Skip to main content
SpringerLink
Log in

CRISPR/Cas9-Edited Rice: A New Frontier for Sustainable Agriculture

  • Chapter
  • First Online:
New Frontiers in Stress Management for Durable Agriculture

Abstract

With the exponential increase in the world’s human population, improving agricultural productivity is among the top of the researchers’ agendas till the 2050 deadline. One of the potential solutions to this global issue is genome editing because of the precision, fastness, and probably low cost involved compared to other traditional methods. It is in the spotlight especially from the last decade due to the discovery of sequence-specific-based nuclease technology including CRISPR/Cas9 tool. Initially, this tool was applied only in protoplasts and calli. However, due to the modifications in vectors, Cas9 variants, cassettes, cloning systems, multiplexing, and delivery methods, this platform has revolutionized the plant science field. It has been exploited in such a manner that about 16 crop plants have been already edited in the last few years. Out of all crops, most of the editing has been done in the case of rice (Oryza sativa L., Family: Poaceae), a cereal staple food. Therefore, in the current chapter, we have highlighted about the CRISPR/Cas9-edited rice for agronomic traits, stress tolerance/resistance, and biofortification. Additionally, we have presented an overview of various tools, databases, and commercial service providers devoted solely to CRISPR/Cas9 genome-editing technology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abuajah CI, Ogbonna AC, Osuji CM (2015) Functional components and medicinal properties of food: a review. J Food Sci Technol 52(5):2522–2529

    Article  CAS  PubMed  Google Scholar 

  • Abbott TR, Qi LS (2018) Evolution at the cutting edge: CRISPR-mediated directed evolution. Mol Cell 72(3):402–403

    Article  CAS  PubMed  Google Scholar 

  • Alagoz Y, Gurkok T, Zhang B, Unver T (2016) Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep 6:30910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alok A, Kumar J, Jogam P, Sandhya D (2018) CRISPR/Cas9-mediated gene editing tool and fathomless genetic and metabolic engineering applications in plants. In: Recent trends and techniques in plant metabolic engineering. Springer, Singapore, pp 167–179

    Chapter  Google Scholar 

  • Arzani A, Ashraf M (2016) Smart engineering of genetic resources for enhanced salinity tolerance in crop plants. Crit Rev Plant Sci 35(3):146–189

    Article  CAS  Google Scholar 

  • Ashkani S, Rafii MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, Tanweer FA, Akhtar MS, Nasehi A (2015) Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop. Front Plant Sci 6:886

    Article  PubMed  PubMed Central  Google Scholar 

  • Atkins P, Bowler I (2016) Food in society: economy, culture, geography. Routledge, Abingdon

    Book  Google Scholar 

  • Anamika MS, Singh B, Patra A, Islam MA (2019) Databases: a weapon from the arsenal of bioinformatics for plant abiotic stress research. In: Recent approaches in omics for plant resilience to climate change. Springer, Cham, pp 135–169

    Chapter  Google Scholar 

  • Azadi P, Bagheri H, Nalousi AM, Nazari F, Chandler SF (2016) Current status and biotechnological advances in genetic engineering of ornamental plants. Biotechnol Adv 34(6):1073–1090

    Article  PubMed  Google Scholar 

  • Azzam O, Chancellor TC (2002) The biology, epidemiology, and management of rice tungro disease in Asia. Plant Dis 86(2):88–100

    Article  CAS  PubMed  Google Scholar 

  • Bado S, Forster BP, Nielen S, Ali AM, Lagoda PJ, Till BJ, Laimer M (2015) Plant mutation breeding: current progress and future assessment. Plant Breed Rev 39:23–88

    Google Scholar 

  • Bado S, Yamba NG, Sesay JV, Laimer M, Forster BP (2017) Plant mutation breeding for the improvement of vegetatively propagated crops: successes and challenges. CAB Reviews 12(028):1–21

    Article  Google Scholar 

  • Bae S, Park J, Kim JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30(10):1473–1475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baltes NJ, Voytas DF (2015) Enabling plant synthetic biology through genome engineering. Trends Biotechnol 33(2):120–131

    Article  CAS  PubMed  Google Scholar 

  • Baltes NJ, Gil-Humanes J, Voytas DF (2017) Genome engineering and agriculture: opportunities and challenges. In: Progress in molecular biology and translational science, vol 149. Academic Press, Cambridge, pp 1–26

