استفاده از رگرسیون برای بررسی ارتباط نشانگرهای مولکولی SCoT با صفات زراعی و فیزیولوژیک ریحان تحت شرایط تنش خشکی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه بیوتکنولوژی، پژوهشگاه علوم و تکنولوژی پیشرفته و علوم محیطی، دانشگاه تحصیلات تکمیلی صنعتی و فناوری پیشرفته، کرمان، ایران.

2 دانشیار، گروه بیوتکنولوژی، پژوهشگاه علوم و تکنولوژی پیشرفته و علوم محیطی، دانشگاه تحصیلات تکمیلی صنعتی و فناوری پیشرفته، کرمان، ایران

چکیده

هدف: ریحان (Ocimum basilicum) یکی از گیاهان دارویی و سبزی بسیار مهم است که در سطح جهان کشت و مصرف می‌شود. یکی از جنبه‌های ضروری برنامه‌های اصلاح نباتات مطالعه همبستگی بین چندشکلی DNA و تنوع صفات فنوتیپی است. هدف از این تحقیق بررسی تنوع ژنتیکی پنج رقم ریحان در شرایط تنش خشکی با استفاده از نشانگر SCoT و صفات و همچنین انجام تجزیه و تحلیل ارتباط بین صفات و نشانگرها با رگرسیون گام به گام است.
مواد و روش‌ها: در این پژوهش، پنج ژنوتیپ ریحان تحت شرایط تنش خشکی به صورت طرح اسپیلت پلات بر پایه طرح کاملا تصادفی با سه تکرار در گلدان و در شرایط گلخانه‌ای مورد مطالعه قرار گرفتند. فاکتور اصلی شامل تنش خشکی در دو سطح (نرمال و تنش خشکی) و عامل فرعی شامل ژنوتیپ (5 سطح) بود و صفات ریخت‌شناسی و فیزیولوژیک آن‌ها ارزیابی گردیدند. همچنین DNA ژنومی آن‌ها از برگ استخراج گردید و تنوع ژنوتیپی ژنوتیپ‌ها بر اساس هشت آغازگر SCoT بررسی شد و در نهایت ارتباط بین صفات و نشانگرها با رگرسیون گام به گام مشخص گردید.
نتایج: همبستگی صفات در دو شرایط نشان داد که عملکرد برگ همبستگی مثبت و معنی‌داری با صفات صفات ارتفاع بوته و کلروفیل کل داشت. درصد تغییرات صفات در شرایط تنش نشان داد که صفات طول ریشه، کلروفیل a و کلروفیل کل بیشترین کاهش را داشتند و تجزیه خوشه‌ای براساس آنها، ژنوتیپ‌ها را در سه گروه و صفات را نیز در سه گروه قرار داد. هشت آغازگر در مجموع تعداد 101 نوار چندشکل تکثیر کردند و ScoT1 با 17 نوار چندشکل، بیشترین نوار رو تولید کرد. تجزیه خوشه‌ای به روش جفت گروه بدون وزن با میانگین حسابی و معیار شباهت دایس بر اساس داده‌های SCoT، پنج ژنوتیپ ریحان را در سه گروه قرار دادند. نتایج تجزیه رگرسیون نشان داد که به ترتیب در شرایط نرمال و تنش خشکی، 15 و 12 نشانگر (آلل) با صفات مورد مطالعه رابطه معنی‌داری پیدا کردند.
نتیجه‌گیری: انتخاب بر اساس نشانگرهای مولکولی روشی سریع برای برنامه‌های اصلاحی ارائه می‌دهد. اطلاعات ژنتیکی به دست آمده نشانگرها در این مطالعه نقش مهم آنها را نشان داد. بنابراین در کنار صفات، انتخاب ژنوتیپ‌های برتر و جمعیت‌های با ارزش بالا در برنامه‌های اصلاحی امکان‌پذیر است. یافته‌ها نشان داد که نشانگرهای خاصی با صفات متعدد مرتبط هستند و بر اهمیت حیاتی این ویژگی در اصلاح گیاهان برای بهبود همزمان صفات متعدد تأکید کرد. بینش این مطالعه در مورد نشانگرها دارای پتانسیل برای کاربرد در برنامه‌های به‌نژادی است.

