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:: Volume 7, Issue 1 (2020) ::
pgr 2020, 7(1): 161-180 Back to browse issues page
Identification of Genes and Molecular Markers Associated with Germination Components in F9 Lines of Rice under Osmotic Stress
Abbas Saberi Kuchesfahani , Atefeh Sabouri * , Amin Abedi , Ali Aalami , Teimour Razavipour
Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran , a.sabouri@guilan.ac.ir
Abstract:   (8140 Views)

water stress and, in this regard, it is necessary to improve rice cultivars to tolerance to environmental stresses. In this research 154 recombinant inbred lines (F9) derived from a cross between Shah-Pasand and IR28 in three conditions (non-stress, osmotic stress -0.3 and -0.6 Mpa induced through polyethylene glycol-6000) were evaluated as a factorial experiment in randomized complete block design. In addition, for molecular polymorphism experiment, 110 SSR and EST-SSR markers were assessed on parents of population and among them, 41 markers identified which had proper polymorphism between two parents. The regression analysis between germination components and molecular markers revealed the most coefficient of determination were found in RM211 for allometric coefficient (17%) under non-stress, RMES10-1 for Plumule dry weight (18%) under -0.3 MPa; and RM273 for germination uniformity (22.7%) under -0.6 MPa. RM3496, RM452, and RMES6-1 in three conditions had the most number of significant relationships with six, three and eight traits, respectively, and they can be a suitable candidate for simultaneous improvement of several traits in breeding programs of marker-assisted selection. In addition, after the identification of significant markers associated with germination components, the closest genes to these markers were identified using bioinformatic analysis, and the analysis of their expression were performed by rice transcriptome database. According to the results, the maximum gene expression pattern under drought stress and under non-stress conditions were related to loci LOC_Os01g57220 and LOC_Os01g26039, respectively and this information could be applied in breeding programs.

Keywords: Marker assisted selection, Environmental stress, Microsatellite markers
Full-Text [PDF 858 kb]   (1370 Downloads)    
Type of Study: Research | Subject: Molecular genetics
References
1. Abdul-Baki, A.A. and Anderson, J.D. (1973). Vigor determination in soybean seed by multiple criteria. Crop Science, 13: 630-633.
2. Agrawal, R. (1980). Seed Technology. Pub. Co. PVT. LTD. New Dehli, IND.
3. Blasi, É.A., Buffon, G., Rativa, A.G., Lopes, M.C., Berger, M., Santid, L., Lavallée-Adame, M., Yates, J., Schwambachg, J., Beys-da-Silvad, W. and Sperottoa, R. (2017). High infestation levels of Schizotetranychus oryzae severely affects rice metabolism. Journal of Plant Physiology, 219: 100-111.
4. Bolser, D., Staines, D.M., Pritchard, E. and Kersey, P. (2016). Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. Plant Bioinformatics. Humana Press, New York, USA. [DOI:10.1007/978-1-4939-3167-5_6]
5. Camberato, J., and Mccarty, B. (1999). Irrigation water quality: part I. salinity. South Carolina Turfgrass Foundation New, 6(2): 6-8.
6. Chen, C., Chen, H., He, Y. and Xia, R. (2018). TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface, BioRxiv.1: 289660.
7. Collard, B.C., Beredo, J.C., Lenaerts, B., Mendoza, R., Santelices, R., Lopena, V., Verdeprado, H., Raghavan, C., Gregorio, G.B., Vial, L. and Demont, M. (2017). Revisiting rice breeding methods-evaluating the use of rapid generation advance (RGA) for routine rice breeding. Plant Production Science, 20(4): 337-352.
8. Djanaguiraman, M., Senthil, A. and Ramadass, R. (2004). Mechanism of salt tolerance in rice genotypes during germination and seedling growth. Indian Journal of Agricultural Research, 38(1): 73-76.
9. Edwards, J.D., Baldo, A.M. and Mueller, L.A. (2016). Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data. Database, 107: 1- 6.
10. Fazeli Kakhki, F., Nazemi, A., Parsa, M. and Kafi, M. (2015). Evaluation of germination indices and seedling growth in sesame ecotypes (Sesamum indicum L.) under salinity conditions. Environmental Stress in Crop Science, 7(2): 217-232 (In Persian).
11. Hussain, F. (1989). Field and Laboratory Manual of Plant Ecology. National Academy of Higher Education. University Grants Commissionو Islamabad, PK.
12. IBM Corp. (2016). IBM SPSS Statistics for Windows, Version 24.0. Armonk, IBM, New York, USA.
13. Jafarzadeh-Razmi, M., Navabpour, S., Sabouri, H. and Ramzanpour, S.S. (2020). qGW, a stable and major QTL for increasing of grain weight in rice (Oryza sativa L.). Plant Genetic Researches, 6(2): 173-182 (In Persian).
