Physiological Response of Selected Rice Accessions to Salinity and In Silico Analysis of DREB1A Gene Among Diploid Oryza Species
DOI:
https://doi.org/10.56919/usci.1222.014Keywords:
Salinity, Rice, DREB1A, Diploid Oryza, Transcription FactorAbstract
The responses of selected rice accessions to variant salt concentrations and in-silico analysis of DREB1A gene among diploid Oryza species were evaluated. Ten (10) rice accessions were selected based on their popularity in farmer's fields. Seedlings of each variety (one per pot) were watered with variant salt concentrations of 0mM, 100mM and 200mM for 21 days. The morpho-physiological characters (plant height, number of tillers, root length and dry weight) were evaluated using a standard evaluation system for rice. The reference sequences of OsDREB1A and AtDREB1A were used as queries to search against the 10 diploid Oryza species in the BLASTN of the PlantEnsembl database to reveal DREB1A orthologs. The retrieved DREB1A orthologs were used to compute the physicochemical properties of their proteins, gene motifs, intron-exon architecture and phylogenetic relationship. The studied accessions showed significant differences (p<0.05) in morpho-physiological responses to salinity. The accessions Zaqama, Yar-Garnaki, Yar-Yuti, Samira and Chana-Beru performed better under salt stress and there was no significant difference (p>0.05) between the control and salt-treated groups. Additionally, the in-silico analysis of DREB1A gene identified 10 orthologs with conserved single transcript, AP2 domain and unstable protein (characteristics of TFs) across the 10 diploid Oryza species. Phylogenetic analysis revealed 3 clusters of African rice and its progenitor, Asian rice and their relatives and O. brachyantha/O. punctata complex, similar to the evolution of rice species. Conclusively, salt stress affects rice in a concentration-dependent manner and DREB1A gene is a conserved plant transcription factor (TF) across diploid Oryza species.
References
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W. and Noble, W. S. (2009). MEME Suite: tools for motif discovery and searching. Nucleic Acids Residue 37(Suppl 2): W202–W208. https://doi.org/10.1093/nar/gkp335.
Cao, Y., Duan, L., Li, H., Sun, X., Zhao, Y. and Xu, C. (2001). Functional analysis of Xa3/Xa26 family members in rice resistance to Xanthomonas Oryzae pv. Oryzae. Theoretical and Applied Genetics 115(7), 887–895. http://www.ncbi.nlm.nih.gov/pubmed/176 57469.
Chen, H., An, R., Tang, J. H., Cui, X. H., Hao, F. S., Chen, J. and Wang, X. C. (2007). Over-expression of a vacuolar Na+/H+ antiporter gene improves salt tolerance in upland rice. Molecular Breeding 19, 215–225. https://doi.org/10.1007/s11032-006-9048-8.
Cominelli, E., Conti, L., Tonelli, C. and Galbiati, M. (2013). Challenges and perspectives to improve crop drought and salinity tolerance. New Biotechnology 30, 355-361. https://doi.org/10.1016/j.nbt.2012.11.001.
Dubouzet, J.G.; Sakuma, Y.; Ito, Y.; Kasuga, M.; Dubouzet, E.D.; Miura, S.; Seki, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. OsDREB genes in rice Oryza sativa L.; encoded transcription activators that function in drought, high salt- and cold-responsive gene expression. Plant Journal 2003, 33, 751–763. https://doi.org/10.1046/j.1365-313X.2003.01661.x.
Eckardt, N. A. (2009). The future of science: Food and water for life. Plant Cell 21, 368–372. https://doi.org/10.1105/tpc.109.066209.
Fathelrahman, S. A., Alsadig, A. I. and Dagash, Y. I. (2015). Genetic Variability in Rice Genotypes (Oryza Sativa L.) in Yield and Yield Component under Semi-Arid Zone (Sudan). Journal of Forest Products and Industries, 4(2): 21-32.
FAO (2009). Declaration of the World Summit on Food Security. Rome, Italy, 16–18 November 2009. http://www.Fao.Org/wsfs/world-summit/wsfs-challenges/en/. Accessed on 20 August 2016. https://doi.org/10.1080/09614524.2010.491540.
Filiz, E.; Tombuloglu, H. In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses. Appl. Biochem. Biotechnol. 2014, 174, 1272–1285. https://doi:10.1007/s12010-014-1093-x.