کلیدواژه‌ها

عنوان مقاله [English]

Using regression to investigate the relationship between SCoT molecular markers and agronomic and physiological traits of basil under drought stress conditions

نویسندگان [English]

  • Atousa Keshavarzi 1
  • Mehdi Rahimi 2
  • Amin Baghizadeh 2
1 Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
2 Corresponding author. Associate Professor, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
چکیده [English]

Objective: Basil (Ocimum basilicum) is one of the most important medicinal as well as vegetables plants that are cultivated and consumed worldwide One of the essential aspects of plant breeding programs is to study the correlation between DNA polymorphisms and phenotypic trait diversity. The purpose of this research is to investigate the genetic diversity of five basil cultivars under drought stress conditions using SCoT markers and traits, and also to analyze the relationship between traits and markers by stepwise regression.
Materials and Methods: In this research, five basil genotypes were studied under drought stress in the form of a split plot based on a completely randomized design with three replications in pots and under greenhouse conditions. The main plot included drought stress in two levels (normal and drought stress) and the sub plot factor included genotype (5 levels) and their morphological and physiological traits were evaluated. Also, their genomic DNA was extracted from the leaves, and the genotypic diversity of the genotypes was investigated based on eight SCoT primers, and finally, the relationship between the traits and markers was determined by stepwise regression.
Results: Correlation of traits in two conditions showed that leaf yield had a positive and significant correlation with traits of plant height and total chlorophyll. The percentage of trait changes under stress conditions showed that root length, chlorophyll a and total chlorophyll traits had the greatest decrease and cluster analysis based on them placed the genotypes in three groups and the traits in three groups. Eight primers amplified a total of 101 polymorphic bands and ScoT1 produced the most bands with 17 polymorphic bands. Cluster analysis by UPGMA and dice similarity criterion based on SCoT data were placed five basil genotypes in three groups. The results of regression analysis showed that in normal and drought stress conditions, 15 and 12 markers (alleles) had a significant relationship with the studied traits, respectively.
Conclusion: Selection based on molecular markers provides a rapid method for breeding programs. The obtained genetic information of markers in this study showed their important role. Therefore, in addition to traits, it is possible to select superior genotypes and high value populations in breeding programs. The findings showed that certain markers are associated with multiple traits and emphasized the critical importance of this trait in plant breeding for simultaneous improvement of multiple traits. Insights from this study on markers have potential for application in breeding programs.

کلیدواژه‌ها [English]

