References
- Barman HN, Sheng Z, Fiaz S, Zhong M, Wu Y, Cai Y, Wang W, Jiao G, Tang S, Wei X, et al. Generation of a new thermo-sensitive genic male sterile rice line by targeted mutagenesis of TMS5 gene through CRISPR/Cas9 system. BMC Plant Biol. 2019;19(1):109. doi:https://doi.org/10.1186/s12870-019-1715-0.
- Sheng Z, Fiaz S, Li Q, Chen W, Wei X, Xie L, Jiao G, Shao G, Tang S, Wang, et al. Molecular breeding of fragrant early-season hybrid rice using the BADH2 gene. Pak J Bot. 2019;51(6):2089–2095.
- Taiz, L Zeiger E. Plant physiology, 4th edn. Sinauer Associates, Massachusetts. 2006; p.690.
- Ghoneim A, Ebid A. Combined effects of soil water regimes and rice straw incorporation into the soil on 15N, P, K Uptake, rice yield and selected soil properties. Int J Plant Soil Sci. 2015;5(6):339–49. doi:https://doi.org/10.9734/IJPSS/2015/15472.
- Noor M. Nitrogen management and regulation for optimum NUE in maize–A mini review. Cogent Food Agric. 2017;3:1348214.
- Fageria N, Baligar VC, Li YC. The role of nutrient efficient plants in improving crop yields in the twenty first century. J Plant Nutr. 2008;31(6):1121–57. doi:https://doi.org/10.1080/01904160802116068.
- Good AG, Shrawat AK, Muench DG. Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production? Trends Plant Sci. 2004;9(12):597–605. doi:https://doi.org/10.1016/j.tplants.2004.10.008.
- Moose S, Below F. Biotechnology approaches to improving maize nitrogen use efficiency. In: Kriz AL, Larkins BA, editors. Molecular genetic approaches to maize improvement, biotechnology in agriculture and forestry. Berlin (Heidelberg): Springer; 2009, 65–77. doi:https://doi.org/10.1007/978-3-540-68922-5_6.
- Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S. Agricultural sustainability and intensive production practices. Nature. 2002;418:671–677.
- Masclaux-Daubresse C, Daniel-Vedele F, Dechorgnat J, Chardon F, Gaufichon L, Suzuki A. Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. Ann Bot. 2010;105(7):1141–57. doi:https://doi.org/10.1093/aob/mcq028.
- Stitt M, Müller C, Matt P, Gibon Y, Carillo P, Morcuende R, Scheible WR, Krapp A. Steps towards an integrated view of nitrogen metabolism. J Exp Bot. 2002;53(370):959–70. doi:https://doi.org/10.1093/jexbot/53.370.959.
- Ng J, Han M, Beatty P, Good A. Genes, meet gases: the role of plant nutrition and genomics in addressing greenhouse gas emissions. In: Edwards D, Batley J, editors. Plant genomics and climate change. New York (NY): Springer; 2016. p. 149–72.
- Shen J, Li C, Mi G, Li L, Yuan L, Jiang R, Zhang F. Maximizing root/rhizosphere efficiency to improve crop productivity and nutrient use efficiency in intensive agriculture of China. J Exp Bot. 2013;64(5):1181–92. doi:https://doi.org/10.1093/jxb/ers342.
- Wuebbles DJ. Nitrous oxide: No laughing matter. Science. 2009;326(5949):56–57. doi:https://doi.org/10.1126/science.1179571.
- Han M, Wong J, Su T, Beatty PH, Good AG. Identification of nitrogen use efficiency genes in Barley: Searching for QTLs controlling complex physiological traits. Front Plant Sci. 2016a;7:1587–1587. doi:https://doi.org/10.3389/fpls.2016.01587.
- Ray DK, Ramankutty N, Mueller ND, West PC, Foley JA. Recent patterns of crop yield growth and stagnation. Nat Commun. 2012;3(1):1293. doi:https://doi.org/10.1038/ncomms2296.
- McAllister CH, Beatty PH, Good AG. Engineering nitrogen use efficient crop plants: the current status. Plant Biotechnol J. 2012;10(9):1011–25. doi:https://doi.org/10.1111/j.1467-7652.2012.00700.x.
- Tiwari JK, Buckseth, T, Devi S, Varshney S, Sahu S, Patil VU, Zinta R, Ali N, Moudgil V, Singh RK, et al. Physiological and genome-wide RNA-sequencing analyses identify candidate genes in a nitrogen-use efficient potato cv. Kufri Gaurav. Plant Physiology and Biochemistry. 2020a;154:171–183.
- Fiaz S, Ahmad S, Noor M, Wang X, Younas A, Riaz A, Riaz A, Ali F. Applications of the CRISPR/Cas9 system for rice grain quality improvement: Perspectives and opportunities. Int J Mol Sci. 2019;20(4):888. doi:https://doi.org/10.3390/ijms20040888.