14. Kavousi, M. (2001). Study of Interaction Effects Between Different Levels of Nitrogen and Potassium on Rice Yield. Rice Research Institute of Iran. Research Report, Rasht, IR (In Persian).
15. Kawahara, Y., Bastide, M., Hamilton, J.P., Kanamori, H., McCombie, W.R., Ouyang, Sh., Schwartz, D.C., Tanaka, T., Wu, J., Zhou, Sh., Childs, K.L., Davidson, R.M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S.Sh., Kim, J., Numa, H., Itoh, T., Buell, C.R. and Matsumoto, T. (2013). Improvement of the (Oryza sativa L.) Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1): 4.
16. Kim, S. H., Bhat, P. R., Cui, X., Walia, H., Xu, J., Wanamaker, S., Ismai, A. M., Wilson, C. and Close, T.J. (2009). Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. BMC Plant Biology, 9(1): 65.
17. Michel, B.E. and Kaufman, M.R. (1973). The osmotic potential of polyetylene glycol 6000. Plant Physiology, 51: 914-916.
18. Millan, T., Clarke, H.J., Siddique, K.H., Buhariwalla, H.K., Gaur, P.M., Kumar, J., Jagdish, K., Gil, J., Kahland G. and Winter, P. (2006). Chickpea molecular breeding: new tools and concepts. Euphytica, 147(1-2): 81-103.
19. Mirarab-Razi, S.M., Shirzadian-Khorramabad, R., Sabouri, H., Rabiei, B. and Hosseini Moghadam, H. (2019). Response of Iranian Rice Recombinant Inbred Lines (Oryza sativa L.) to Salt Stress in Seedling Stage. Journal of Crop Breeding, 11(29): 65-84.
20. Mohammadi, M., Xavier, A., Beckett, T., Beyer, S., Chen, L., Chikssa, H., Cross, V., Moreira, F.F., French, E., Gaire, R. and Griebel, S. (2020). Identification, deployment, and transferability of quantitative trait loci from genome-wide association studies in plants. Current Plant Biology, 24: 100145.
21. Monaco, M.K., Stein, J., Naithani, S., Wei, Sh., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S.h., Olson, A., Jiao, Y., Lu, Z.h., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., Eustachio, P.D., Haw, R., Croft, D., Kersey, P.J., Stein, L., Jaiswal, P. and Ware, D. (2013) Comparative plant genomics resources. Nucleic Acids Research, 42:1193-1199. [DOI:10.1093/nar/gkt1110]
22. Nasiri, E., Sabouri, A., Forghani. and Esfahani, M. (2018). Grouping of rice genotypes based on grain iron, zinc, manganese and protein and performance measurement of linked microsatellite markers. Plant Genetic Researches, 5(2): 73-84.
23. Rabiei, B. and Sabouri, H. (2008). Mapping of Genes Controlling Quantitative Traits. Guilan University Press, Rasht, IR (In Persian).
24. Sabouri, A., Dadras, A.R., Khoshchehreh, H., Vatanparast, A. and Afltooni, H. (2019). Investigation of rice recombinant inbred lines based on drought tolerance using tolerance indices and SSR marker. Iranian Journal of Field Crop Science, 49(4): 13-24.
25. Sabouri, A., Afshari, R., Raiesi, T., Raouf, H.B., Nasiri, E., Esfahani, M., Kafi-Ghasemi, A. and Kumar, A. (2018). Superior adaptation of aerobic rice under drought stress in Iran and validation test of linked SSR markers to major QTLs by MLM analysis across two years. Molecular Biology Reports, 45(5): 1037-1053.
26. Sabouri, H., Rezai, A., Moumeni, A. and Kavousi, M. (2007). Investigation of genetic diversity of Iranian rice genotypes under salinity condition: compare means, sensitive and tolerance index. In: Bocchi, S., Ferrero, A. and Porro, A., Eds., Proceedings of the 4th International Temperate Rice Conference, Tipografia Fiordo, Novara, , Italy
27. Sabouri, H., Biabani, A., Sabouri, A. and Mohammad-Esmaili, M. (2010). The study of QTLs related to seed vigour under stress caused to Sorbitol in rice. Journal of Plant Production Research, 17(2): 123-136 (In Persian).
28. Saghai-Maroof, M.A., Biyashev, R.M., Yang, G.P., Zhang, Q. and Allard, R.W. (1994). Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 91(12): 5466-5570.
29. Segal, R. and Le Nguyet, M. (2019). Unfair Harvest: The State of Rice in Asia. Oxford, UK.
30. Singh, R.K., Gregorio, G.B. and Jain, R.K. (2007). QTL mapping for salinity tolerance in rice. Physiology and Molecular Biology of Plants, 13(2): 87-99.
