, identify consensus genomic regions (Meta-QTLs, MQTLs), and overcome the limitations of individual QTL mapping studies.
Materials and methods: In this study, studies reporting QTLs associated with photosynthesis-related traits in rice were first collected and reviewed. Among the 27 identified studies, 17 studies comprising 129 eligible QTLs were finally selected for the meta-analysis. A consensus map was then constructed, and MQTL regions were identified in centiMorgans (cM) according to the software guidelines. Subsequently, genes and molecular markers located within or adjacent to the MQTL regions were identified. Finally, the functional pathways of the candidate genes were analyzed using relevant bioinformatics databases and tools.
Results: A total of 32 MQTLs were identified. Chromosomes 1 and 3 each contained five MQTLs, representing the highest number, whereas chromosome 9 contained only two MQTLs. No MQTLs were detected on Chromosomes 7, 8, 10, or 11. Candidate genes within the MQTL regions were identified using online databases and bioinformatics tools. Overall, 131 gene IDs were found in 29 MQTLs. MQTL6.3 contained the largest number of candidate genes (59), while MQTL1.2, MQTL3.2, and MQTL4.3 each contained only one gene. No candidate genes were identified in MQTL12.3 or MQTL3.1. Several important genes, including OsCML19, OsSTA36, OsRDCP4, OsPP2C60, OsSEC18, OsZIP54, and OsUCL18, were identified as promising candidates. Gene ontology and pathway analyses indicated that environmental stresses such as cold, heat, and salinity affect photosynthesis and chlorophyll content by activating biological processes related to protein folding, cell wall metabolism, hydrogen peroxide response, and root development. In addition, molecular functions associated with transcription factor binding, nitrate reductase activity, and molybdenum cofactor binding were significantly enriched.
Conclusion: Although QTL mapping in individual studies is challenged by environmental effects, differences among parental genotypes, genetic background, and chromosome map characteristics, the QTL meta-analysis conducted in the present study provided a comprehensive chromosomal map, enabling the simultaneous analysis of the collected QTLs and the identification of significant meta-QTLs (MQTLs). Investigation of the genomic regions underlying these MQTLs led to the identification of key genes involved in stress responses, stress-responsive pathways, and their encoded protein products, ultimately revealing the identification of important biological and functional pathways at the cellular and molecular levels. These findings may improve our understanding of the molecular mechanisms underlying photosynthesis and provide a basis for more effective crop breeding. However, the results of QTL meta-analysis depend on the quality and diversity of the primary studies, including population type, marker density, statistical methods, environmental conditions, and developmental stage. In the present study, due to the limited number of studies addressing photosynthesis-related traits, all available data were included without accounting for variation in environmental conditions and developmental stages. Therefore, the identified MQTLs and candidate genes require validation in independent populations and environments through fine mapping, gene expression analysis, and molecular approaches.

کلیدواژه‌ها [English]

  • Chlorophyll content
  • Gene ontology
  • Meta-QTL
  • QTL mapping

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بیوتکنولوژی و بیوشیمی غلات
دوره 5، شماره 1 - شماره پیاپی 1
فروردین 1405
صفحه 87-118

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