- Fiaz S, Wang X, Younas A, Alharthi B, Riaz A, Ali H. Apomixis and strategies to induce apomixis to preserve hybrid vigor for multiple generations. GM Crops Food. 2021;12(1):57–70. doi:https://doi.org/10.1080/21645698.2020.1808423.
- Gallais A, Hirel B. An approach to the genetics of nitrogen use efficiency in maize. J Exp Bot. 2004;55(396):295–306. doi:https://doi.org/10.1093/jxb/erh006.
- Li H, Hu B, Chu C. Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. J Exp Bot. 2017a;68(10):2477–88. doi:https://doi.org/10.1093/jxb/erx101.
- Ribaut J-M, Fracheboud Y, Monneveux P, Banziger M, Vargas M, Jiang C. Quantitative trait loci for yield and correlated traits under high and low soil nitrogen conditions in tropical maize. Mol Breed. 2007;20(1):15–29. doi:https://doi.org/10.1007/s11032-006-9041-2.
- Zhang M, Gao M, Zheng H, Yuan Y, Zhou X, Guo Y, Zhang G, Zhao Y, Kong F, An Y, et al. QTL mapping for nitrogen use efficiency and agronomic traits at the seedling and maturity stages in wheat. Mol Breed. 2019a;39(5):71. doi:https://doi.org/10.1007/s11032-019-0965-8.
- Kindu GA, Tang J, Yin X, Struik PC. Quantitative trait locus analysis of nitrogen use efficiency in barley (Hordeum vulgare L.). Euphytica. 2014;199(1–2):207–21. doi:https://doi.org/10.1007/s10681-014-1138-9.
- Dechorgnat J, Nguyen CT, Armengaud P, Jossier M, Diatloff E, Filleur S, Daniel-Vedele F. From the soil to the seeds: the long journey of nitrate in plants. J Exp Bot. 2011;62(4):1349–59. doi:https://doi.org/10.1093/jxb/erq409.
- Léran S, Varala K, Boyer J-C, Chiurazzi M, Crawford N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, et al. A unified nomenclature of Nitrate transporter 1/peptide transporter family members in plants. Trends Plant Sci. 2014;19(1):5–9. doi:https://doi.org/10.1016/j.tplants.2013.08.008.
- Li BZ, Merrick M, Li SM, Li HY, Zhu SW, Shi WM, Su YH. Molecular basis and regulation of ammonium transporter in rice. Rice. 2009; Sci.16:314–22. doi:https://doi.org/10.1016/S1672-6308(08)60096-7.
- Kirk GJD, Kronzucker HJ. The potential for nitrification and nitrate uptake in the rhizosphere of wetland plants: a modelling study. Ann Bot. 2005;96(4):639–46. doi:https://doi.org/10.1093/aob/mci216.
- Fan X, Xie D, Chen J, Lu H, Xu Y, Ma C, Xu G. Over-expression of OsPTR6 in rice increased plant growth at different nitrogen supplies but decreased nitrogen use efficiency at high ammonium supply. Plant Sci. 2014;227:1–1. doi:https://doi.org/10.1016/j.plantsci.2014.05.013.
- Han Y-L, Song H-X, Liao Q, Yu Y, Jian S-F, Lepo JE, Liu Q, Rong X-M, Tian C, Zeng J, et al. Nitrogen use efficiency is mediated by vacuolar nitrate sequestration capacity in roots of brassica napus. Plant Physiol. 2016b;170(3):1684. doi:https://doi.org/10.1104/pp.15.01377.
- Tabuchi M, Sugiyama K, Ishiyama K, Inoue E, Sato T, Takahashi H. Expression of the nitrate transporter gene OsNRT1.1A/OsNPF6.3 confers high yield and early maturation in Rice. Plant Cell. 2018;30:638–51. doi:https://doi.org/10.1105/tpc.17.00809.
- Cai C, Wang J-Y, Zhu Y, Shen Q-R, Li B, Tong Y, Li Z-S. Gene structure and expression of the high-affinity nitrate transport system in rice roots. J Integr Plant Biol. 2008;Biology 50(4):443–51. doi:https://doi.org/10.1111/j.1744-7909.2008.00642.x.
- Inostroza-Blancheteau C, Aquea F, Moraga F, Ibañez C, Renge LZ, Reyes-Díaz M. Genetic engineering and molecular strategies for nutrient manipulation in plants. In: Naeem M, Ansari A, Gill S, editors. Essential plant nutrients. Cham, Switzerland : Springer; 2017, 405–441. doi:https://doi.org/10.1007/978-3-319-58841-4_17.
- Meyer C, Stitt M. Nitrate reduction and signaling. In: Lea PJ, Morot-Gaudry JF, editors. Plant nitrogen. Berlin/Heidelberg (Germany): Springer; 2001. p. 37.–59.
- Tabuchi M, Abiko T, Yamaya T. Assimilation of ammonium ions and reutilization of nitrogen in rice (Oryza sativa L.). J Exp Bot. 2007;58(9):2319–27. doi:https://doi.org/10.1093/jxb/erm016.
