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Association analysis of salt tolerance in sunflower (Helianthus annuus L.) using retrotransposon markers | ||
Iranian Journal of Genetics and Plant Breeding | ||
دوره 11، شماره 2 - شماره پیاپی 22، دی 2022، صفحه 29-46 اصل مقاله (1.13 M) | ||
نوع مقاله: Research paper | ||
شناسه دیجیتال (DOI): 10.30479/ijgpb.2023.19245.1354 | ||
نویسندگان | ||
Soheila Ahmadpour1؛ Reza Darvishzadeh* 2؛ Omid Sofalian1؛ Naser Abbaspour3؛ Hossein Abbasi Holasou4؛ Muhammad Sajjad5 | ||
1Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil, Iran. | ||
2Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran. | ||
3Department of Biology, Faculty of Science, Urmia University, Urmia, Iran. | ||
4Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran. | ||
5Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan. | ||
تاریخ دریافت: 01 شهریور 1402، تاریخ بازنگری: 22 مهر 1402، تاریخ پذیرش: 20 آبان 1402 | ||
چکیده | ||
Salinity is a serious impediment to agricultural production in the world. Development of salt tolerant hybrid varieties using marker aided selection (MAS) is a pioneering strategy to combat salinity stress. Here we used retrotransposon based molecular markers and salinity tolerance related characters in a panel of eighty-four sunflower inbred lines for marker-trait association (MTA) analysis. Characters such as grain yield per plant, leaf relative water content (RWC), K+, Na+ and Cl- concentration in leaf lamina and petiole were measured separately under normal and 8 ds/m salt stress conditions. The impact of salinity was significant on grain yield, RWC, Na+ concentrations in lamina and petiole as well as on K+ to Na+ ratio. To study genomic variability and survey of LTR retrotransposons activity, the lines were fingerprinted with retrotransposon-based DNA markers; IRAP and REMAP. In hierarchical cluster analysis using IRAP+REMAP markers data, the 84 inbred lines were categorized in four main groups, whereas in Bayesian model-based cluster analysis, the lines were assigned into 2 subpopulations (K=2). A mixed linear model was implemented to detect marker–trait associations incorporating membership coefficient of individuals in the subpopulation (Q matrix) and relationship coefficient (kinship matrix) as covariates in the model. In association analysis by using IRAP+REMAP markers; 8 and 12 loci were identified to be significantly linked with the studied characters in normal and salt stress states, respectively. After developing specific primers for identified markers, they could be potentially applied in marker aided selection (MAS) programs to achieve suitable parental lines and also the improvement of traits of interest. | ||
کلیدواژهها | ||
Abiotic stress؛ LTR؛ Molecular markers؛ QTL analysis؛ Sunflower | ||
عنوان مقاله [English] | ||
تجزیه ارتباط برای تحمل به تنش شوری در آفتابگردان (Helianthus annuus L.) با استفاده از نشانگرهای رتروترنسپوزون | ||
نویسندگان [English] | ||
سهیلا احمدپور1؛ رضا درویش زاده2؛ امید سفالیان1؛ ناصر عباسپور3؛ حسین عباسی هولاسو4؛ محمد سجاد5 | ||
1گروه زراعت و اصلاح نباتات، دانشکده کشاورزی، دانشگاه محقق اردبیلی، اردبیل، ایران. | ||
2گروه تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران. | ||
3گروه زیست شناسی، دانشکده علوم، دانشگاه ارومیه، ارومیه، ایران. | ||
4گروه اصلاح نباتات و بیوتکنولوژی، دانشکده کشاورزی، دانشگاه تبریز، تبریز، ایران. | ||
5گروه علوم زیستی، دانشگاه COMSATS اسلام آباد (CUI)، اسلام آباد، پاکستان. | ||
چکیده [English] | ||
