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Burgos, N., Sales, M., Song, J., Ren, Y., & de los Reyes, B. (2014). N-starvation and supplementation in weedy red rice. BioStudies, E-GEOD-59438. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-GEOD-59438. Cai, H., Lu, Y., Xie, W., Zhu, T., & Lian, X. (2012). Transcriptome response to nitrogen starvation in rice. Journal of Biosciences, 37, 731-747. https://doi.org/10.1007/s12038-012-9242-2 Cao, P., Jung, K. H., Choi, D., Hwang, D., Zhu, J., & Ronald, P. C. (2012). The rice oligonucleotide array database: an atlas of rice gene expression. Rice, 5, 1-9. https://doi.org/10.1186/1939-8433-5-17 Chaturvedi, I. (2005). Effect of nitrogen fertilizers on growth, yield and quality of hybrid rice (Oryza sativa). Journal of Central European Agriculture, 6(4), 611-618. https://hrcak.srce.hr/17330 Chen, X. P., Zhu, Y. G., Hong, M. N., Kappler, A., & Xu, Y. X. (2008). Effects of different forms of nitrogen fertilizers on arsenic uptake by rice plants. Environmental Toxicology and Chemistry: An International Journal, 27(4), 881-887. https://doi.org/10.1897/07-368.1 Curie, C., & Briat, J. F. (2003). Iron transport and signaling in plants. Annual Review of Plant Biology, 54(1), 183-206. https://doi.org/10.1146/annurev.arplant.54.031902.135018 Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003). DAVID: database for annotation, visualization, and integrated discovery. Genome Biology, 4, 1-11. https://doi.org/10.1186/gb-2003-4-9-r60 Durrani, I. S., Jan, A., Shah, S., Iqbal, A., Ahmad, D., Khan, H., & Naqvi, S. M. S. (2020). Bioinformatics studies of OSGLP8-12 gene from oryza sativa (japonica) reveal its role in conferring resistance against disease and stresses. Pakistan Journal of Botany, 52(2), 461-467. http://dx.doi.org/10.30848/PJB2020-2(23 Ethan, S., Odunze, A. C., Abu, S. T., & Iwuafor, E. N. O. (2011). Effect of water management and nitrogen rates on iron concentration and yield in lowland rice. Agriculture and Biology Journal of North America, 2(4), 622-629. 10.5251/abjna.2011.2.4.622.629 Feng, H., Fan, X., Miller, A. J., & Xu, G. (2020). Plant nitrogen uptake and assimilation: regulation of cellular pH homeostasis. Journal of Experimental Botany, 71(15), 4380-4392. https://doi.org/10.1093/jxb/eraa150 Groen, S. C., Ćalić, I., Joly-Lopez, Z., Platts, A. E., Choi, J. Y., Natividad, M., ... & Purugganan, M. D. (2020). The strength and pattern of natural selection on gene expression in rice. Nature, 578(7796), 572-576. https://doi.org/10.1038/s41586-020-1997-2 Hsieh., P. H., Kan., C. C., Wu., H. U., Yang., H. C., & Hsieh M. H. (2018). Early molecular events associated with nitrogen deficiency in rice seedling roots.. Scientific Reports, 8(1), 12207-12207. https://doi.org/10.1038/S41598-018-30632-1 Hou, W., Yan, J., Jákli, B., Lu, J., Ren, T., Cong, R., & Li, X. (2018). Synergistic effects of nitrogen and potassium on quantitative limitations to photosynthesis in rice (Oryza sativa L.). Journal of Agricultural and Food Chemistry, 66(20), 5125-5132. https://doi.org/10.1021/acs.jafc.8b01135 Huang, X., Zhang, Y., Wang, L., Dong, X., Hu, W., Jiang, M., ... & Wu, Y. (2021). OsDOF11 affects nitrogen metabolism by sucrose transport signaling in rice (Oryza sativa L.). Frontiers in Plant Science, 12, 703034. https://doi.org/10.3389/fpls.2021.703034 Imam, Y. (2017). Cereal Production. Shiraz, Shiraz University Press. (in Persian) Kobayashi, T., Nozoye, T., & Nishizawa, N. K. (2019). Iron transport and its regulation in plants. Free Radical Biology and Medicine, 133, 11-20. https://doi.org/10.1016/j.freeradbiomed.2018.10.439 Li, Q., Lu, X., Wang, C., Shen, L., Dai, L., He, J., ... & Zeng, D. (2022). Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen‐deficiency tolerance in rice. The Crop Journal, 10(4), 942-951. https://doi.org/10.1016/j.cj.2021.12.006. Liang, T., Yuan, Z., Fu, L., Zhu, M., Luo, X., Xu, W., ... & Wu, X. (2021). Integrative transcriptomic and proteomic analysis reveals an alternative molecular network of glutamine synthetase 2 corresponding to nitrogen deficiency in rice (Oryza sativa L.). International Journal of Molecular Sciences, 22(14), 7674. https://doi.org/10.3390/ijms22147674 Nazish, T., Arshad, M., Jan, S. U., Javaid, A., Khan, M. H., Naeem, M. A., ... & Ali, M. (2021). Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.). Transgenic Research, 1-20. https://doi.org/10.1007/s11248-021-00284-5 Sabouri, H. S. M. Hosseini. (2017). Rice. Gonbad Kavous. Gonbad Kavous University Press and Noruzi. (in Persian) Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L., Lotia, S., ... & Ideker, T. (2012). A travel guide to Cytoscape plugins. Nature Methods, 9(11), 1069-1076. https://doi.org/10.1038/nmeth.2212 Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., ... & Lohmann, J. U. (2005). A gene expression map of Arabidopsis thaliana development. Nature Genetics, 37(5), 501-506. https://doi.org/10.1038/ng1543 Shao, C.