- Thomsen H, Eriksson D, Møller I, Schjoerring J.Cytosolic glutamine synthetase: a target for improvement of crop nitrogen use efficiency? Trends Plant Sci. 2014;19:656–663.
- Schiltz S, Munier-Jolain N, Jeudy C, Burstin J, Salon C. Dynamics of exogenous nitrogen partitioning and nitrogen remobilization from vegetative organs in pea revealed by 15 N in Vivo labeling throughout seed filling. Plant Physiol. 2005;137(4):1463–73. doi:https://doi.org/10.1104/pp.104.056713.
- Bernard SM, Habash DZ. The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling. New Phytol. 2009;182(3):608–20. doi:https://doi.org/10.1111/j.1469-8137.2009.02823.x.
- Xu G, Fan X, Miller A. Plant nitrogen assimilation and use efficiency. Ann Rev Plant Biol. 2012;63(1):153–82. doi:https://doi.org/10.1146/annurev-arplant-042811-105532.
- Liu K-H, Huang C-Y, Tsay Y-F. CHL1 is a dual-affinity nitrate transporter of Arabidopsis involved in multiple phases of nitrate uptake. Plant Cell. 1999;11(5):865–74. doi:https://doi.org/10.1105/tpc.11.5.865.
- Fraisier V, Gojon A, Tillard P, Daniel-Vedele F. Constitutive expression of a putative high-affinity nitrate transporter in Nicotiana plumbaginifolia: evidence for post-transcriptional regulation by a reduced nitrogen source. Plant J. 2000;23(4):489–96. doi:https://doi.org/10.1046/j.1365-313x.2000.00813.x.
- Okamoto M, Kumar A, Li WB, Wang Y, Siddiqi MY, Crawford NM, Glass ADM. High-affinity nitrate transport in roots of arabidopsis depends on expression of the NAR2 -like gene AtNRT3.1. Plant Physiol. 2006;140(3):1036–46. doi:https://doi.org/10.1104/pp.105.074385.
- Kumar A, Kaiser BN, Siddiqi MY, Glass ADM. Functional characterisation of OsAMT1.1 overexpression lines of rice, Oryza sativa L. Fun Plant Biol. 2006;33(4):339–46. doi:https://doi.org/10.1071/FP05268.
- Brauer EK, Rochon A, Bi Y-M, Bozzo GG, Rothstein SJ, Shelp BJ. Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase. Physiol Plant. 2011;141(4):361–72.doi:https://doi.org/10.1111/j.1399-3054.2011.01443.x.
- Hoshida H, Tanaka Y, Hibino T, Hayashi Y, Tanaka A, Takabe T, Takabe T. Enhanced tolerance to salt stress in transgenic rice that overexpresses chloroplast glutamine synthetase. Plant Mol Biol. 2000;43(1):103–11. doi:https://doi.org/10.1023/A:1006408712416.
- Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T. Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice. J Exp Bot. 2002;53(370):917–25. doi:https://doi.org/10.1093/jexbot/53.370.917.
- Good AG, Johnson SJ, De Pauw M, Carroll RT, Savidov N. Engineering nitrogen use efficiency with alanine aminotransferase. Can J Botany-Revue Canadienne De Botanique. 2007;85:252–62.
- Bi Y-M, Kant S, Clarke J, Gidda S, Ming F, Xu J, Rochon A, Shelp BJ, Hao L, Zhao R, et al. Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. Plant Cell Environ. 2009;32(12):1749–60. doi:https://doi.org/10.1111/j.1365-3040.2009.02032.x.
- Canas RA, Yesbergenova-Cuny Z, Belanger L, Rouster J, Brule L, Gilard F, Quilleré I, Sallaud C, Hirel B. NADH-GOGAT overexpression does not improve maize (Zea mays L.) performance even when pyramiding with NAD-IDH, GDH and GS. Plants. 2020;9(2):130. doi:https://doi.org/10.3390/plants9020130.
- Abiko T, Wakayama M, Kawakami A, Obara M, Kisaka H, Miwa T, Aoki N, Ohsugi R. Changes in nitrogen assimilation, metabolism, and growth in transgenic rice plants expressing a fungal NADP(H)-dependent glutamate dehydrogenase (gdhA). Planta. 2010;232(2):299–311. doi:https://doi.org/10.1007/s00425-010-1172-3.
- Lee S, Park J, Lee J, Shin D, Marmagne A, Lim PO, Masclaux-Daubresse C, An G, Nam HG. OsASN1 overexpression in rice increases grain protein content and yield under nitrogen-limiting conditions. Plant Cell Physiol. 2020b;61(7):1309–20. doi:https://doi.org/10.1093/pcp/pcaa060.
- Wu J, Zhang Z, Zhang Q, Han X, Gu X, Lu T. The molecular cloning and clarification of a photorespiratory mutant, oscdm1, using enhancer trapping. Front Genet. 2015;6:226. doi:https://doi.org/10.3389/fgene.2015.00226.