Ganie, S. A. Pani, D. R and Mondal T. K (2017). Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PLoS ONE 12(8), e0182469. https://doi.org/10.1371/journal.pone.0182469.
Gumi, A. M., Guha, P. K., Mazumder, A., Jayaswal, P. and Mondal, T. K. (2018). Characterization of OglDREB2A gene from African rice (Oryza glaberrima), comparative analysis and its transcriptional regulation under salinity stress. 3 Biotech 8, 91-96. https://doi.org/10.1007/s13205-018-1098-1.
Guo, B., Wei, Y., Xu, R., Lin, S., Luan, H., Lv, C., Zhang, X., Song, X. and Xu, R. (2016). Genome-wide analysis of APETALA2/ethylene-responsive factor (AP2/ERF) gene family in barley (HordeumÀvulgare L.). PLoS ONE 11, e0161322. https://doi.org/10.1371/jourlnal.ponel.0161l322.
Hu, J., Xiao, C., Cheng, M. X., Gao, G. J., Zhang, Q. L. and He, Y. Q. (2015). A new finely mapped Oryza australiensis-derived QTL in rice confers resistance to brown planthopper. Gene 561(1):132–137. http://www.ncbi.nlm.nih.gov/pubmed/25682936. https://doi.org/10.1016/j.gene.2015.02.026.
Hussain, S., Ramzan, M., Aslam, M., Zaheen, M. and Ehsan, S. M. (2005). Effect of Various Stand Establishment Method on Yield and Yield Components of Rice. Proceedings of the International Seminar on Rice Crop. October 23. Rice Research Institute, Kala Shah Kau, Pakistan. 212-220.
Islam, F., Yasmeen, T., Ali, S., Ali, B., Farooq, M. A. and Gill, R. A. (2015b). Priming-induced antioxidative responses in two wheat cultivars under salinity stress. Acta Physiologiae Plantarum 37, 153-161. https://doi.org/10.1007/s11738-015-1897-5.
Islam, T., Manna, M. and Reddy, M. K. (2015a). Glutathione peroxidase of Pennisetum glaucum (PgGPx) is a functional Cd21 dependent peroxiredoxin that enhances tolerance against salinity and drought stress. PLoS ONE 10, e0143344. https://doi.org/10.1371/journal.pone.0143344.
Jin, M., Kumar, S. and Weemhoff, J. (2017). Cytochrome P450-mediated phytoremediation using transgenic plants: a need for engineered cytochrome P450 enzymes. Journal of Petroleum and Environmental Engineering 29(6), 997–1003
Kersey, P. J., Allen, J. E., Armean, I., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C. and Humphrey, J. (2016). Ensembl genomes 2016: more genomes, more complexity. Nucleic Acid Research 44(D1), D574–D580. https://doi.org/10.1093/nar/gkv1209.
Lafitte, H. R., Ismail, A. M. and Bennett, J. (2004). Abiotic stress tolerance in rice for Asia: Progress and future. In Proceedings of the 4th International Crop Science Congress, Brisbane, Australia, 26 September–1 October 2004.
Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought and low-temperature responsive gene expression, respectively, in Arabidopsis. Plant Cell 10, 1391–1406. https://doi.org/10.1105/tpc.10.8.1391.
Liu, S., Wang, X., Wang, H., Xin, H., Yang, X., Yan, J., Li, J., Tran, L. S. P., Shinozaki, K., Yamaguchi-Shinozaki, K. and Qin, F. (2013). Genome wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L. PLoS Genetics 9, https://doi.org/10.1371/journal.pgen.1003790
Matlin, A. J., Clark, F. and Smith, C. W. J. (2005). Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386–398. https://doi.org/10.1038/nrm1645.
Matsukura, S., Mizoi, J., Yoshida, T., Todaka, D., Ito, Y., Maruyama, K., Shinozaki, K., Yamaguchi-Shinozaki, K. (2010). Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress responsive genes. Molecular Genetics and Genomics 283, 185-196. https://doi.org/10.1007/s00438-009-0506-y.
Munns, R. (2002). Comparative physiology of salt and water stress. Plant Cell Environment 25, 239-250. https://doi.org/10.1046/j.0016-8025.2001.00808.x.
Qin, F., Kakimoto, M., Sakuma, Y., Maruyama, K., Osakabe, Y., Tran, L. S., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2007). Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. Plant Journal 50, 54–69. https://doi.org/10.1111/j.1365-313X.2007.03034.x.
