PERTANIKA JOURNAL OF SOCIAL SCIENCES AND HUMANITIES

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• Abdullah‐Zawawi, M. R., Afiqah‐Aleng, N., Ikhwanuddin, M., Sung, Y. Y., Tola, S., Fazhan, H., & Waiho, K. (2021). Recent development in ecdysone receptor of crustaceans: Current knowledge and future applications in crustacean aquaculture. Reviews in Aquaculture, 13(4), 1938-1957. https://doi.org/10.1111/raq.12552

• Ai, Z., Wang, G., Liang, C., Liu, H., Zhang, J., Xue, S., & Liu, G. (2017). The effects of nitrogen addition on the uptake and allocation of macro- and micronutrients in Bothriochloa ischaemum on Loess Plateau in China. Frontiers in Plant Science, 8, 1476. https://doi.org/10.3389/fpls.2017.01476

• Awasthi, S., Chauhan, R., Indoliya, Y., Chauhan, A. S., Mishra, S. K., Agrawal, L., Dwivedi, S., Singh, S. N., Srivastava, S., Singh, P. C., Chauhan, P. S., Chakrabarty, D., Srivastava, S., & Tripathi, R. D. (2021). Microbial consortium mediated growth promotion and arsenic reduction in rice: An integrated transcriptome and proteome profiling. Ecotoxicology and Environmental Safety, 228, 113004. https://doi.org/10.1016/j.ecoenv.2021.113004

• Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Research, 37(suppl_2), W202–W208. https://doi.org/10.1093/nar/gkp335

• Bao, A., Liang, Z., Zhao, Z., & Cai, H. (2015). Overexpressing of OsAMT1-3, a high affinity ammonium transporter gene, modifies rice growth and carbon-nitrogen metabolic status. International Journal of Molecular Sciences, 16(5), 9037-9063. https://doi.org/10.3390/ijms16059037

• 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, 17. https://doi.org/10.1186/1939-8433-5-17

• Chen, J., Qi, T., Hu, Z., Fan, X., Zhu, L., Iqbal, M. F., Yin, X., Xu, G., & Fan, X. (2019). OsNAR2.1 positively regulates drought tolerance and grain yield under drought stress conditions in rice. Frontiers in Plant Science, 10, 197. https://doi.org/10.3389/fpls.2019.00197

• Coneva, V., Simopoulos, C., Casaretto, J. A., El-Kereamy, A., Guevara, D. R., Cohn, J., Zhu, T., Guo, L., Alexander, D. C., Bi, Y. M., McNicholas, P. D., & Rothstein, S. J. (2014). Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics, 15, 1056. https://doi.org/10.1186/1471-2164-15-1056

• Djaman, K., Mel, V., Ametonou, F., El-Namaky, R., Diallo, M., & Koudahe, K. (2018). Effect of nitrogen fertilizer dose and application timing on yield and nitrogen use efficiency of irrigated hybrid rice under semi-arid conditions. Journal of Agricultural Science and Food Research, 9(2), 1000223.

• Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. https://doi.org/10.1093/nar/gkh340

• Fenchel, T., King, G. M., & Blackburn, T. H. (2012). Transport mechanisms. Bacterial Biogeochemistry, 3(10), 35–47. https://doi.org/10.1016/b978-0-12-415836-8.00002-5

• Ferreira, L. M., de Souza, V. M., Tavares, O. C. H., Zonta, E., Santa-Catarina, C., de Souza, S. R., Fernandes, M. S., & Santos, L. A. (2015). OsAMT1.3 expression alters rice ammonium uptake kinetics and root morphology. Plant Biotechnology Reports, 9(4), 221–229. https://doi.org/10.1007/s11816-015-0359-2

• Food and Agriculture Organization of the United Nations. (2017). The future of food and agriculture – Trends and challenges. FAO. https://www.fao.org/3/i6583e/i6583e.pdf

