Agnihotri, A., Gupta, P., Dwivedi, A. and Seth, C.S. (2018). Counteractive mechanism (s) of salicylic acid in response to lead toxicity in Brassica juncea (L.) Czern. cv. Varuna. Planta, 248(1): 49-68. https://doi.org/10.1007/s00425-018-2867-0
Ali, J., Jewel, Z.A., Mahender, A., Anandan, A., Hernandez, J. and Li, Z. (2018). Molecular genetics and breeding for nutrient use efficiency in rice. International Journal of Molecular Sciences, 19(6): 1762. https://doi.org/10.3390/ijms19061762
Armijo, G. and Gutiérrez, R.A. (2017). Emerging players in the nitrate signaling pathway. Molecular Plant, 10(8): 1019-1022. https://doi.org/10.1016/j.molp.2017.07.006
Bernard, S.M. and Habash, D.Z. (2009). The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling. New Phytologist, 182(3): 608-620. https://doi.org/10.1111/j.1469-8137.2009.02823.
Biswas, K.K., Palchoudhury, S., Chakraborty, P., Bhattacharyya, U.K., Ghosh, D.K., Debnath, P., Ramadugu, C., Keremane, M.L., Khetarpal, R.K. and Lee, R.F. (2019). Codon usage bias analysis of citrus tristeza virus: Higher codon adaptation to citrus reticulata host. Viruses, 11(4): 331. https://doi.org/10.3390/v11040331
Chen, H., Sun, S., Norenburg, J.L. and Sundberg, P. (2014). Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea). PloS One, 9(1): e85631. https://doi.org/10.1371/journal .pone.0085631
Chin, C.H., Chen, S.H., Wu, H.H., Ho, C.W., Ko, M.T. and Lin, C.Y. (2014). CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Systems Biology, 8(Suppl 4): 1-7. https://doi.org/10.1186/1752-0509-8-S4-S11
Clément, G., Moison, M., Soulay, F., Reisdorf-Cren, M. and Masclaux-Daubresse, C. (2018). Metabolomics of laminae and midvein during leaf senescence and source–sink metabolite management in Brassica napus L. leaves. Journal of Experimental Botany, 69(4): 891-903. https://doi.org/10.1093/jxb/erx253
Cramer, G.R., Läuchli, A. and Epstein, E. (1986). Effects of NaCl and CaCl2 on ion activities in complex nutrient solutions and root growth of cotton. Plant Physiology, 81(3): 792-797. https://doi.org/10.1104/pp.81.3.792
Delamare, J., Brunel-Muguet, S., Morvan-Bertrand, A., Cantat, O., Firmin, S., Trinsoutrot-Gattin, I., Le Franc, L. and Personeni, E. (2023). Thermopriming effects on root morphological traits and root exudation during the reproductive phase in two species with contrasting strategies: Brassica napus (L.) and Camelina sativa (L.) Crantz. Environmental and Experimental Botany, 210: 105318. https://doi.org/10.1016/j.envexpbot.2023.105318
Gao, Z., Wang, Y., Chen, G., Zhang, A., Yang, S., Shang, L., Wang, D., Ruan, B., Liu, C., Jiang, H., Dong, G., Zhu, L., Hu, J., Zhang, G., Zeng, D., Guo, L., Xu, G., Teng, S., Harberd, N. and Qian, Q. (2019). The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency. Nature Communications, 10(1): 5207. https://doi.org/10.1038/s41467-019-13110-8
Gaufichon, L., Masclaux‐Daubresse, C., Tcherkez, G., Reisdorf‐Cren, M., Sakakibara, Y., Hase, T., Clement, G., Avice, J. C., Grandjean, O., Marmagne, A., Mercey, S. B., Azzopardi, M., Soulay, F. and Suzuki, A. (2013). Arabidopsis thaliana ASN2 encoding asparagine synthetase is involved in the control of nitrogen assimilation and export during vegetative growth. Plant, Cell & Environment, 36(2): 328-342. https://doi.org/10.1111/j.1365-3040.2012.02576.x