- Ji Y, Huang W, Wu B, Fang Z, Wang X, Gibbs D. The amino acid transporter AAP1 mediates growth and grain yield by regulating neutral amino acid uptake and reallocation in Oryza sativa. J Exp Bot. 2020;71(16):4763–77. doi:https://doi.org/10.1093/jxb/eraa256.
- Lu K, Wu B, Wang J, Zhu W, Nie H, Qian J, Huang W, Fang Z. Blocking amino acid transporter OsAAP3 improves grain yield by promoting outgrowth buds and increasing tiller number in rice. Plant Biotechnol J. 2018;16(10):1710–22. doi:https://doi.org/10.1111/pbi.12907.
- Wang J, Wu B, Lu K, Wei Q, Qian J, Chen Y, et al. The amino acid Permease 5 (OsAAP5) regulates tiller number and grain yield in Rice. Plant Physiol. 2019;180:1031–1045.
- Peng B, Kong H, Li Y, Wang L, Zhong M, Sun L, Gao G, Zhang Q, Luo L, Wang G, et al. OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nat Commun. 2014;5(1):4847. doi:https://doi.org/10.1038/ncomms5847.
- Heuer S, Lu X, Chin JH, Tanaka JP, Kanamori H, Matsumoto T, De Leon T, Ulat VJ, Ismail AM, Yano M, et al. Comparative sequence analyses of the major quantitative trait locus p hosphorus up take 1 (Pup1) reveal a complex genetic structure. Plant Biotechnol J. 2009;7(5):456–71. doi:https://doi.org/10.1111/j.1467-7652.2009.00415.x.
- Sun H, Qian Q, Wu K, Luo J, Wang S, Zhang C, Ma Y, Liu Q, Huang X, Yuan Q, et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice. Nat Genet. 2014;46(6):652–56. doi:https://doi.org/10.1038/ng.2958.
- Zhang Y, Tan L, Zhu Z, Yuan L, Xie D, Sun C. TOND1 confers tolerance to nitrogen deficiency in rice. Plant J. 2015b;81(3):367–76. doi:https://doi.org/10.1111/tpj.12736.
- Li S, Tian Y, Wu K, Ye Y, Yu J, Zhang J, Liu Q, Hu M, Li H, Tong Y, et al. Modulating plant growth–metabolism coordination for sustainable agriculture. Nature. 2018;560(7720):595–600. doi:https://doi.org/10.1038/s41586-018-0415-5.
- Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, et al.Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat. Genet. 2013;45:1097–1102.
- Yu CY, Liu YH, Zhang AD, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan YB. MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice. Plos One. 2015;10(8):e0135196. doi:https://doi.org/10.1371/journal.pone.0135196.
- Liang C, Wang Y, Zhu Y, Tang J, Hu B, Liu L, Ou S, Wu H, Sun X, Chu J, et al. OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice. Pro Nat Acad Sci. 2014;111(27):10013–18. doi:https://doi.org/10.1073/pnas.1321568111.
- Bak RO, Gomez-Ospina N, Porteus MH. Gene editing on center stage. Trends Genet. 2018;34(8):600–11. doi:https://doi.org/10.1016/j.tig.2018.05.004.
- Jiang S, Shen Q. Principles of gene editing techniques and applications in animal husbandry. Biotech. 2019;9:28. doi:https://doi.org/10.1007/s13205-018-1563-x.
- Barrangou R, Doudna J. Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016;34(9):933–41. doi:https://doi.org/10.1038/nbt.3659.
- Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA. RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 2018;7(7). doi:https://doi.org/10.7554/eLife.32724.
- Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotech. 2013;31:233–239.
- Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23. doi:https://doi.org/10.1126/science.1231143.
- Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013;31:230–232.
- Mali P, Yang L, Esvelt K, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science (New York, N.Y.).2013;339:823–826.
- Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, Voytas DF, Hsieh T-F, Zhang Y, Qi Y, et al. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol. 2015;169(2):971–85. doi:https://doi.org/10.1104/pp.15.00636.
- Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu J-L, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol. 2013;31(8):686–88. doi:https://doi.org/10.1038/nbt.2650.
- Bin Moon S, Lee JM, Kang JG, Lee N-E, Ha D-I, Kim DY, Kim SH, Yoo K, Kim D, Ko J-H, et al. Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3ʹ-overhang. Nat Commun. 2018;9(1):3651. doi:https://doi.org/10.1038/s41467-018-06129-w.
- Liu Y, Han J, Chen Z, Wu H, Dong H, Nie G. Engineering cell signaling using tunable CRISPR–Cpf1-based transcription factors. Nat Commun. 2017;8(1):2095. doi:https://doi.org/10.1038/s41467-017-02265-x.
- Zetsche B, Gootenberg J, Abudayyeh OO, Slaymaker IM, Makarova K, Essletzbichler P, Volz S, Joung J, Van der Oost J, Regev A, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759–71. doi:https://doi.org/10.1016/j.cell.2015.09.038.