• Forde, B. G. (2000). Nitrate transporters in plants: Structure, function and regulation. Biochimica et Biophysica Acta-Biomembranes, 1465(1–2), 219–235. https://doi.org/10.1016/S0005-2736(00)00140-1

• García, M. J., Angulo, M., García, C., Lucena, C., Alcántara, E., Pérez-Vicente, R., & Romera, F. J. (2021). Influence of ethylene signaling in the crosstalk between Fe, S, and P deficiency responses in Arabidopsis thaliana. Frontiers in Plant Science, 12, 643585. https://doi.org/10.3389/fpls.2021.643585

• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Eds.), The proteomics protocols handbook (pp. 571–607). Humana. https://doi.org/10.1385/1592598900

• Hoang, D. T., Hiroo, T., & Yoshinobu, K. (2019). Nitrogen use efficiency and drought tolerant ability of various sugarcane varieties under drought stress at early growth stage. Plant Production Science, 22(2), 250-261. https://doi.org/10.1080/1343943X.2018.1540277

• Hossain, M. A., Lee, Y., Cho, J. I., Ahn, C. H., Lee, S. K., Jeon, J. S., Kang, H., Lee, C. H., An, G., & Park, P. B. (2010). The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice. Plant Molecular Biology, 72(4), 557–566. https://doi.org/10.1007/s11103-009-9592-9

• Huang, S., Zhao, C., Zhang, Y., & Wang, C. (2018). Nitrogen use efficiency in rice. In A. Amanullah & S. Fahad (Eds.), Nitrogen in agriculture – Updates. IntechOpen. https://doi.org/10.5772/intechopen.69052

• Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., Langendijk-Genevaux, P. S., Pagni, M., & Sigrist, C. J. A. (2006). The PROSITE database. Nucleic Acids Research, 34(suppl_1), D227–D230. https://doi.org/10.1093/nar/gkj063

• Ishimaru, Y., Suzuki, M., Tsukamoto, T., Suzuki, K., Nakazono, M., Kobayashi, T., Wada, Y., Watanabe, S., Matsuhashi, S., Takahashi, M., Nakanishi, H., Mori, S., & Nishizawa, N. K. (2006). Rice plants take up iron as an Fe3+-phytosiderophore and as Fe2+. Plant Journal, 45(3), 335–346. https://doi.org/10.1111/j.1365-313X.2005.02624.x

• Izawa, T., Foster, R., & Chua, N. H. (1993). Plant bZIP protein DNA binding specificity. Journal of Molecular Biology, 230(4), 1131–1144. https://doi.org/10.1006/jmbi.1993.1230

• Jin, Z., Zhu, Y., Li, X., Dong, Y., & An, Z. (2015). Soil N retention and nitrate leaching in three types of dunes in the Mu Us desert of China. Scientific Reports, 5, 14222. https://doi.org/10.1038/srep14222

• Kabange, N. R., Park, S. Y., Lee, J. Y., Shin, D., Lee, S. M., Kwon, Y., Cha, J. K., Cho, J. H., Duyen, D. Van, Ko, J. M., & Lee, J. H. (2021). New insights into the transcriptional regulation of genes involved in the nitrogen use efficiency under potassium chlorate in rice (Oryza sativa L.). International Journal of Molecular Sciences, 22(4), 2192. https://doi.org/10.3390/ijms22042192

• Khan, M. R., Khan, I., Ibrar, Z., Léon, J., & Naz, A. A. (2017). Drought-responsive genes expressed predominantly in root tissues are enriched with homotypic cis-regulatory clusters in promoters of major cereal crops. Crop Journal, 5(3), 195–206. https://doi.org/10.1016/j.cj.2016.10.001

• Khazanah Research Institute. (2019). The status of the paddy and rice industry in Malaysia. Khazanah Research Institute. http://www.krinstitute.org/assets/contentMS/img/template/editor/20190409_RiceReport_Full%20Report_Final.pdf