    Google Scholar 

  • Banasik A, Kanellopoulos A, Claassen GD, Bloemhof-Ruwaard JM, van der Vorst JG (2017) Assessing alternative production options for eco-efficient food supply chains using multi-objective optimization. Ann Oper Res 250(2):341–362

    Article  Google Scholar 

  • Banerjee A, Roychoudhury A (2019) Genetic engineering in plants for enhancing arsenic tolerance. In: Transgenic plant technology for remediation of toxic metals and metalloids. Academic Press, Cambridge, pp 463–475

    Chapter  Google Scholar 

  • Baret PV, Vanloqueren G (2017) How agricultural research systems shape a technological regime that develops genetic engineering but locks out agroecological innovations. In: Food sovereignty, agroecology and biocultural diversity. Routledge, Abingdon, pp 77–112

    Google Scholar 

  • Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9(1):39

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belkhodja R (2018) Breeding small grain cereal crops in a climate change scenario. https://hdl.handle.net/20.500.11766/9623

  • Bhowmik P, Ellison E, Polley B, Bollina V, Kulkarni M, Ghanbarnia K, Song H, Gao C, Voytas DF, Kagale S (2018) Targeted mutagenesis in wheat microspores using CRISPR/Cas9. Sci Rep 8

    Google Scholar 

  • Bilichak A, Eudes F (2016) Genetic engineering of plants using Zn fingers, TALENs, and CRISPRs. In: Genome stability. Academic Press, Cambridge, pp 187–201

    Chapter  Google Scholar 

  • Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493(7432):429

    Article  CAS  PubMed  Google Scholar 

  • Butt H, Jamil M, Wang JY, Al-Babili S, Mahfouz M (2018) Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis. BMC Plant Biol 18(1):174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cai L, Cao Y, Xu Z, Ma W, Zakria M, Zou L, Cheng Z, Chen G (2017) A transcription activator-like effector Tal7 of Xanthomonasoryzaepv. oryzicola activates rice gene Os09g29100 to suppress rice immunity. Sci Rep 7(1):5089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cazzolla Gatti R (2016) Trends in human development and environmental protection. Int J Environ Stud 73(2):268–276

    Article  Google Scholar 

  • Certo MT, Gwiazda KS, Kuhar R, Sather B, Curinga G, Mandt T, Brault M, Lambert AR, Baxter SK, Jacoby K, Ryu BY (2012) Coupling endonucleases with DNA end–processing enzymes to drive gene disruption. Nat Methods 9(10):973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chancellor TCB, Holt J, Villareal S, Tiongco ER, Venn J (2006) Spread of plant virus disease to new plantings: a case study of rice tungro disease. Adv Virus Res 66:1–29

    Article  CAS  PubMed  Google Scholar 

  • Chao S, Cai Y, Feng B, Jiao G, Sheng Z, Luo J, Tang S, Wang J, Wei X, Hu P (2019) Editing of the rice isoamylase gene ISA1 provides insights into its function in starch formation. Rice Sci 26(2):77–87

    Article  Google Scholar 

  • Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B (2017) An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize. Plant Biotechnol J 15(2):257–268

    Article  CAS  PubMed  Google Scholar 

  • Chari R, Mali P, Moosburner M, Church GM (2015) Unraveling CRISPR/Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 12(9):823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Wang Y, Zhang R, Zhang H, Gao C (2019) CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu Rev Plant Biol 70:667–697

    Article  CAS  PubMed  Google Scholar 

  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186(2):757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Roffler S, Ohyanagi H, Wicker T (2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16(1):538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de los Campos G, Burgueño J, González-Camacho JM, Pérez-Elizalde S, Beyene Y, Dreisigacker S (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22(11):961–975

    Article  CAS  PubMed  Google Scholar 

  • Daboussi F, Stoddard TJ, Zhang F (2015) Engineering meganuclease for precise plant genome modification. In: Advances in new technology for targeted modification of plant genomes. Springer, New York, pp 21–38

    Google Scholar 

  • Darwin C (2010) The variation of animals and plants under domestication. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Dhakate P, Sharma P, Mehta S, Akter J, Bhatt V, Chandanshive S, Chakravarty D, Rahman M, Islam MA (2019) Beneficial role of metalloids in plants: molecular understanding and applicability. In: Recent approaches in omics for plant resilience to climate change. Springer, Cham, pp 357–387

    Chapter  Google Scholar 

  • Dillard HR (2019) Global food and nutrition security: from challenges to solutions. Food Sec 11:249–252