شوری یک مانع جدی برای تولید محصولات کشاورزی در جهان است. توسعه واریتههای متحمل به شوری با استفاده از انتخاب به کمک نشانگر یک استراتژی پیشگام برای مبارزه با شوری است. بدین منظور برای تجزیه ارتباط تحمل به شوری در 84 لاین آفتابگردان از نشانگرهای مولکولی مبتنی بر رتروترنسپوزون استفاده شد و صفاتی مانند عملکرد دانه در بوته، RWC، غلظت پتاسیم، سدیم و کلر در برگ و دمبرگ اندازهگیری شد. تأثیر شوری بر عملکرد دانه، RWC، میزان سدیم در برگ و دمبرگ و همچنین بر نسبت پتاسیم به سدیم معنیدار بود. برای مطالعه تنوع ژنومی و بررسی فعالیت رتروترانسپوزونهای LTR، لاینهای خالص آفتابگردان با نشانگرهای DNA مبتنی بر رتروترنسپوزون نظیر IRAP و REMAP انگشتنگاری شدند. با استفاده از مجموع دادههای نشانگرهای IRAP و REMAP، در تجزیه کلاستر به روش سلسله مراتبی 84 لاین در چهار گروه اصلی دستهبندی شدند؛ در حالی که لاینها با روش بیزین در 2 زیرجمعیت (K=2) گروهبندی شدند. مدل خطی مخلوط برای شناسایی ارتباط نشانگر-صفت که ضریب عضویت افراد در هر زیرجمعیت و ضریب خویشاوندی را به عنوان متغیرهای کمکی در مدل ترکیب میکند، اجرا شد. در تجزیه ارتباط با استفاده از نشانگرهای REMAP+IRAP 8 و 12 جایگاه بهترتیب با صفات مورد مطالعه در شرایط نرمال و تنش شوری مرتبط بودند. نشانگرهای DNA شناسایی شده در این تحقیق میتواند در برنامههای انتخاب به کمک نشانگر برای دستیابی به لاینهای مناسب والدین و همچنین بهبود صفات مورد مطالعه استفاده شود | ||
کلیدواژهها [English] | ||
تنش غیر زیستی, توالی طولانی تکراری, نشانگرهای مولکولی, تجزیه QTL, آفتابگردان | ||
مراجع | ||
Abd El-Aty M., Amer Kh., Eldegwy I., and Elakhdar A. (2011). Genetic studies on yield and its components in some barley crosses. Journal of Plant Production, 11: 1537-1550. Abdollahi Mandoulakani B., Nasri Sh., Dashchi S., Arzhang S., Bernousi I., and Abbasi Holasou H. (2016). Preliminary evidence for associations between molecular markers and quantitative traits in a set of bread wheat (Triticum aestivum L.) cultivars and breeding lines. Comptes Rendus Biologies, 340(6-7): 307-313. DOI: http://dx.doi.org/10.1016/j.crvi.2017.05.001. Andersen J. R., Zein I., Wenzel G., Krützfeldt B., Eder J., Ouzunova M., and Lübberstedt T. (2007). High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theoretical and Applied Genetics, 114: 307-319. Arraouadi S., Badri M., Abdelly Ch., Huguet T., and Aouani M. E. (2011). QTL mapping of physiological traits associated with salt tolerance in Medicago truncatula recombinant inbred lines. Genomics, 99: 118-125. Arora S. (2017). Diagnostic properties and constraints of salt-affected soils. In: Arora S., Singh A. K., Singh Y. P. (Eds.), Bioremediation of salt affected soils: an Indian perspective. Springer, 41-52 Ashraf M. Y., and Wu L. (1994). Breeding for salinity tolerance in plants. Critical Reviews in Plant Sciences, 13: 17-42. Ashwath M. N., Lavale S. A., Santhoshkumar A. V., Mohapatra S. R., Bhardwaj A., Dash U., Shiran K., Samantara K., and Wani S. H. (2023). Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees. Functional & Integrative Genomics, 23(4): 297. DOI: https://doi.org/10.1007/s10142-023-01224-8. Basirnia A., Darvishzadeh R., and Abdollahi Mandoulakani B. (2014a). Retrotransposon insertional polymorphism in sunflower (Helianthus annuus L.) lines revealed by IRAP and REMAP markers. Plant Biosystems, 150(4): 641-652. DOI: 10.1080/11263504.2014.970595. Basirnia A., Hatami Maleki H., Darvishzadeh R., and Ghavami F. (2014b). Mixed linear model association mapping for low chloride accumulation rate in oriental-type tobacco (Nicotiana tabacum L.) germplasm. Journal of Plant Interactions, 9: 666-672. Bazin J., Langlade N., Vincourt P., Arribat S., Balzergue S., El-Maarouf-Bouteau H., and Bailly C. (2011). Targeted mRNA oxidation regulates sunflower seed dormancy alleviation during dry after-ripening. Plant Cell, 23: 2196-2208. Boyer J. S., James R. A., Munns R., Condon T. A. G., and Passioura J. B. (2008). Osmotic adjustment leads to anomalously low estimates of relative water content in wheat and barley. Functional Plant Biology, 35: 1172-1182. Chen Z., Zhou M., Newman I. A., Mendham N. J., Zhang G., and Shabala S. (2007). Potassium and sodium relations in salinised barley tissues as a basis of differential