Goel, P. and Singh, A.K. (2015). Abiotic stresses downregulate key genes involved in nitrogen uptake and assimilation in Brassica juncea L. Plos One, 10(11): e0143645. https://doi.org/10.1371/journal.pone.0143645
Han, M.L., Lv, Q.Y., Zhang, J., Wang, T., Zhang, C.X., Tan, R.J., Wang, Y.L., Zhong, L.Y., Gao, Y.Q., Chao, Z.F., Li, Q.Q., Chen, G.Y., Shi, Z., Lin, H.X. and Chao, D.Y. (2022). Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of Nitrate Reductase 1.2 in rice. Molecular Plant, 15(1): 167-178. https://doi.org/10.1016/j.molp.2021.09.005
Hasnain, A., Irfan, M., Bashir, A., Maqbool, A. and Malik, K.A. (2020). Transcription factor TaDof1 improves nitrogen and carbon assimilation under low-nitrogen conditions in wheat. Plant Molecular Biology Reporter, 38(3): 441-451. https://doi.org/10.1007/s11105-020-01208-z
He, X., Zhang, H., Ye, X., Hong, J. and Ding, G. (2021). Nitrogen assimilation related genes in Brassica napus: Systematic characterization and expression analysis identified hub genes in multiple nutrient stress responses. Plants, 10(10): 2160. https://doi.org/10.3390/plants10102160
Hershberg, R. and Petrov, D.A. (2008). Selection on codon bias. Annual Review of Genetics, 42(1): 287-299. https://doi.org/10.1146/annurev.genet.42.110807.091442
Hoshida, H., Tanaka, Y., Hibino, T., Hayashi, Y., Tanaka, A., Takabe, T. and Takabe, T. (2000). Enhanced tolerance to salt stress in transgenic rice that overexpresses chloroplast glutamine synthetase. Plant Molecular Biology, 43(1): 103-111. https://doi.org/10.1023/A:1006408712416
Hu, J., Zhao, X., Zhang, Z. and Yu, J. (2007). Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Research in Microbiology, 158(4): 363-370. https://doi.org/10.1016/j.resmic.2007.02.007
Hua, Y.P., Zhou, T., Huang, J.Y., Yue, C.P., Song, H.X., Guan, C.Y. and Zhang, Z.H. (2020). Genome-wide differential DNA methylation and miRNA expression profiling reveals epigenetic regulatory mechanisms underlying nitrogen-limitation-triggered adaptation and use efficiency enhancement in allotetraploid rapeseed. International Journal of Molecular Sciences, 21(22): 8453. https://doi.org/10.3390/ijms21228453
Huang, H., Rong, X., Song, H., Liu, Q., Liao, Q., Luo, J., Gu, J., Guan, C., Gong, J. and Zhang, Z. (2013). Effect of nitrate reductase (NR) inhibitor on NR activity in oilseed rape (Brassica napus L.) and its relation to nitrate content. Acta Agronomica Sinica, 39: 1668–1673. https://doi.org/10.3724/SP.J.1006.2013.01668
Huo, X., Liu, S., Li, Y., Wei, H., Gao, J., Yan, Y., Zhang, G. and Liu, M. (2021). Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJournal, 9: e10450. https://doi.org/10.7717/peerj.10450
Johnson, M.M., Hockenberry, A.J., McGuffie, M.J., Vieira, L.C. and Wilke, C.O. (2023). Growth-dependent gene expression variation influences the strength of codon usage biases. Molecular Biology and Evolution, 40(9): msad189. https://doi.org/10.1093/molbev/msad189
Joudaki, F., Ismaili, A., Sohrabi, S. S., Hosseini, S. Z. and Ahmadi, H. (2024). Conserved microRNAs and their target genes in Quercus infectoria. Plant Genetic Research, 10(2): 103-118 (In Persian). http://dx.doi.org/10.22034/PGR.10.2.8
Klimenko, S.B., Peshkova, A.A. and Dorofeev, N.V. (2006). Nitrate reductase activity during heat shock in winter wheat. Journal of Stress Physiology & Biochemistry, 2(1): 50-55.