    Article  Google Scholar 

  • Ding D, Chen K, Chen Y, Li H, Xie K (2018) Engineering introns to express RNA guides for Cas9-and Cpf1-mediated multiplex genome editing. Mol Plant 11(4):542–552

    Article  CAS  PubMed  Google Scholar 

  • Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE (2014) Rational design of highly active sgRNAs for CRISPR/Cas9–mediated gene inactivation. Nat Biotechnol 32(12):1262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33(18):5978–5990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Endo A, Masafumi M, Kaya H, Toki S (2016) Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida. Sci Rep 6:38169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eş I, Gavahian M, Marti-Quijal FJ, Lorenzo JM, Khaneghah AM, Tsatsanis C, Kampranis SC, Barba FJ (2019) The application of the CRISPR/Cas9 genome editing machinery in food and agricultural science: current status, future perspectives, and associated challenges. Biotechnol Adv 37(3):410–421

    Article  CAS  PubMed  Google Scholar 

  • Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23(10):1229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L (2014a) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in arabidopsis. Proc Natl Acad Sci 111(12):4632–4637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L (2014b) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in arabidopsis. Proc Natl Acad Sci U S A 111(12):4632–4637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Figueroa A (2019) Population and the quality of society. In: The quality of society. Palgrave Macmillan, Cham, pp 115–137

    Chapter  Google Scholar 

  • Fukuoka S, Yamamoto SI, Mizobuchi R, Yamanouchi U, Ono K, Kitazawa N, Yasuda N, Fujita Y, Nguyen TT, Koizumi S, Sugimoto K (2014) Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast. Sci Rep 4:4550

    Article  CAS  Google Scholar 

  • Gaj T, Gersbach CA, Barbas CF III (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao C (2018) The future of CRISPR technologies in agriculture. Nat Rev Mol Cell Biol 19(5):275–276

    Article  CAS  PubMed  Google Scholar 

  • Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, Wu Y, Zhao P, Xia Q (2015) CRISPR/Cas9-mediated targeted mutagenesis in nicotianatabacum. Plant Mol Biol 87(1–2):99–110

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296(5565):92–100

    Article  CAS  PubMed  Google Scholar 

  • Glenn KC, Alsop B, Bell E, Goley M, Jenkinson J, Liu B, Martin C, Parrott W, Souder C, Sparks O, Urquhart W (2017) Bringing new plant varieties to market: plant breeding and selection practices advance beneficial characteristics while minimizing unintended changes. Crop Sci 57(6):2906–2921

    Article  Google Scholar 

  • Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17(1):148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heigwer F, Kerr G, Boutros M (2014) E-CRISP: fast CRISPR target site identification. Nat Methods 11(2):122

    Article  CAS  PubMed  Google Scholar 

  • Hensel G, Kumlehn J (2019) Genome engineering using TALENs. In: Barley. Humana Press, New York, NY, pp 195–215

    Chapter  Google Scholar 

  • Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170

    Article  CAS  PubMed  Google Scholar 

  • Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31(9):827

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hsu PD, Lander ES, Zhang F (2014) Development and applications of CRISPR/Cas9 for genome engineering. Cell 157(6):1262–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu X, Wang C, Fu Y, Liu Q, Jiao X, Wang K (2016) Expanding the range of CRISPR/Cas9 genome editing in rice. Mol Plant 9(6):943–945

    Article  CAS  PubMed  Google Scholar 

  • Hu X, Wang C, Liu Q, Fu Y, Wang K (2017) Targeted mutagenesis in rice using CRISPR-Cpf1 system. J Genet Genomics 44(1):71–73

    Article  PubMed  Google Scholar 

  • Huang TK, Puchta H (2019) CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. Plant Cell Rep 38(4):443–453

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Zeng X, Li J, Zhao D (2017) Construction and analysis of tify1a and tify1b mutants in rice (Oryza sativa) based on CRISPR/Cas9 technology. J Agric Biotechnol 25(6):1003–1012

    Google Scholar 

  • Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41(20):e188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jun R, Xixun H, Kejian W, Chun W (2019) Development and application of CRISPR/Cas system in rice. Ric Sci 26(2):69–76

    Article  Google Scholar 

  • Kamburova VS, Nikitina EV, Shermatov SE, Buriev ZT, Kumpatla SP, Emani C, Abdurakhmonov IY (2017) Genome editing in plants: an overview of tools and applications. Int J Agron 2017:1–15