  • Association analysis
  • grouping
  • molecular marker
  • trait correlation

مراجع

افکاری احمد (1396) تأثیر تنش خشکی و مقادیر کود نیتروژنه بر میزان و عملکرد اسانس و برخی ویژگی‌های فیزیولوژیکی گیاه دارویی ریحان (Ocimum basilicum L.) تحقیقات گیاهان دارویی و معطر ایران 33(6(پیاپی 86))، 1059-1047.
کریمی سمیه، زاهدی بهمن، مومیوند حسن (1399) بررسی تأثیر تنش کم آبی بر رشد میزان اسانس و برخی صفات فیزیولوژیک چهار رقم ریحان (Ocimum basilicum L.). پژوهش‌های تولید گیاهی 27(2)، 213-201.
References
AbdoliNasab M, Rahimi M (2020) Association analysis of traits in watermelon genotypes using molecular markers. Iran J Sci Technol Trans A Sci 44, 361-369.
Abecasis GR, Cardon LR, Cookson WO et al. (2001) Association analysis in a variance components framework. Genet Epidemiol 21, S341-S346.
Abuhashem YS, Khalil HB, El-Tahawey MA et al. (2023) Exploring the morphological and genetic diversity of Egyptian basil landraces (Ocimum sp.) for future breeding strategies. Beni-Suef Univ J Basic Appl Sci 12, Article number: 70.
Afkari A (2018) Effects of drought stress and nitrogen fertilizer rate on some physiological characteristics, essential oil percentage, and yield of basil (Ocimum basilicum L.). Iranian J Medicinal Aromat Plants Res 33, 1047-1059 (In Persian).
Aghaei M, Darvishzadeh R, Hassani A (2012) Molecular characterisation and similarity relationships among Iranian basil (Ocimum basilicum L.) accessions using inter simple sequence repeat markers. Rev Cienc Agron 43, 312-320.
Al-Ashkar I, Alderfasi A, Ben Romdhane W et al. (2020) Morphological and genetic diversity within salt tolerance detection in eighteen wheat genotypes. Plants 9, Article 287.
Arabsalehi F, Rahimmalek M, Sabzalian MR (2022) Morpho-physiological and molecular characterization reveal low genetic variation for conservation of endangered Iranian moshgak (Ducrosia anethifolia Boiss). Biochem Genet 66, 2587–2610.
Asghari J, Mahdavikia H, Rezaei-Chiyaneh E et al. (2023) Selenium nanoparticles improve physiological and phytochemical properties of basil (Ocimum basilicum L.) under drought stress conditions. Land 12, Article 164.
Azizi A, Ardalani H, Honermeier B (2016) Statistical analysis of the associations between phenolic monoterpenes and molecular markers, AFLPs and SAMPLs in the spice plant Oregano. Herba Pol 62, 42-56.
Bates LS, Waldren Ra, Teare I (1973) Rapid determination of free proline for water-stress studies. Plant Soil 39, 205-207.
Begna T (2021) Role and economic importance of crop genetic diversity in food security. Int J Agric Sci Food Technol 7, 164-169.
Bhandari H, Bhanu A, Srivastava K et al. (2017) Assessment of genetic diversity in crop plants - an overview. Adv Plants Agric Res 7, 279-286.
Botstein D, White RL, Skolnick M et al. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32, 314– 331.
Collard BC, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27, 86-93.
De Masi L, Siviero P, Esposito C et al. (2006) Assessment of agronomic, chemical and genetic variability in common basil (Ocimum basilicum L.). Eur Food Res Technol 223, 273-281.
Doyle J (1991) DNA protocols for plants. In: Molecular techniques in taxonomy. Hewitt GM, Johnston AWB & Young JPW (eds). Springer, Norwich, England. pp. 283-293.
Esposito MA, Gatti I, Cravero VP et al. (2013) Combining abilities and heterotic groups in'Pisum sativum'L. Aust J Crop Sci 7, 1634-1641.
Farhangian-Kashani S, Azadi A, Khaghani S et al. (2021) Association analysis and evaluation of genetic diversity in wheat genotypes using SSR markers. Biol Futura 72, 441-452.
Gebhardt C, Ballvora A, Walkemeier B et al. (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13, 93-102.
Giachino RRA, Sönmez Ç, Tonk FA et al. (2014) RAPD and essential oil characterization of Turkish basil (Ocimum basilicum L.). Plant Syst Evol 300, 1779-1791.
Golkar P, Nourbakhsh V (2019) Analysis of genetic diversity and population structure in Nigella sativa L. using agronomic traits and molecular markers (SRAP and SCoT). Ind Crops Prod 130, 170-178.
Gonda I, Faigenboim A, Adler C et al. (2020) The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding. DNA Res 27, dsaa027.
Hamidi M, Tohidi Moghadam H, Nasri M et al. (2023) How do mycorrhiza and plant growth stimulants improve the qualitative and quantitative yields of basil (Ocimum basilicum L.) under different irrigation regimes? Gesunde Pflanzen 75, 165-177.
Hammer Ø, Harper D, Ryan P (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeont Electr 4, 9pp.
Henry RJ (2012) Molecular markers in plants. Wiley, USA.
Jambhale V, Awari V, Aher A et al. (2023) Assessment of genetic variability in Ocimum spp. Pharma Innov J 12, 3016-3020.
Javanmardi J, Khalighi A, Kashi A et al. (2002) Chemical characterization of basil (Ocimum basilicum L.) found in local accessions and used in traditional medicines in Iran. J Agric Food Chem 50, 5878-5883.
Kafi MA, Mahdavi Damghani M (2003) Mechanisms of Environmental Stress Resistance in Plants. Ferdwsi University of Mashhad Press, Iran.
Karimi S, Zahedi B, Mumivand H (2020) Evaluation of the effect of drouth stress on growth, esential oil and some physiological traits of four basil (Ocimum basilicum L.) cultivars. J Plant Prod Res 27, 201-213 (In Persian).
Khadka K, Earl HJ, Raizada MN et al. (2020) A physio-morphological trait-based approach for breeding drought tolerant wheat. Front Plant Sci 11, Article 715.
Khalid KA (2006) Influence of water stress on growth, essential oil, and chemical composition of herbs [Ocimum sp.]. Int Agrophysics 20, 289-296.