Kolbert, Z., Ortega, L. and Erdei, L. (2010). Involvement of nitrate reductase (NR) in osmotic stress-induced NO generation of Arabidopsis thaliana L. roots. Journal of Plant Physiology, 167(1): 77-80. https://doi.org/10.1016/j.j plph.2009.08.013
Kumar, R., Taware, R., Gaur, V.S., Guru, S.K. and Kumar, A. (2009). Influence of nitrogen on the expression of TaDof1 transcription factor in wheat and its relationship with photo synthetic and ammonium assimilating efficiency. Molecular Biology Reports, 36(8): 2209-2220. https://doi.org/10.1007/s11033-008-9436-8
Lammerts van Bueren, E.T. and Struik, P.C. (2017). Diverse concepts of breeding for nitrogen use efficiency. A review. Agronomy for Sustainable Development, 37(5): 50. https://doi.org/10.1007/s13593-017-0457-3
Lea, U.S., Slimestad, R., Smedvig, P. and Lillo, C. (2007). Nitrogen deficiency enhances expression of specific MYB and bHLH transcription factors and accumulation of end products in the flavonoid pathway. Planta, 225(5): 1245-1253. https://doi.org/10.1007/s00425-006-0414-x
Lee, H.J., Abdula, S.E., Jang, D.W., Park, S.H., Yoon, U.H., Jung, Y.J., Kang, K.K., Nou, I.S. and Cho, Y.G. (2013). Overexpression of the glutamine synthetase gene modulates oxidative stress response in rice after exposure to cadmium stress. Plant Cell Reports, 32(10): 1521-1529. https://doi.org/10.1007/s00299-013-1464-8
Lee, S., Park, J., Lee, J., Shin, D., Marmagne, A., Lim, P.O., Masclaux-Daubresse, C., An, G. and Nam, H.G. (2020). OsASN1 overexpression in rice increases grain protein content and yield under nitrogen-limiting conditions. Plant and Cell Physiology, 61(7): 1309-1320. https://doi.org/10.1093/pcp/pcaa060
Li, G., Pan, Z., Gao, S., He, Y., Xia, Q., Jin, Y. and Yao, H. (2019). Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis. Genes & Genomics, 41(10): 1173-1181. https://doi.org/10.1007/s13258-019-00847-1
Li, M., Xu, J., Gao, Z., Tian, H., Gao, Y. and Kariman, K. (2020). Genetically modified crops are superior in their nitrogen use efficiency-A meta-analysis of three major cereals. Scientific Reports, 10(1): 8568. https://doi.org/10.1038/s41598-020-65684-9
Liu, H.C., Lämke, J., Lin, S. Y., Hung, M.J., Liu, K.M., Charng, Y.Y. and Bäurle, I. (2018). Distinct heat shock factors and chromatin modifications mediate the organ‐autonomous transcriptional memory of heat stress. The Plant Journal, 95(3): 401-413. https://doi.org/10.1111/tpj.13958
Liu, X., Hu, B. and Chu, C. (2022a). Nitrogen assimilation in plants: current status and future prospects. Journal of Genetics and Genomics, 49(5): 394-404. https://doi.org/10.1016/j.jgg.2021.12.006
Liu, H., Able, A.J. and Able, J.A. (2022b). Priming crops for the future: rewiring stress memory. Trends in Plant Science, 27(7): 699-716. https://doi.org/10.1016/j.tplants.2021.11.015
Livak, K.J. and Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods, 25(4): 402-408. https://doi.org/10.1006/meth.2001.1262
Marchi, L., Degola, F., Polverini, E., Tercé-Laforgue, T., Dubois, F., Hirel, B. and Restivo, F.M. (2013). Glutamate dehydrogenase isoenzyme 3 (GDH3) of Arabidopsis thaliana is regulated by a combined effect of nitrogen and cytokinin. Plant Physiology and Biochemistry, 73: 368-374. https://doi.org/10.1016/j.plaphy.2013.10.019
Meyer, C. and Stitt, M. (2001). Nitrate Reduction and Signalling. In: Lea, P.J. and Morot-Gaudry, J.F., Eds., Plant Nitrogen, pp. 61–78. Springer-Verlag, Berlin, DA. https://doi.org/10.1007/978-3-662-04064-5_2
Miller, A.J. and Cramer, M.D. (2005). Root nitrogen acquisition and assimilation. Plant and Soil, 274(1): 1-36. https://doi.org/10.1007/s11104-004-0965-1
Moayedinezhad, A., Mohammadparast, B., Hosseini Salekdeh, G., Mohsenifard, E. and Nejatian, M.A. (2019). Upstream regulatory elements, potential targets and expression patterns of three drought responsive miRNAs in two grapevine cultivars. Plant Genetic Research, 6(1): 115-126 (In Persian). https://doi.org/10.29252/pgr.6.1.115
Nair, A.U., Bhukya, D.P.N., Sunkar, R., Chavali, S. and Allu, A.D. (2022). Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants. Journal of Experimental Botany, 73(11): 3355-3371. https://doi.org/10.1093/jxb/erac089