31. Solis, J., Gutierrez, A., Mangu, V., Sanchez, E., Bedre, R., Linscombe, S. and Baisakh, N. (2018). Genetic mapping of quantitative trait loci for grain yield under drought in rice under controlled greenhouse conditions. Frontiers in Chemistry, 5: 129.
32. Soltani, A. and Maddah, V. (2010). Simple, Applied Programs for Education and Research in Agronomy, Niak Press, Tehran, IR (In Persian).
33. Srividhya, A., Ramanarao, P.V., Sridhar, S., Jayaprada, M., Anuradha, G., Srilakshmi, B., Reddy, H.K., Hariprasad, A.S., Siddiq, E.A. and Vemireddy, L.R. (2011). Molecular mapping of QTLs for drought related traits at seedling stage under PEG induced stress conditions in rice. American Journal of Plant Sciences, 2(02): 190.
34. Swamy, B.M., Vikram, P., Dixit, S., Ahmed, H.U. and Kumar, A. (2011). Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics, 12(1): 319.
35. Thomson, M., De-Ocampo, M., Egdane, J., Katimbang, M., Akhlasur-Rahman, M., Singh, R. K., Gregorio, G.B. and Ismail M.A. (2007). QTL mapping and marker-assisted backcrossing for improved salinity tolerance in rice, The 6th Asian Crop Science Association Conference and 2th International Conference on Rice for the Future, 5-9 November, Bangkok, Thailand.
36. Tsonev, T.D., Lazova, G.N., Stoinova, Z.G. and Popova, L.P. (1998). A possible role forjasmonic acid in adaptation of barley seedling to salinity stress. Journal of Plant Growth Regulation, 17(3): 153-159.
37. Tuberosa, R., Gill, B.S. and Quarrie, S.A. (2002). Cereal genomics: ushering in a brave new world. Plant Molecular Biology, 48(5-6): 445-449.
38. Tuyen, D.D. and Prasad, D.T. (2008). Evaluating difference of yield trait among rice genotypes (Oryza sativa L.) under low moisture condition using candidate gene markers. Omonrice, 16: 24-33.
39. Vaid, N., Pandey, P.K. and Tuteja, N. (2012). Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice. Plant Molecular Biology, 80(4-5): 365-388.
40. Verma, S.K., Saxena, R.R., Saxena, R.R., Xalxo, M.S. and Verulkar, S.B. (2014). QTL for grain yield under water stress and non-stress conditions over years in rice (Oryza sativa L.). Australian Journal of Crop Science, 8(6): 916-926.
41. Vikram, P., Swamy, B.M., Dixit, S., Ahmed, H.U., Cruz, M.T.S., Singh, A.K. and Kumar, A. (2011). qDTY 1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics, 12(1): 89.
42. Wang, Z., Wang, J., Bao, Y., Wu, Y. and Zhang, H. (2011). Quantitative trait loci controlling rice seed germination under salt stress. Euphytica, 178(3): 297-307.
43. Wenhui, W.A.N.G., Linlin, W.A.N.G., Yujun, Z.H.U., Yeyang, F.A.N. and Jieyun, Z.H.U.A.N. G. (2019). Fine-mapping of qTGW1. 2a, a quantitative trait locus for 1000-grain weight in rice. Rice Science, 26(4): 220-228.
44. Willenborg, C.J., Wildeman, J.C., Miller, A.K., Rossnagel, B.G. and Shirtliffe, S.J. (2005). Oat germination characteristics differ among genotypes, seed sizes, and osmotic potentials. Crop Science, 45(5): 2023-2029.
45. Xia, L., Zou, D., Sang, J., Xu, X., Yin, H., Li, M., Wu, S., Hu, S., Hao, L. and Zhang, Z. (2017). Rice expression database (RED): an integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 44(5): 235-41.
46. Zhang, J., Jia, W., Yang, J. and Ismail, A.M. (2006). Role of ABA in integrating plant responses to drought and salt stresses. Journal of Field Crops Research, 97: 111-119.
47. Zhang, J., Li, Y., Guo, J., Du, B., He, G., Zhang, Y., Chen, R. and Li, J. (2018). Lipid profiles reveal different responses to brown planthopper infestation for pest susceptible and resistant rice plants. Metabolomics, 14(9): 120.
48. Zheng, M., Tao, Y., Hussain, S., Jiang, Q., Peng, S., Huang, J., Cui, K. and Nie, L. (2016). Seed priming in dry direct-seeded rice: consequences for emergence, seedling growth and associated metabolic events under drought stress. Plant Growth Regulation, 78(2): 167-178.
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Saberi Kuchesfahani A, Sabouri A, Abedi A, Aalami A, Razavipour T. Identification of Genes and Molecular Markers Associated with Germination Components in F9 Lines of Rice under Osmotic Stress. pgr 2020; 7 (1) :161-180
URL: http://pgr.lu.ac.ir/article-1-203-en.html


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Volume 7, Issue 1 (2020) Back to browse issues page
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