- Zhang X, Wang J, Cheng Q, Zheng X, Zhao G, Wang J. Multiplex gene regulation by CRISPR-ddCpf1. Cell Discov. 2017;3(1):17018. doi:https://doi.org/10.1038/celldisc.2017.18.
- Park J, Bae S, Valencia A. Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. Bioinformatics. 2018;34(6):1077–79. doi:https://doi.org/10.1093/bioinformatics/btx695.
- Yin K, Gao C, Qiu J-L. Progress and prospects in plant genome editing. Nat Plants. 2017;3(8):17107. doi:https://doi.org/10.1038/nplants.2017.107.
- Zhang Y, Li D, Zhang D, Zhao X, Cao X, Dong L, Liu J, Chen K, Zhang H, Gao C, et al. Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits. Plant J. 2018;94(5):857–66. doi:https://doi.org/10.1111/tpj.13903.
- Komor AC, Kim YB, Packer MS, Zuris JA, Liu D. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–24. doi:https://doi.org/10.1038/nature17946.
- Marx V. Base editing a CRISPR way. Nat Methods. 2018;15(10):767–70. doi:https://doi.org/10.1038/s41592-018-0146-4.
- Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464–71. doi:https://doi.org/10.1038/nature24644.
- Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature. 2019;565(7737):91–95. doi:https://doi.org/10.1038/s41586-018-0785-8.
- Eid A, Alshareef S, Mahfouz MM. CRISPR base editors: genome editing without double-stranded breaks. Biochem J. 2018;475(11):1955–64. doi:https://doi.org/10.1042/BCJ20170793.
- Rees HA, Komor AC, Yeh W-H, Caetano-Lopes J, Warman M, Edge ASB, Liu DR. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat Commun. 2017;8(1):15790. doi:https://doi.org/10.1038/ncomms15790.
- Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):149–57. doi:https://doi.org/10.1038/s41586-019-1711-4.
- Lin Q, Zong Y, Xue C, Wang S, Jin S, Zhu Z, Wang Y, Anzalone AV, Raguram A, Doman JL, et al. Prime genome editing in rice and wheat. Nat Biotechnol. 2020;38(5):582–85. doi:https://doi.org/10.1038/s41587-020-0455-x.
- Tiwari JK, Buckseth T, Singh, RK, Kumar M, Kant S. Prospects of improving nitrogen use efficiency in potato: lessons from transgenics to genome editing strategies in plants. Front. Plant Sci. 2020b;11:597481.
- Andrews M, Lea PJ, Raven JA, Lindsey K. Can genetic manipulation of plant nitrogen assimilation enzymes result in increased crop yield and greater N-use efficiency? An assessment. Ann Appl Biol. 2004;145(1):25–40. doi:https://doi.org/10.1111/j.1744-7348.2004.tb00356.x.
- Lea PJ, Azevedo RA. Nitrogen use efficiency. 2. Amino acid metabolism. Ann. Appl Biol. 2007;151(3):269–75. doi:https://doi.org/10.1111/j.1744-7348.2007.00200.x.
- Martin A, Lee J, Kichey T, Gerentes D, Zivy M, Tatout C, Dubois F, Balliau T, Valot B, Davanture M, et al. Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell. 2006;18(11):3252–74. doi:https://doi.org/10.1105/tpc.106.042689.
- Habash DZ, Massiah AJ, Rong HL, Wallsgrov RM, Leigh RA. The role of cytosolic glutamine synthetase in wheat. Ann Appl Biol. 2001;138(1):83–89. doi:https://doi.org/10.1111/j.1744-7348.2001.tb00087.x.
- Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Dua VK, Chakrabarti SK. Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress. Scientific Reports. 2020c;10:1152.
- Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One. 2020d;15:e0233076.
- Li Y, Ouyang J, Wang Y, Hu R, Xia K, Duan J, Wang Y, Tsay Y-F, Zhang M. Disruption of the rice nitrate transporter OsNPF2.2 hinders root-to-shoot nitrate transport and vascular development. Scientific Reports. 2015a;5(1):9635. doi:https://doi.org/10.1038/srep09635.
- Suenaga A, Moriya K, Sonoda Y, Ikeda A, Von Wirén N, Hayakawa T, Yamaguchi J, Yamaya T. Constitutive expression of a novel-type ammonium transporter OsAMT2 in rice plants. Plant Cell Physiol. 2003;44(2):206–11. doi:https://doi.org/10.1093/pcp/pcg017.
- Bao A, Liang Z, Zhao Z, Cai H. Overexpressing of OsAMT1-3, a high affinity ammonium transporter gene, modifies rice growth and carbon-nitrogen metabolic status. Int J Mol Sci. 2015;16(12):9037–63. doi:https://doi.org/10.3390/ijms16059037.
- Sonoda Y, Ikeda A, Saiki S, Wirén NV, Yamaya T, Yamaguchi J. Distinct expression and function of three ammonium transporter genes (OsAMT1;1 – 1;3) in Rice. Plant Cell Physiol. 2003;44(7):726–34. doi:https://doi.org/10.1093/pcp/pcg083.