Nath Choudhury, M., Uddin, A. and Chakraborty, S. (2017) Codon usage bias and its influencing factors for Y-linked genes in human. Computational Biology and Chemistry, 69: 77–86. https://doi.org/10.1016/j.compbiolchem.2017.05.005
Nguyen, G.N., Rothstein, S.J., Spangenberg, G. and Kant, S. (2015). Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. Frontiers in Plant Science, 6: 629. https://doi.org/10.3389/fpls.2015.00629
Peña, P.A., Quach, T., Sato, S., Ge, Z., Nersesian, N., Changa, T., Dweikat, I., Soundararajan, M. and Clemente, T.E. (2017). Expression of the maize Dof1 transcription factor in wheat and sorghum. Frontiers in Plant Science, 8: 434. https://doi.org/10.3389/fpls.2017.00434
Peng, M., Hannam, C., Gu, H., Bi, Y.M. and Rothstein, S.J. (2007). A mutation in NLA, which encodes a RING‐type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation. The Plant Journal, 50(2): 320-337. https://doi.org/10.1111/j.1365-313X.2007.03050.x
Pfaffl, M.W., Horgan, G.W. and Dempfle, L. (2002). Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Research, 30(9): e36-e36. https://doi.org/10.1093/nar/30.9.e36
Plotkin, J.B. and Kudla, G. (2011). Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews Genetics, 12(1): 32-42. https://doi.org/10.1038/nrg2899
Rani, A., Singh, S., Yadav, P., Arora, H., Kaur, I. and Dhaka, N. (2023). MicroRNAs for understanding and improving agronomic traits in oilseed Brassicas. Plant Gene, 34: 100422. https://doi.org/10.1016/j.plgene.2023.100422
Rueda‐López, M., Crespillo, R., Cánovas, F. M. and Ávila, C. (2008). Differential regulation of two glutamine synthetase genes by a single Dof transcription factor. The Plant Journal, 56(1): 73-85. https://doi.org/10.1111/j.1365-313X.2008.03573.x
Samantaray, D., Vankanavath, A.B., Kadumuri, R.V., Ramadurai, D., Chavali, S. and Allu, A.D. (2023). Thermopriming mitigates the effects of heat stress by modulating the expression of Heat shock factors in Brassica juncea (Indian mustard). Environmental and Experimental Botany, 211: 105371. https://doi.org/10.1016/j.envexpbot. 2023.105371
Sedaghatmehr, M., Stüwe, B., Mueller-Roeber, B. and Balazadeh, S. (2022). Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6. Journal of Experimental Botany, 73(18): 6394-6404. https://doi.org/10.1093/jxb/erac257
Sharp, P.M. and Li, W.H. (1986). An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24(1): 28-38. https://doi.org/10.1007/BF02099948
Sharp, P.M. and Li, W.H. (1987). The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3): 1281-1295. https://doi.org/10.1093/nar/15.3.1281
Sharp, P.M., Stenico, M., Peden, J.F. and Lloyd, A.T. (1993). Codon usage: mutational bias, translational selection, or both?. Biochemical Society Transactions, 21(4): 835-841. https://doi.org/10.1042/bst0210835
Shen, Z., Gan, Z., Zhang, F., Yi, X., Zhang, J. and Wan, X. (2020). Analysis of codon usage patterns in citrus based on coding sequence data. BMC Genomics, 21(Suppl 5): 234. https://doi.org/10.1186/s12864-020-6641-x
Srivastava, S., Chanyal, S., Dubey, A., Tewari, A.K. and Taj, G. (2019). Patterns of codon usage bias in WRKY genes of Brassica rapa and Arabidopsis thaliana. Journal of Agricultural Science, 11(4): 76. https://doi.org/10.5539/jas.v11n4p76
Sueoka, N. (1988). Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences, 85(8): 2653-2657. https://doi.org/10.1073/pnas.85.8.2653
Tang, Y., Sun, X., Hu, C., Tan, Q. and Zhao, X. (2013). Genotypic differences in nitrate uptake, translocation and assimilation of two Chinese cabbage cultivars [Brassica campestris L. ssp. Chinensis (L.)]. Plant Physiology and Biochemistry, 70: 14-20. https://doi.org/10.1016/j.plaphy.2013.04.027
Tang, W., He, X., Qian, L., Wang, F., Zhang, Z., Sun, C., Lin, L. and Guan, C. (2019). Comparative transcriptome analysis in oilseed rape (Brassica napus) reveals distinct gene expression details between nitrate and ammonium nutrition. Genes, 10(5): 391. https://doi.org/10.3390/genes10050391