• Kumar, S., Kumar, S., & Mohapatra, T. (2021). Interaction between macro‐ and micro-nutrients in plants. Frontiers in Plant Science, 12, 665583. https://doi.org/10.3389/fpls.2021.665583

• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054

• Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P., & Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1), 325–327. https://doi.org/10.1093/nar/30.1.325

• Letunic, I., & Bork, P. (2007). Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics, 23(1), 127–128. https://doi.org/10.1093/bioinformatics/btl529

• Liang, G., Zhang, H., Li, Y., Pu, M., Yang, Y., Li, C., Lu, C., Xu, P., & Yu, D. (2020). Oryza sativa FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT/OsbHLH156) interacts with OsIRO2 to regulate iron homeostasis. Journal of Integrative Plant Biology, 62(5), 668–689. https://doi.org/10.1111/jipb.12933

• Little, D. Y., Rao, H., Oliva, S., Daniel-Vedele, F., Krapp, A., & Malamy, J. E. (2005). The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues. Proceedings of the National Academy of Sciences of the United States of America, 102(38), 13693–13698. https://doi.org/10.1073/pnas.0504219102

• Liu, W., Xie, Y., Ma, J., Luo, X., Nie, P., Zuo, Z., Lahrmann, U., Zhao, Q., Zheng, Y., Zhao, Y., Xue, Y., & Ren, J. (2015). IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics, 31(20), 3359–3361. https://doi.org/10.1093/bioinformatics/btv362

• Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., Hurwitz, D. I., Lanczycki, C. J., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C., & Bryant, S. H. (2015). CDD: NCBI’s conserved domain database. Nucleic Acids Research, 43(D1), D222–D226. https://doi.org/10.1093/nar/gku1221

• Matthews, D. E., Carollo, V. L., Lazo, G. R., & Anderson, O. D. (2003). GrainGenes, the genome database for small-grain crops. Nucleic Acids Research, 31(1), 183–186. https://doi.org/10.1093/nar/gkg058

• Mering, C. Von, Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research, 31(1), 258–261. https://doi.org/10.1093/nar/gkg034

• Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., & Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research, 49(D1), D412–D419. https://doi.org/10.1093/nar/gkaa913

• Obara, M., Tamura, W., Ebitani, T., Yano, M., Sato, T., & Yamaya, T. (2010). Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions. Theoretical and Applied Genetics, 121, 535-547. https://doi.org/10.1007/s00122-010-1328-3

• Orsel, M., Krapp, A., & Daniel-Vedele, F. (2002). Analysis of the NRT2 nitrate transporter family in Arabidopsis. Structure and gene expression. Plant Physiology, 129(2), 886–896. https://doi.org/10.1104/pp.005280

• Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., & Vandepoele, K. (2015). PLAZA 3.0: An access point for plant comparative genomics. Nucleic Acids Research, 43(D1), D974–D981. https://doi.org/10.1093/nar/gku986

• Qian, X., Shen, Q., Xu, G., Wang, J., & Zhou, M. (2004). Nitrogen form effects on yield and nitrogen uptake of rice crop grown in aerobic soil. Journal of Plant Nutrition, 27(6), 1061–1076. https://doi.org/10.1081/PLN-120037536

• Ranade-Malvi, U. (2011). Interaction of micronutrients with major nutrients with special reference to potassium. Karnataka Journal of Agricultural Sciences, 24(1), 106–109.