Quan, R., Wang, J., Hui, J., Bai, H., Lyu, X., Zhu, Y., Zhang, H., Zhang, Z., Li, S., & Huang, R. (2017). Improvement of Salt Tolerance Using Wild Rice Genes. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.02269.
Rashid, M., Nuruzzaman, M., Hassan, L. and Begum, S. (2017). Genetic Variability Analysis for Various Yield Attributing Traits in Rice Genotypes. Journal of the Bangladesh Agricultural University 15 (1): 15-19. https://doi.org/10.3329/jbau.v15i1.33525.
Ruan, C. J., Da Silva, J. A. T., Mopper, S., Qin, P. and Lutts, S. (2010). Halophyte improvement for a salinized world. Critical Reviews in Plant Sciences 29, 329-359. https://doi.org/10.1080/07352689.2010.524517.
Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2006). Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18, 1292–1309. https://doi.org/10.1105/tpc.105.035881.
Seck, P. A., Tollens, E., Wopereis, M. C. S., Diagne, A. and Bamba, I. (2010). Rising trends and variability of rice prices: threats and opportunities for Sub-Saharan Africa. Food Policy 35, 403–411. https://doi: 10.1016/j.foodpol.2010.05.003.
Sweeney, M. and McCouch, S. (2007). The complex history of the domestication of Rice. Annals of Botany 100, 951–957. https://doi.org/10.1093/aob/mcm128.
Szakonyi, D. and Duque, P. (2018). Alternative Splicing as a Regulator of Early Plant Development. Front. Plant Sci. 9, 1174. doi:10.3389/fpls.2018.01174.
Tamura, K. J., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2011). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725–2729. https://doi.org/10.1093/molbev/mst197.
United Nations Population Fund (2014). Linking Population, Poverty and Development. http://www.unfpa.org/pds/trends.htm.
Upadhyaya, H. D. (1996). Crop Germplasm and wild relatives: a source of novel variation for crop improvement. Korean Journal of Crop Sciences 53, 12–17.
Upadhyaya, H. D., Reddy, L. J., Gowda, C. L. L. and Singh, S. (2009). Phenotypic diversity in cold-tolerant peanut (Arachis hypogaea L.) germplasm. Euphytica 165, 279–291. https://doi: 10.1007/s10681-008-9786-2
Van Ittersum, M. K., Van Bussel, L. G. J., Wolf, J., Grassini, P., Van Wart, J., Guilpart, N., Claessens, L., De Groot, H., Wiebe, K., Mason-D'Croz, D., Yang, H., Boogaard, H., Van Oort, P. A. J., Van Loon, M. P., Saito, K., Adimo, O., Adjei-Nsiah, S., Agali, A., Bala, A., Chikowo, R., Kaizzi, K., Kouressy, M., Makoi, J. H. J. R., Ouattara, K., Tesfaye, K. and Cassman, K. G. (2016). Can sub-Saharan Africa feed itself? Proceedings of National Academy of Science U. S. A. 113, 14964–14969. https://doi.org/10.1073/pnas.1610359113.
Van-Oort, P. A. J. and Zwart, S. J. (2018). Projected climate conditions for rice production systems in Africa. Africa Rice GIS Report – 1. Africa Rice Center, Cotonou, Benin.
Wambugu, P. W., Ndjiondjop, N., & Henry, R. (2019). Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud.). Plants 8(10), 376. https://doi.org/10.3390/plants8100376.
Wang, F. Wang, C. Liu, P. Lei, C. Hao, W. Gao, Y. Liu, Y. G and Zhao, K (2019). Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OSERF922. PLoS ONE 11, e0154027. https://doi.org/10.1371/journal.pone.0154027.
Wuchty, S., Oltvai, Z. N. and Barabási, A. L. (2003). Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genetics 35, 176–179. https://doi.org/10.1038/ng1242.
Yamaguchi-Shinozaki, K. and Shinozaki, K. (1994). A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature or high-salt stress. Plant Cell 6, 251–264. https://doi.org/10.1105/tpc.6.2.251.
Zhu, J. K. (2001). Plant salt tolerance. Trends Plant Science 6, 66–71. https://doi.org/10.1016/S1360-1385(00)01838-0.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2022 UMYU Scientifica
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