salt tolerance. Functional Plant Biology, 34: 150-162. Chérel I. (2004). Regulation of K+ channel activities in plants: from physiological to molecular aspects. Journal of Experimental Botany, 55: 337-351. Darvishzadeh R. (2016). Population structure, linkage disequilibrium and association mapping for morphological traits in sunflower (Helianthus annuus L.). Biotechnology & Biotechnological Equipment 30(2): 236-246. DOI: http://dx.doi.org/10.1080/13102818.2015.1136568. Evanno G., Regnaut S., and Goudet J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14: 2611-2620. FAO (2016). FAO web site. www.fao.org. Fernandez P., Soria M., Blesa D., DiRienzo J., Moschen S., Rivarola M., Clavijo B. J., Gonzalez S., Peluffo L., Príncipi D., Dosio G., Aguirrezabal L., García-García F., and Dosio G. (2012). Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray. PLoS One, 7: e45899. Flint-Garcia S. A., Thornsberry J. M., and Buckler E. S. (2003). Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 54: 357-374. Francois L. E. (1996). Salinity effects on four sunflower hybrids. Agronomy Journal, 88: 215-219. Funk V. A., Bayer R. J., Keeley S., Chan R., Watson L., Gemeinholzer B., Schilling E., Panero J. L., Baldwin B. G., Garcia-Jagas N., Susanna A., and Jansen R. K. (2005). Everywhere but Antarctica: Using a supertree to understand the diversity and distribution of the Compositae. Biologiske Skrifter, 55: 343-374. Ghavami F., Elias E. M., Mamidi S., Ansari O., Sargolzaei M., Adhikari T., Mergoum M., Kianian S. F. (2011). Mixed model association mapping for Fusarium head blight resistance in Tunisian-derived durum wheat populations. G3: Genes, Genomes, Genetics, 1(3): 209-218. DOI: https://doi.org/10.1534/g3.111.000489. Gupta P. K., Rustgi S., and Kulwal P. L. (2005). Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology, 57: 461-485. Han X., Kang Y., Wan S., and Li X. (2022). Effect of salinity on oleic sunflower (Helianthus annuus L.) under drip irrigation in arid area of Northwest China. Agricultural Water Management, 259: 107267. Huang X. H., Wei X. H., Sang T., Zhao Q., Feng Q., Zhao Y., Li C. Y., Zhu C. R., Lu T. T., Zhang Z. W., Li M., Fan D. L., Guo Y. L., Wang A. H., Wang L., Deng L. W., Li W. J., Lu Y. Q., Weng Q. J., Liu K. Y., Huang T., Zhou T. Y., Jing Y. F., Li W., Lin Z., Buckler E. S., Qian Q., Zhang Q. F., Li J. Y., and Han B. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42: 961-965. Hussain M. K., and Rehman O. U. (1993). Breeding sunflower for salt tolerance; Physiological basis for salt tolerance in sunflower (Helianthus annuus L.). Helia, 16: 77-84 Jannatdoust M., Darvishzadeh R., Ziaeifard R., Ebrahimi M. A., Hatami Maleki H., Gholinezhad E., and Hatamnia A. A. (2016). Analysis of genetic diversity and population structure of confectionery sunflower (Helianthus annuus L.) native to Iran. Journal of Crop Science and Biotechnology, 19: 37-44. Jun T. H., Van K., Kim M. Y., Lee S. H., and Walker D. R. (2008). Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica, 162: 179-191. Kalendar R., and Schulman A. H. (2006). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1: 2478-2484. Khalifani S., Darvishzadeh R., and Morsali Aghajari F. (2023). Studying salinity stress in sunflower with focusing on mechanisms and approaches. Crop Biotechnology, 12(40): 15-40. DOI: 10.30473/cb.2023.68177.1911. Khalifani S., Darvishzadeh R., Azad N., and Rahmani R. S. (2022). Prediction of sunflower grain yield under normal and salinity stress by RBF, MLP and, CNN models. Industrial Crops and Products, 189: 115762. DOI: https://doi.org/10.1016/j.indcrop.2022.115762. Khatoon A., Qureshi M. S., and Hussain M. K. (2000). Effect of salinity on some yield parameters of sunflower (Helianthus annuus L.). International Journal of Agriculture and Biology, 2(4): 382-384. Kumar P., Choudhary M., Halder T., Prakash N. R., Singh V., Vineeth V. T., Sheoran S., Ravikiran T. K., Longmei N., Rakshit S., and Siddique K. H. M. (2022). Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops. Heredity, 128: 497-518. DOI: https://doi.org/10.1038/s41437-022-00516-2. Liu L., Wang L., Yao J., Zheng Y., and Zhao C. (2010). Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.). Molecular Plant Breeding, 1: 1-10. Liu X., and Baird W. M. (2003). Differential expression of genes regulated in response to drought or salinity stress in sunflower. Crop Science, 43: 678-687. Long N. V., Dolstra O., Malosetti M., Kilian B., Graner A., Visser R. G., and Van Der Linden C. G. (2013). Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theoretical and Applied Genetics,126: 2335-2351. Luan Z., Xiao M., Zhou D., Zhang H., Tian Y., Wu Y., Guan B., and Song Y. (2014). Effects of salinity, temperature, and polyethylene glycol on the seed germination of sunflower (Helianthus annuus L.). Scientific World Journal, 170418: 1-9. Mackay I., and Powell W. (2007). Methods for linkage disequilibrium mapping in crops. Trends in Plant Science 12: 57-63. Morsali Aghajari F. (2015). Identification of QTL controlling traits in sunflower under different levels of salt stress. M.Sc. Thesis, Urmia University, Urmia, Iran, pp. 192. Munns R. (2002). Comparative physiology of salt and water stress. Plant, Cell & Environment, 25: 239-250. Munns R. (2005). Genes and salt tolerance: bringing them together. New Phytologist, 167: 645-663. Munns R., James R. A., and Läuchli A. (2006). Approaches to increasing the salt tolerance of wheat and other cereals. Journal of Experimental Botany, 57: 1025-1043. Munns R., and Tester M. (2008). Mechanisms of salinity tolerance. Annual Review of Plant Biology, 59: 651-681. Nordborg M., and Tavaré S. (2002). Linkage disequilibrium: what history has to tell us. Trends in Genetics, 18: 83-90. Oraguzie N. C., Wilcox P. L., Rikkerink E. H., and de Silva H. N. (2007). Linkage disequilibrium. In: Association mapping in plants, Springer, New York, 11-39. Pritchard J. K., Stephens M., and Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. Rasoulzadeh Aghdam M., Reza D., Sepehr E., and Alipour H. (2021). Association analysis of agronomic traits of oilseed sunflower (Helianthus annuus L.) lines with REMAP and IRAP markers under optimum and phosphorus deficit stress. Iranian Journal of Field Crop Science, 52: 179-196. Rehman O. U., and Hussain M. K. (1998). Effect of salinity on growth and development of cultivated sunflower (Helianthus annuus L.). Pakistan Journal of Science, 50: 45-52. Rengel D., Arribat S., Maury P., Martin-Magniette M. L., Hourlier T., Laporte M., Varès D., Carrère S., Grieu P., Balzergue S., and Gouzy J. (2012). A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments. PloS One, 7: e45249. Reynolds M. P., Mujeeb Kazi A., and Sawkins M. (2005). Prospects for utilising plant adaptive mechanisms to improve wheat and other crops in drought and salinity prone environments. Annals of Applied Biology, 146: 239-259. Rosenberg N. A., Pritchard J. K., Weber J. L., Cann H. M., Kidd K. K., Zhivotovsky L. A., and Feldman M. W. (2002). Genetic structure of human populations. Science, 298: 2381-2385. Sahranavard A. F., Darvishzadeh R., Ghadimzadeh M., Azizi H., and Aboulghasemi Z. (2015). Identification of SSR loci related to some important agro morphological traits in different oily sunflower (Helianthus annuus L.) lines using association mapping. Crop Biotechnology, 10: 73-87. Shabala S., Shabala L., and Van Volkenburgh E. (2003). Effect of calcium on root development and root ion fluxes in salinised barley seedlings. Functional Plant Biology, 30: 507-514. Shehzad T., Iwata H., and Okuno K. (2009). Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breeding Science, 59: 217-227 Srivastava A. K., Shankar A., Nalini Chandran A. K., Sharma M., Jung K. H., Suprasanna P., and Pandey G. K. (2020). Emerging concepts of potassium homeostasis in plants. Journal of Experimental Botany, 71(2): 608-619. DOI: 10.1093/jxb/erz458. Stich B., Maurer H. P., Melchinger A. E., Frisch M., Heckenberger M., van der Voort J. R., Peleman J., Sørensen A. P., and Reif J. C. (2006). Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers. Molecular Breeding, 17: 217-226. Stich B., Melchinger A. E., Frisch M., Maurer H. P., Heckenberger M., and Reif J. C. (2005). Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theoretical and Applied Genetics, 111: 723-730. Stich B., Melchinger A. E., Piepho H. P., Hamrit S., Schipprack W., Maurer H. P., and Reif J. C. (2007). Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations. Theoretical and Applied Genetics, 115: 529-536. Tamura K., Dudley J., Nei M., Kumar S., and Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24: 1596-1599. Teakle N. L., and Tyerman S. D. (2010) Mechanisms of Cl- transport contributing to salt tolerance. Plant, Cell & Environment, 33: 566-589. Tester M., and Davenport R. (2003). Na+ tolerance and Na+ transport in higher plants. Annals of Botany, 91: 503-527. Tuberosa R., Salvi S., Sanguineti M. C., Landi P., Maccaferri M., and Conti S. (2002). Mapping QTLs regulating morpho-physiological traits and yield: Case studies, shortcomings and perspectives in drought-stressed maize. Annals of Botany, 89: 941-963. Van Zelm E., Zhang Y., and Testerink C. (2020). Salt Tolerance Mechanisms of Plants. Annual Review of Plant Biology, 29(71): 403-433. DOI: 10.1146/annurev-arplant-050718-100005. Vukich M., Giordani T., Natali L., and Cavallini A. (2009). Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.). BMC Plant Biology, 9: 150. DOI: https://doi.org/10.1186/1471-2229-9-150. Wang M., Jiang N., Jia T., Leach L., Cockram J., Waugh R., and Luo Z. (2012). Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theoretical and Applied Genetics, 124: 233-246. White P. J., and Broadley M. R. (2001). Chloride in soils and its uptake and movement within the plant: a review. Annals of Botany, 88: 967-988. Wade S. (2023). Bayesian cluster analysis. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 381(2247): 20220149. DOI: http://doi.org/10.1098/rsta.2022.0149. Wu H., and Li Z. (2019). The importance of Cl- exclusion and vacuolar Cl- sequestration: Revisiting the role of Cl- transport in plant salt tolerance. Frontiers in Plant Science, 10: 1418. DOI: https://doi.org/10.3389/fpls.2019.01418. Yagcioglu M., Gulsen O., Yetisir H., Solmaz I., and Sari N. (2016). Preliminary studies of genom-wide association mapping for some selected morphological characters of watermelons. Scientia Horticulturae, 210: 277-284. Yu J., Pressoir G., Briggs W. H., Vroh B. I., Yamasaki M., Doebley J. F., McMullen M. D., Gaut B. S., Nielsen D. M., Holland J. B., Kresovich S., and Buckler E. S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38: 203-208. Yu J., and Buckler E. S. (2006). Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology, 17(2): 155-160. Zhao K., Aranzana M. J., Kim S., Lister C., Shindo C., Tang C., Toomajian C., Zheng H., Dean C., Marjoram P., and Nordborg M. (2007). An Arabidopsis example of association mapping in structured samples. PLOS Genetics, 3: e4:0071-0082. Zhu Ch., Gore M., Bucker E. S., and Yu J. (2008). Status and prospects of association mapping in plants. Plant Genome, 1: 5-20. Zhu J. K. (2003). Regulation of ion homeostasis under salt stress. Current Opinion in Plant Biology, 6: 441-44. | ||
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