Kordrostami M, Rahimi M (2015) Molecular markers in plants: concepts and applications. Genete 3rd Millenn 13, 4024-4031.
Kumar RR, Reddy LPA, Patel RP (2012) Genetic association for oil yield and its component traits in different Ocimum species. Electron J Plant Breed 3, 794-799.
Labra M, Miele M, Ledda B et al. (2004) Morphological characterization, essential oil composition and DNA genotyping of Ocimum basilicum L. cultivars. Plant Sci 167, 725-731.
Lambert SM, Borba EL, Machado MC et al. (2006) Allozyme diversity and morphometrics of Melocactus paucispinus (Cactaceae) and evidence for hybridization with M. concinnus in the Chapada Diamantina, North-eastern Brazil. Ann Bot 97, 389-403.
Lee S-J, Umano K, Shibamoto T et al. (2005) Identification of volatile components in basil (Ocimum basilicum L.) and thyme leaves (Thymus vulgaris L.) and their antioxidant properties. Food Chem 91, 131-137.
Lichtenthaler HK (1987) [34] Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. In: Methods in enzymology. Elsevier. pp. 350-382.
Liu BH (1998) Statistical genomics: Linkage, mapping and QTL analysis. CRC Press, Boca Raton, Florida, USA.
Louwaars NP (2018) Plant breeding and diversity: A troubled relationship? Euphytica 214, 1-9.
Luo C, He X-H, Chen H et al. (2010) Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochem Syst Ecol 38, 1176-1184.
Luo C, He X-h, Chen H et al. (2011) Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochem Syst Ecol 39, 676-684.
Luo Z, Chen Z, Liu M et al. (2022) Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm. BMC Genom 23, 1-17.
Mandel JR, Nambeesan S, Bowers JE et al. (2013) Association mapping and the genomic consequences of selection in sunflower. PLoS Genet 9, Article: e1003378, 1003313pages.
Moghaddam M, Omidbeygi R, Salimi A et al. (2014) An Assessment of genetic diversity among Iranian populations of basil (Ocimum spp.) using morphological traits. Iran J Hortic Sci 44, 227-243.
Nei M (1972) Genetic distance between populations. Am Nat 106, 283-292.
Pandey Y, Chaturvedi T, Swaroop H et al. (2023) Phytochemical and genetic marker (SCoT and CBDP) based study of genetic diversity and population structure in natural populations of Cannabis sativa L.: A high-value sustainable biodiversity of North-Indian Himalaya. Ind Crops Prod 200, Article 116892.
Patel RP, Singh R, Lal RK et al. (2018) Genetic variability of agronomic traits and chemo diversity in the genus Ocimum. Trends Phytochem Res 2, 103-110.
Pathirana R, Carimi F (2022) Management and utilization of plant genetic resources for a sustainable agriculture. Plants 11, Article 2038.
Pawlak K, Kołodziejczak M (2020) The role of agriculture in ensuring food security in developing countries: Considerations in the context of the problem of sustainable food production. Sustainability 12, Article 5488.
Powell W, Morgante M, Andre C et al. (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2, 225-238.
Pritchard JK, Stephens M, Rosenberg NA et al. (2000) Association mapping in structured populations. Am J Hum Genet 67, 170-181.
Rahimi M (2021) Genetic diversity, population structure and screening of molecular markers associated to agronomic traits in Safflower (Carthamus tinctorius L.). Iran J Sci Technol Trans A Sci 45, 1549-1560.
Rahimi M, Kordrostami M, SafaeiChaeikar S (2019) Genetic variation, population structure and the possibility of association mapping of biochemical and agronomic traits using dominant molecular markers in Iranian tea accessions. Iran J Sci Technol Trans A Sci 43, 2769-2780.
Rahimi M, Nazari L, Kordrostami M et al. (2018) SCoT marker diversity among Iranian Plantago ecotypes and their possible association with agronomic traits. Sci Hortic 233, 302-309.
Rahimi M, Ranjbaran E (2023) Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers. Physiol Mol Biol Plants 29, 421-433.
Reynolds M, Chapman S, Crespo-Herrera L et al. (2020) Breeder friendly phenotyping. Plant Sci 295, Article 110396.
Sawant SV, Singh PK, Gupta SK et al. (1999) Conserved nucleotide sequences in highly expressed genes in plants. J Genet 78, 123-131.
Shannon CE (2001) A mathematical theory of communication. ACM SIGMOBILE Mob Comput Commun Rev 5, 3-55.
Sheller M, Tóth EG, Ciocîrlan E et al. (2023) Genetic diversity and population structure of Scots Pine (Pinus sylvestris L.) in Middle Siberia. Forests 14, Article 119.
Singh Y, Gaurav S, Kumar P et al. (2015) Genetic variability and correlation coeff icient in F2 segregating population of basil (Ocimum basilicum L.). Med Plants - Int J Phytomed Relat Ind 7, 196-207.
Stankovic S, Zdravkovic-Korac S, Vujicic M, Jevremovic, S et al. (2019) Genetic diversity and population structure of basil (Ocimum basilicum L.) germplasm from Iran and other countries using ISSR markers. Ind Crops Prod 137, 111–119.
Tessier C, David J, This P et al. (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet 98, 171– 177.
Wang Z, Li G, Sun H et al. (2018) Effects of drought stress on photosynthesis and photosynthetic electron transport chain in young apple tree leaves. Biol Open 7, bio035279.
Wei T, Simko V, Levy M et al. (2017) Package ‘corrplot’. Statistician 56, e24.
Yaldiz G, Camlica M (2021) Agro‐morphological and phenotypic variability of sweet basil genotypes for breeding purposes. Crop Sci 61, 621-642.
Yeh FC (1999) POPGENE (version 1.3. 1). Microsoft Window-Bases Freeware for Population Genetic Analysis. http://www ualberta ca/~ fyeh.
مجله بیوتکنولوژی کشاورزی
دوره 16، شماره 2
خرداد 1403
صفحه 25-50

فایل ها

هم رسانی

ارجاع به این مقاله

آمار