- Lin C-M, Koh S, Stacey G, Yu S-M, Lin T-Y, Tsay Y-F. Cloning and functional characterization of a constitutively expressed nitrate transporter gene, OsNRT1, from rice. Plant Physiol. 2000;122(2):379–88. doi:https://doi.org/10.1104/pp.122.2.379.
- Fan X, Tang Z, Tan Y, Zhang Y, Luo B, Yang M, Lian X, Shen Q, Miller AJ, Xu G, et al. Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields. Proc Nat Acad Sci USA. 2016b;113(26):7118–23. doi:https://doi.org/10.1073/pnas.1525184113.
- Wang W, Hu B, Yuan, D, Liu Y, Che R, Hu Y, et al. Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice. Plant Cell. 2018; 30: 638–651.
- Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, et al. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet. 2015;47(7):834–38. doi:https://doi.org/10.1038/ng.3337.
- Araki R, Hasegawa H. Expression of rice (Oryza Sativa L.) genes involved in high-affinity nitrate transport during the period of nitrate induction. Breed Sci. 2006;56(3):295–302. doi:https://doi.org/10.1270/jsbbs.56.295.
- Yan M, Fan X, Feng H, Miller AJ, Shen Q, Xu G. Rice OsNAR2.1 interacts with OsNRT2.1, OsNRT2.2 and OsNRT2.3a nitrate transporters to provide uptake over high and low concentration ranges. Plant Cell Environ. 2011;34(8):1360–72. doi:https://doi.org/10.1111/j.1365-3040.2011.02335.x.
- Cai H, Zhou Y, Xiao J, Li X, Zhang Q, Lian X. Overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice. Plant Cell Rep. 2009;28(3):527–37. doi:https://doi.org/10.1007/s00299-008-0665-z.
- Tamura W. Kojima, S, Toyokawa A, Watanabe H, Tabuchi-Kobayashi M, Hayakawa T, et al. Disruption of a Novel NADH-Glutamate Synthase2 Gene Caused Marked Reduction in Spikelet Number of Rice. Front. Plant Sci.2011;2:57–57.
- Yamaya T, Kusano M. Evidence supporting distinct functions of three cytosolic glutamine synthetases and two NADH-glutamate synthases in rice. J Exp Bot. 2014;65(19):5519–25. doi:https://doi.org/10.1093/jxb/eru103.
- Ishiyama K, Inoue E, Tabuchi M, Yamaya T, Takahashi H. Biochemical Background and compartmentalized functions of cytosolic glutamine synthetase for active ammonium assimilation in rice roots. Plant Cell Physiol. 2004;45(11):1640–47. doi:https://doi.org/10.1093/pcp/pch190.
- Brugière N, Dubois F, Masclaux C, Sangwan RS, Hirel B. Immunolocalization of glutamine synthetase in senescing tobacco (Nicotiana tabacum L.) leaves suggests that ammonia assimilation is progressively shifted to the mesophyll cytosol. Planta. 2000;211(4):519–27. doi:https://doi.org/10.1007/s004250000309.
- Obara M, Sato T, Sasaki S, Kashiba K, Nagano A, Nakamura I, Ebitani T, Yano M, Yamaya T. Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice. Theor Appl Genet. 2004;110(1):1–11. doi:https://doi.org/10.1007/s00122-004-1828-0.
- Hu H-C, Wang -Y-Y, Tsay Y. AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. Plant J. 2009;57(2):264–78. doi:https://doi.org/10.1111/j.1365-313X.2008.03685.x.
- Kurai T, Wakayama M, Abiko T, Yanagisawa S, Aoki N, Ohsugi R. Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions. Plant Biotech J. 2011;9(8):826–37. doi:https://doi.org/10.1111/j.1467-7652.2011.00592.x.
- Noguero M, Lacombe B. Transporters involved in root nitrate uptake and sensing by arabidopsis. Front Plant Sci. 2016;7:1391. doi:https://doi.org/10.3389/fpls.2016.01391.
- Iwamoto M, Tagiri A. MicroRNA-targeted transcription factor gene RDD1 promotes nutrient ion uptake and accumulation in rice. Plant J. 2016;85(4):466–77. doi:https://doi.org/10.1111/tpj.13117.
- Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X, et al. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet. 2009;41(4):494–97. doi:https://doi.org/10.1038/ng.352.
- Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW, et al. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell. 2007;19(3):731–49. doi:https://doi.org/10.1105/tpc.106.047688.
- Chen X, Yao Q, Gao X, Jiang C, Harberd NP, Fu X. Shoot-to-root mobile transcription factor HY5 coordinates plant carbon and nitrogen acquisition. Curr Biol. 2016;26(5):640–46. doi:https://doi.org/10.1016/j.cub.2015.12.066.
- Kumagai E, Araki T, Kubota F. Effects of nitrogen supply restriction on gas exchange and photosystem 2 function in flag leaves of a traditional low-yield cultivar and a recently improved high-yield cultivar of rice (Oryza sativa L.). Photosynthetica. 2007;45(4):489. doi:https://doi.org/10.1007/s11099-007-0084-3.