-H., Qiu, C.-F., Qian, Y.-F., & Liu, G.-R. (2020). Nitrate deficiency decreased photosynthesis and oxidation-reduction processes, but increased cellular transport, lignin biosynthesis and flavonoid metabolism revealed by RNA-Seq in Oryza sativa leaves. PLoS One, 15(7), e0235975. https://doi.org/10.1371/journal.pone.0235975 Sherman, B. T., Hao, M., Qiu, J., Jiao, X., Baseler, M. W., Lane, H. C., ... & Chang, W. (2022). DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research, 50(W1), W216-W221. https://doi.org/10.1093/nar/gkac194 Sun, J., Ye, M., Peng, S., & Li, Y. (2016). Nitrogen can improve the rapid response of photosynthesis to changing irradiance in rice (Oryza sativa L.) plants. Scientific Reports, 6(1), 31305. https://doi.org/10.1038/srep31305 Sun, L., Di, D. W., Li, G., Li, Y., Kronzucker, H. J., & Shi, W. (2020). Transcriptome analysis of rice (Oryza sativa L.) in response to ammonium resupply reveals the involvement of phytohormone signaling and the transcription factor OsJAZ9 in reprogramming of nitrogen uptake and metabolism. Journal of Plant Physiology, 246, 153137. https://doi.org/10.1016/j.jplph.2020.153137 Tabuchi, M., Abiko, T., & Yamaya, T. (2007). Assimilation of ammonium ions and reutilization of nitrogen in rice (Oryza sativa L.). Journal of Experimental Botany, 58(9), 2319-2327. https://doi.org/10.1093/jxb/erm016 Tantray, A. Y., Bashir, S. S., & Ahmad, A. (2020). Low nitrogen stress regulates chlorophyll fluorescence in coordination with photosynthesis and Rubisco efficiency of rice. Physiology and Molecular Biology of Plants, 26, 83-94. https://doi.org/10.1007/s12298-019-00721-0 Ueda, Y., Ohtsuki, N., Kadota, K., Tezuka, A., Nagano, A. J., Kadowaki, T., ... & Yanagisawa, S. (2020). Gene regulatory network and its constituent transcription factors that control nitrogen‐deficiency responses in rice. New Phytologist, 227(5), 1434-1452. https://doi.org/10.1111/nph.16627 Varotto, C., Maiwald, D., Pesaresi, P., Jahns, P., Salamini, F., & Leister, D. (2002). The metal ion transporter IRT1 is necessary for iron homeostasis and efficient photosynthesis in Arabidopsis thaliana. The Plant Journal, 31(5), 589-599. https://doi.org/10.1046/j.1365-313X.2002.01381.x Wairich, A., de Oliveira, B. H. N., Arend, E. B., Duarte, G. L., Ponte, L. R., Sperotto, R. A., ... & Fett, J. P. (2019). The combined strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa). Scientific Reports, 9(1), 16144. https://doi.org/10.1038/s41598-019-52502-0 Wang, D., Xu, T., Yin, Z., Wu, W., Geng, H., Li, L., ... & Lian, X. (2020). Overexpression of OsMYB305 in rice enhances the nitrogen uptake under low-nitrogen condition. Frontiers in plant science, 11, 369. https://doi.org/10.3389/fpls.2020.00369 Wang, F., Wang, Y., Ying, L., Lu, H., Liu, Y., Liu, Y., ... & Mao, C. (2023). Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice. Frontiers in Plant Science, 14, 1164441. https://doi.org/10.3389/fpls.2023.1164441 Wang, L., Xie, W., Chen, Y., Tang, W., Yang, J., Ye, R., ... & Zhang, Q. (2010). A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal, 61(5), 752-766. https://doi.org/10.1111/j.1365-313X.2009.04100.x Wang, Y., Wang, D., Tao, Z., Yang, Y., Gao, Z., Zhao, G., & Chang, X. (2021). Impacts of nitrogen deficiency on wheat (Triticum aestivum L.) grain during the medium filling stage: transcriptomic and metabolomic comparisons. Frontiers in Plant Science, 12, 674433. https://doi.org/10.3389/fpls.2021.674433 Wang, Y., Zhang, P., Li, M., Guo, Z., Ullah, S., Rui, Y., & Lynch, I. (2020). Alleviation of nitrogen stress in rice (Oryza sativa) by ceria nanoparticles. Environmental Science: Nano, 7(10), 2930-2940. https://doi.org/10.1039/D0EN00757A Wen, B., Li, C., Fu, X., Li, D., Li, L., Chen, X., ... & Gao, D. (2019). Effects of nitrate deficiency on nitrate assimilation and chlorophyll synthesis of detached apple leaves. Plant Physiology and Biochemistry, 142, 363-371. https://doi.org/10.1016/j.plaphy.2019.07.007 Yang, S. Y., Hao, D. L., Song, Z. Z., Yang, G. Z., Wang, L., & Su, Y. H. (2015). RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies. Gene, 555(2), 305-317. http://dx.doi.org/10.1016/j.gene.2014.11.021 Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R. Y., ... & Margalit, H. (2004). Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction. Proceedings of the National Academy of Sciences, 101(16), 5934-5939. https://doi.org/10.1073/pnas.0306752101 Zakari, S. A., Asad, M. A. U., Han, Z., Zhao, Q., & Cheng, F. (2020). Relationship of nitrogen deficiency-induced leaf senescence with ROS generation and ABA concentration in rice flag leaves. Journal of Plant Growth Regulation, 39, 1503-1517. https://doi.org/10.1007/s00344-020-10128-x