Thomsen, H.C., Eriksson, D., Møller, I.S. and Schjoerring, J.K. (2014). Cytosolic glutamine synthetase: a target for improvement of crop nitrogen use efficiency?. Trends in Plant Science, 19(10): 656-663. https://doi.org/10.1016/j.tplants.2014.06.002
Ueda, Y. and Yanagisawa, S. (2018). Transcription Factor-Based Genetic Engineering to Increase Nitrogen Use Efficiency. In: Shrawat, A., Zayed, A. and Lightfoot, D., Eds., Engineering Nitrogen Utilization in Crop Plants, PP. 37-55. Springer, Cham. https://doi.org/10.1007/978-3-319-92958-3_3
Wang, G., Ding, G., Li, L., Cai, H., Ye, X., Zou, J. and Xu, F. (2014). Identification and characterization of improved nitrogen efficiency in interspecific hybridized new-type Brassica napus. Annals of Botany, 114(3): 549-559. https://doi.org/10.1093/aob/mcu135
Wang, F., Yoshida, H. and Matsuoka, M. (2021a). Making the ‘Green Revolution’truly green: improving crop nitrogen use efficiency. Plant and Cell Physiology, 62(6): 942-947. https://doi.org/10.1093/pcp/pcab051
Wang, Y., Hua, Y.P., Zhou, T., Huang, J.Y. and Yue, C.P. (2021b). Genomic identification of nitrogen assimilation-related genes and transcriptional characterization of their responses to nitrogen in allotetraploid rapeseed. Molecular Biology Reports, 48(8): 5977-5992. https://doi.org/10.1007/s11033-021-06599-0
Wong, H.K., Chan, H.K., Coruzzi, G.M. and Lam, H.M. (2004). Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis. Plant Physiology, 134(1): 332-338. https://doi.org/10.1104/pp.103.033126
Xu, Y., Liu, K., Han, Y., Xing, Y., Zhang, Y., Yang, Q. and Zhou, M. (2021). Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris. Microbial Cell Factories, 20(1): 91. https://doi.org/10.1186/s12934-021-01580-9
Yan, L. U., Gong, Y., Luo, Q., Dai, G.X., Teng, Z., He, Y., Wu, X., Liu, C., Tang, D., Ye, N., Deng, G., Lin, J. and Liu, X. (2021). Heterologous expression of fungal AcGDH alleviates ammonium toxicity and suppresses photorespiration, thereby improving drought tolerance in rice. Plant Science, 305: 110769. https://doi.org/10.1016/j.plantsci.2020.110769
Yanagisawa, S., Akiyama, A., Kisaka, H., Uchimiya, H. and Miwa, T. (2004). Metabolic engineering with Dof1 transcription factor in plants: improved nitrogen assimilation and growth under low-nitrogen conditions. Proceedings of the National Academy of Sciences, 101(20): 7833-7838. https://doi.org/10.1073/pnas.0402267101
Yang, M., Liu, J., Yang, W., Li, Z., Hai, Y., Duan, B., Zhang, H., Yang, X. and Xia, C. (2023a). Analysis of codon usage patterns in 48 Aconitum species. BMC Genomics, 24(1): 703. https://doi.org/10.1186/s12864-023-09650-5
Yang, Q., Xin, C., Xiao, Q.S., Lin, Y.T., Li, L. and Zhao, J.L. (2023b). Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. Frontiers in Plant Science, 14: 1304264. https://doi.org/10.3389/fpls.2023.1304264
Yu, J.L., Zhu, Z.K., Zhang, Z.H., Shu, J.B., Yang, C., Song, H.X. and Guan, C. (2014). Influence of glutamine synthase and glutamate synthase on N reutilization in Brassica napus under different nitrogen condition. Crops, 6: 81-85.
Yu, J., Xuan, W., Tian, Y., Fan, L., Sun, J., Tang, W., Chen, G., Wang, B., Liu, Y., Wu, W., Liu, X., Jiang, X., Zhou, C., Dai, Z., Xu, D., Wang, C. and Wan, J. (2021). Enhanced OsNLP4‐OsNiR cascade confers nitrogen use efficiency by promoting tiller number in rice. Plant Biotechnology Journal, 19(1): 167-176. https://doi.org/10.1111/pbi.13450
Zhang, Z.H., Zhou, T., Liao, Q., Yao, J.Y., Liang, G.H., Song, H.X., Guan, C.Y. and Hua, Y.P. (2018). Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation. BMC Plant Biology, 18(1): 322. https://doi.org/10.1186/s12870-018-1507-y
Zhou, T., Wu, P., Yue, C., Huang, J., Zhang, Z. and Hua, Y. (2022). Transcriptomic dissection of allotetraploid rapeseed (Brassica napus L.) in responses to nitrate and ammonium regimes and functional analysis of BnaA2. Gln1; 4 in Arabidopsis. Plant and Cell Physiology, 63(6): 755-769. https://doi.org/10.1093/pcp/pcac037
Zou, X., Guan, M. and Guan, C. (2022). Studies on plant morphological and physiological characteristics of high nitrogen absorption in Brassica napus L. Crops, 5: 97–103.