- Ranathunge K, El-Kereamy A, Gidda S, Bi Y-M, Rothstein SJ. AMT1;1 transgenic rice plants with enhanced NH4+ permeability show superior growth and higher yield under optimal and suboptimal NH4+ conditions. J Exp Bot. 2014;65(4):965–79. doi:https://doi.org/10.1093/jxb/ert458.
- Shrawat AK, Carroll RT, DePauw M, Taylor GJ, Good AG. Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression of alanine aminotransferase. Plant Biotechnol J. 2008;6(7):722–32. doi:https://doi.org/10.1111/j.1467-7652.2008.00351.x.
- Yanagisawa S, Akiyama A, Kisaka H, Uchimiya H, Miwa T. Metabolic engineering with Dof1 transcription factor in plants: improved nitrogen assimilation and growth under low-nitrogen conditions. Pro Nat Aca Sci. 2004;101(20):7833–38. doi:https://doi.org/10.1073/pnas.0402267101.
- Bao A, Zhao Z, Ding G, Shi L, Xu F, Cai H, Wilson RA. Accumulated expression level of cytosolic glutamine synthetase 1 gene (OsGS1;1 or OsGS1;2) alter plant development and the carbon-nitrogen metabolic status in rice. PLoS One. 2014;9(4):e95581. doi:https://doi.org/10.1371/journal.pone.0095581.
- James D, Borphukan B, Fartyal D, Ram B, Singh J, Manna M, Sheri V, Panditi V, Yadav R, Achary VMM, et al. Concurrent overexpression of OsGS1;1 and OsGS2 genes in transgenic Rice (Oryza sativa L.): impact on tolerance to abiotic stresses. Front Plant Sci. 2018;9:786. doi:https://doi.org/10.3389/fpls.2018.00786.
- Lee S, Marmagne A, Park J, Fabien C, Yim Y, Kim S-J, Kim T-H, Lim PO, Masclaux‐Daubresse C, Nam HG, et al. Concurrent activation of OsAMT1;2 and OsGOGAT1 in rice leads to enhanced nitrogen use efficiency under nitrogen limitation. Plant J. 2020a;103(1):7–20. doi:https://doi.org/10.1111/tpj.14794.
- Lee S, Park J, Lee J, Shin D, Marmagne A, Lim PO, Masclaux-Daubresse C, An G, Nam HG. OsASN1 overexpression in Rice increases grain protein content and yield under nitrogen-limiting conditions. Plant Cell Physiol. 2020b;61(7):1309–20.
- Du C-Q, Lin J-Z, Dong L-A, Liu C, Tang D-Y, Yan L, Chen M-D, Liu S, Liu X-M. Overexpression of an NADP(H)-dependent glutamate dehydrogenase gene, TrGDH, from Trichurus improves nitrogen assimilation, growth status and grain weight per plant in rice. Breed Sci. 2019;69(3):429–38. doi:https://doi.org/10.1270/jsbbs.19014.
- Sisharmini A, Apriana A, Khumaida N, Trijatmiko KR, Purwoko BS. Expression of a cucumber alanine aminotransferase2 gene improves nitrogen use efficiency in transgenic rice. J Genet Eng Biotechnol. 2019;17(1):9. doi:https://doi.org/10.1186/s43141-019-0010-7.
- Wang J, Wu B, Lu K, Wei Q, Qian J, Chen Y, et al. The amino acid Permease 5 (OsAAP5) regulates tiller number and grain yield in Rice. Plant Physiol.2019;180:1031–1045.
- Pingali PL. Green Revolution: impacts, limits, and the path ahead. Proc Natl Acad Sci USA. 2012;109(31):12302–08. doi:https://doi.org/10.1073/pnas.0912953109.
- De Datta S, Broadbent FE. Development changes related to nitrogen-use efficiency in rice. Field Crops Res. 1993;34(1):47–56. doi:https://doi.org/10.1016/0378-4290(93)90110-9.
- Grover G, Sharma A, Gill HS, Srivastava P, Bains NS, Zhang A. Rht8 gene as an alternate dwarfing gene in elite Indian spring wheat cultivars. PLoS One. 2018;13(6):e0199330. doi:https://doi.org/10.1371/journal.pone.0199330.
- Zaidi SS, Vanderschuren H, Qaim M, Mahfouz MM, Kohli A, Mansoor S, Tester M. New plant breeding technologies for food security. Science. 2019;363(6434):1390–91. doi:https://doi.org/10.1126/science.aav6316.
- Lu Y, Zhu J-K. Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 System. Mol Plant. 2017;10(3):523–25. doi:https://doi.org/10.1016/j.molp.2016.11.013.
- Asano T, Hayashi N, Kobayashi M, Aoki N, Miyao A, Mitsuhara I, Ichikawa H, Komatsu S, Hirochika H, Kikuchi S, et al. A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J. 2012;69(1):26–36. doi:https://doi.org/10.1111/j.1365-313X.2011.04766.x.