• Rao, I. S., Neeraja, C. N., Srikanth, B., Subrahmanyam, D., Swamy, K. N., Rajesh, K., Vijayalakshmi, P., Kiran, T. V., Sailaja, N., Revathi, P., Rao, P. R., Rao, L. V. S., Surekha, K., Babu, V. R., & Voleti, S. R. (2018). Identification of rice landraces with promising yield and the associated genomic regions under low nitrogen. Scientific Reports, 8, 9200. https://doi.org/10.1038/s41598-018-27484-0

• Remans, T., Nacry, P., Pervent, M., Girin, T., Tillard, P., Lepetit, M., & Gojon, A. (2006). A central role for the nitrate transporter NRT2.1 in the integrated morphological and physiological responses of the root system to nitrogen limitation in Arabidopsis. Plant Physiology, 140(3), 909–921. https://doi.org/10.1104/pp.105.075721

• Safavi-Rizi, V., Uellendahl, K., Öhrlein, B., Safavi‐Rizi, H., & Stöhr, C. (2021). Cross‐stress tolerance: Mild nitrogen (N) deficiency effects on drought stress response of tomato (Solanum lycopersicum L.). Plant‐Environment Interactions, 2(5), 217-228. https://doi.org/10.1002/pei3.10060

• Sayers, E. W., Beck, J., Bolton, E. E., Bourexis, D., Brister, J. R., Canese, K., Comeau, D. C., Funk, K., Kim, S., Klimke, W., Marchler-Bauer, A., Landrum, M., Lathrop, S., Lu, Z., Madden, T. L., O’Leary, N., Phan, L., Rangwala, S. H., Schneider, V. A., … Sherry, S. T. (2021). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 49(D1), D10-D17. https://doi.org/10.1093/nar/gkaa892

• Schaeffer, R. D., Kinch, L. N., Liao, Y., & Grishin, N. V. (2016). Classification of proteins with shared motifs and internal repeats in the ECOD database. Protein Science, 25(7), 1188–1203. https://doi.org/10.1002/pro.2893

• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498-504. https://doi.org/10.1101/gr.1239303

• Sharma, S., Kaur, G., Kumar, A., Meena, V., Kaur, J., & Pandey, A. K. (2019). Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress. BMC Molecular Biology, 20, 22. https://doi.org/10.1186/s12867-019-0139-6

• Singh, B. R., Timsina, Y. N., Lind, O. C., Cagno, S., & Janssens, K. (2018). Zinc and iron concentration as affected by nitrogen fertilization and their localization in wheat grain. Frontiers in Plant Science, 9, 307. https://doi.org/10.3389/fpls.2018.00307

• Sonoda, Y., Ikeda, A., Saiki, S., Wirén, N. V., Yamaya, T., & Yamaguchi, J. (2003). Distinct expression and function of three ammonium transporter genes (OsAMT1; 1–1; 3) in rice. Plant and Cell Physiology, 44(7), 726-734. https://doi.org/10.1093/pcp/pcg083

• Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., Xu, W., & Su, Z. (2017). AgriGO v2.0: A GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research, 45(W1), W122–W129. https://doi.org/10.1093/nar/gkx382

• Tong, J., Walk, T. C., Han, P., Chen, L., Shen, X., Li, Y., Gu, C., Xie, L., Hu, X., Liao, X., & Qin, L. (2020). Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses. BMC Plant Biology, 20, 464. https://doi.org/10.1186/s12870-020-02648-1

• Tong, H. H., Chen, L., Li, W. P., Mei, H. W., Xing, Y. Z., Yu, X. Q., Xu, X. Y., Zhang, S. Q., & Luo, L. J. (2011). Identification and characterization of quantitative trait loci for grain yield and its components under different nitrogen fertilization levels in rice (Oryza sativa L.). Molecular Breeding, 28, 495-509. https://doi.org/10.1007/s11032-010-9499-9

• Waese, J., Fan, J., Pasha, A., Yu, H., Fucile, G., Shi, R., Cumming, M., Kelley, L. A., Sternberg, M. J., Krishnakumar, V., Ferlanti, E., Miller, J., Town, C., Stuerzlinger, W., & Provart, N. J. (2017). ePlant: Visualizing and exploring multiple levels of data for hypothesis generation in plant biology. Plant Cell, 29(8), 1806–1821. https://doi.org/10.1105/tpc.17.00073