- Bartkowski B, Theesfeld I, Pirscher F, Timaeus J. Snipping around for food: economic, ethical and policy implications of CRISPR/Cas genome editing. Geoforum. 2018;96:172–80. doi:https://doi.org/10.1016/j.geoforum.2018.07.017.
- Pineda M, Lear A, Collins JP, Kiani S. Safe CRISPR: challenges and Possible Solutions. Trends Biotechnol. 2019;37(4):389–401. doi:https://doi.org/10.1016/j.tibtech.2018.09.010.
- Wyvekens N, Topkar VV, Khayter C, Joung JK, Tsai SQ. Dimeric CRISPR RNA-Guided FokI-dCas9 nucleases directed by truncated gRNAs for highly specific genome editing. Hum Gene Ther. 2015;26(7):425–31. doi:https://doi.org/10.1089/hum.2015.084.
- Garcia Ruiz MT, Knapp AN, Garcia-Ruiz H. Profile of genetically modified plants authorized in Mexico. GM Crops Food. 2018;9(3):152–68. doi:https://doi.org/10.1080/21645698.2018.1507601.
- Eckerstorfer M, Engelhard M, Heissenberger A, Simon S, Teichmann H. Plants developed by new genetic modification techniques—comparison of existing regulatory frameworks in the EU and Non-EU Countries. Front Bioeng Biotechnol. 2019;7:26. doi:https://doi.org/10.3389/fbioe.2019.00026.
- Van Vu T, Sung YW, Kim J, Doan D, Tran M., and Kim J. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. Rice 2019;12:95.
- Waltz E. CRISPR-edited crops free to enter market, skip regulation. Nat. Biotechnol. 2016;34:582.
- Gleim S, Lubieniechi S, Smyth SJ. CRISPR-Cas9 application in canadian public and private plant breeding. The CRISPR J. 2020;3(1):44–51. doi:https://doi.org/10.1089/crispr.2019.0061.
- Spicer A, Molnar A. Gene editing of microalgae: scientific progress and regulatory challenges in Europe. Biology. 2018;7(1):21. doi:https://doi.org/10.3390/biology7010021.
- Gao W, Xu W-T, Huang K-L, Guo M-Z, Luo Y-B. Risk analysis for genome editing-derived food safety in China. Food Control. 2018;84:128–37. doi:https://doi.org/10.1016/j.foodcont.2017.07.032.
- Chimata MK, Bharti G. Regulation of genome edited technologies in India. Transgenic Res. 2019;28(S2):175–81. doi:https://doi.org/10.1007/s11248-019-00148-z.
- Zannoni L. Evolving Regulatory Landscape for Genome-Edited Plants. Crispr J. 2019;2(1):3–8. doi:https://doi.org/10.1089/crispr.2018.0016.
- Rodriguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. Engineering quantitative trait variation for crop improvement by genome editing. Cell. 2017;171(2):470–80. doi:https://doi.org/10.1016/j.cell.2017.08.030.
- Li Z-K, Zhang F. Rice breeding in the post-genomics era: from concept to practice. Curr Opin Plant Biol. 2013;16(2):1–9. doi:https://doi.org/10.1016/j.pbi.2013.03.008.
- Silva NV, Patron NJ, Harwood W. CRISPR-based tools for plant genome engineering. Emerg Top Life Sci. 2017;1(2):135–49. doi:https://doi.org/10.1042/ETLS20170011.
- Xie K, Minkenberg B, Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci U S A. 2015;112(11):3570–75. doi:https://doi.org/10.1073/pnas.1420294112.
- Fonfara I, Richter H, Bratovi M, Le RA, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016;532(7600):517–21. doi:https://doi.org/10.1038/nature17945.
- Wang M, Mao Y, Lu Y, Tao X, and Zhu JK. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol. Plant. 2017;10:1011–1013.
- Khan MHU, Khan SU, Muhammad A, Hu L, Yang Y, Fan C. Induced mutation and epigenetics modification in plants for crop improvement by targeting CRISPR/Cas9 technology. Journal of Cellular Physiology. 2018;233(6):4578–94. doi:https://doi.org/10.1002/jcp.26299.
- Jones HD. Regulatory uncertainty over genome editing. Nat Plants. 2015;1(1):14011. doi:https://doi.org/10.1038/nplants.2014.11.
- Gao X, Chen J, Dai X, Zhang D, Zhao Y. An effective strategy for reliably isolating heritable and Cas9 -free arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing. Plant Physiol. 2016;171(3):1794–800. doi:https://doi.org/10.1104/pp.16.00663.
- Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y, Qiu J-L, Gao C. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat Biotechnol. 2018;36(10):950–53. doi:https://doi.org/10.1038/nbt.4261.
- Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, Guo X, Du W, Zhao Y, Xia L, et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant. 2016;9(4):628–31. doi:https://doi.org/10.1016/j.molp.2016.01.001.