• Wang, H., Yang, Z., Yu, Y., Chen, S., He, Z., Wang, Y., Jiang, L., Wang, G., Yang, C., Liu, B., & Zhang, Z. (2017). Drought enhances nitrogen uptake and assimilation in maize roots. Agronomy Journal, 109(1), 39–46. https://doi.org/10.2134/agronj2016.01.0030

• Wang, M., Zhang, P., Liu, Q., Li, G., Di, D., Xia, G., Kronzucker, H. J., Fang, S., Chu, J., & Shi, W. (2020). TaANR1-TaBG1 and TawAbi5-TaNRT2S/NARs link ABA metabolism and nitrate acquisition in wheat roots. Plant Physiology, 182(3), 1440–1453. https://doi.org/10.1104/PP.19.01482

• Wang, Y. Y., Hsu, P. K., & Tsay, Y. F. (2012). Uptake, allocation and signaling of nitrate. Trends in Plant Science, 17(8), 458–467. https://doi.org/10.1016/j.tplants.2012.04.006

• Wang, Q., Nian, J., Xie, X., Yu, H., Zhang, J., Bai, J., Dong, G., Hu, J., Bai, B., Chen, L., Xie, Q., Feng, J., Yang, X., Peng, J., Chen, F., Qian, Q., Li, J., & Zuo J. (2018). Genetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice. Nature Communications, 9, 735. https://doi.org/10.1038/s41467-017-02781-w

• Waraich, E. A., Ahmad, R., & Ashraf, M. Y. (2011). Role of mineral nutrition in alleviation of drought stress in plants. Australian Journal of Crop Science, 5(6), 764-777

• Wei, J., Zheng, Y., Feng, H., Qu, H., Fan, X., Yamaji, N., Ma, J. F., & Xu, G. (2018). OsNRT2.4 encodes a dual-affinity nitrate transporter and functions in nitrate-regulated root growth and nitrate distribution in rice. Journal of Experimental Botany, 69(5), 1095–1107. https://doi.org/10.1093/jxb/erx486

• Wu, J., Wang, C., Zheng, L., Wang, L., Chen, Y., Whelan, J., & Shou, H. (2011). Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa. Journal of Experimental Botany, 62(2), 667–674. https://doi.org/10.1093/jxb/erq301

• Wu, K., Ali, I., Xie, H., Ullah, S., Iqbal, A., Wei, S., He, L., Huang, Q., Wu, X., Cheng, F., & Jiang, L. (2021). Impact of fertilization with reducing in nitrogen and phosphorous application on growth, yield and biomass accumulation of rice (Oryza sativa L.) under a dual cropping system. PeerJ, 9, e11668. https://doi.org/10.7717/peerj.11668

• Xia, L., Zou, D., Sang, J., Xu, X., Yin, H., Li, M., Wu, S., Hu, S., Hao, L., & Zhang, Z. (2017). Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 44(5), 235–241. https://doi.org/10.1016/j.jgg.2017.05.003

• Xu, G., Fan, X., & Miller, A. J. (2012). Plant nitrogen assimilation and use efficiency. Annual Review of Plant Biology, 63, 153–182. https://doi.org/10.1146/annurev-arplant-042811-105532

• Zhang, X., Liu, H., Zhang, S., Wang, J., & Wei, C. (2019). NH4+-N alleviates iron deficiency in rice seedlings under calcareous conditions. Scientific Reports, 9, 12712. https://doi.org/10.1038/s41598-019-49207-9

• Zhang, Z., Gao, S., & Chu, C. (2020). Improvement of nutrient use efficiency in rice: Current toolbox and future perspectives. Theoretical and Applied Genetics, 133, 1365-1384. https://doi.org/10.1007/s00122-019-03527-6

• Zhao, L., Chen, P., Liu, P., Song, Y., & Zhang, D. (2021). Genetic effects and expression patterns of the nitrate transporter (NRT) gene family in Populus tomentosa. Frontiers in Plant Science, 12, 661635. https://doi.org/10.3389/fpls.2021.661635