    Article  CAS  Google Scholar 

  • Kantar MB, Runck BC, Raghavan B, Joglekar AB, Senay S, Krohn B, Neyhart J, Bradeen J, Soto Gomez M, Kjelgren R (2019) The many-faced Janus of plant breeding. Plants People Planet 1(4):306–309. https://doi.org/10.1002/ppp3.30

  • Kaur K, Tandon H, Gupta AK, Kumar M (2015) CrisprGE: a central hub of CRISPR/Cas-based genome editing. Database 2015:bav055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khalid A, Zhang Q, Yasir M, Li F (2017) Small RNA based genetic engineering for plant viral resistance: application in crop protection. Front Microbiol 8:43

    Article  PubMed  PubMed Central  Google Scholar 

  • Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59(1):1–6

    Article  CAS  PubMed  Google Scholar 

  • Kihoro J, Bosco NJ, Murage H, Ateka E, Makihara D (2013) Investigating the impact of rice blast disease on the livelihood of the local farmers in greater Mwea region of Kenya. Springerplus 2(1):308

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim HJ, Cho SW, Jeong JS, Kim JK, Lim YP, Kim JS, Kang BC (2012) Construction, selection, and application of zinc finger nucleases as a tool for genome editing in rice. 한국원예학회학술발표요지. Seoul National University Open Repository. pp 45–46. http://s-space.snu.ac.kr/handle/10371/121043

  • Kleter GA, Kuiper HA, Kok EJ (2019) Gene-edited crops: towards a harmonized safety assessment. Trends Biotechnol 37(5):443–447

    Article  CAS  PubMed  Google Scholar 

  • Knott GJ, Doudna JA (2018) CRISPR-Cas guides the future of genetic engineering. Science 361(6405):866–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Korotkova AM, Gerasimova SV, Shumny VK, Khlestkina EK (2017) Crop genes modified using the CRISPR/Cas system. Russian J Genet Appl Res 7(8):822–832

    Article  CAS  Google Scholar 

  • Korotkova AM, Gerasimova SV, Khlestkina EK (2019) Current achievements in modifying crop genes using CRISPR/Cas system. Vavilov J Genet Breed 23(1)

    Google Scholar 

  • Kumari P, Rastogi A, Shukla A, Srivastava S, Yadav S (2018) Prospects of genetic engineering utilizing potential genes for regulating arsenic accumulation in plants. Chemosphere 211:397–406

    Article  CAS  PubMed  Google Scholar 

  • Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E (2016) CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res 44(W1):W272–W276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laible G, Wei J, Wagner S (2015) Improving livestock for agriculture–technological progress from random transgenesis to precision genome editing heralds a new era. Biotechnol J 10(1):109–120

    Article  CAS  PubMed  Google Scholar 

  • Langner T, Kamoun S, Belhaj K (2018) CRISPR crops: plant genome editing toward disease resistance. Annu Rev Phytopathol 56:479–512

    Article  CAS  PubMed  Google Scholar 

  • Lassoued R, Macall DM, Hesseln H, Phillips PW, Smyth SJ (2019) Benefits of genome-edited crops: expert opinion. Transgenic Res 28(2):247–256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee JH, Muhsin M, Atienza GA, Kwak DY, Kim SM, De Leon TB, Angeles ER, Coloquio E, Kondoh H, Satoh K, Cabunagan RC (2010) Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to Rice tungro spherical virus. Mol Plant Microbe Interact 23(1):29–38

    Article  CAS  PubMed  Google Scholar 

  • Li C, Zhang B (2019) Genome editing in cotton using CRISPR/Cas9 system. In: Transgenic cotton. Humana Press, New York, pp 95–104

    Chapter  Google Scholar 

  • Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30(5):390

    Article  CAS  PubMed  Google Scholar 

  • Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J, Li J, Gao C (2016a) Gene replacements and insertions in rice by intron targeting using CRISPR–Cas9. Nat Plants 2(10):16139

    Article  CAS  PubMed  Google Scholar 

  • Li T, Liu B, Chen CY, Yang B (2016b) TALEN-mediated homologous recombination produces site-directed DNA base change and herbicide-resistant rice. J Genet Genomics 43(5):297–305

    Article  PubMed  Google Scholar 

  • Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H (2016c) Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci 7:377

    PubMed  PubMed Central  Google Scholar 

  • Li J, Sun Y, Du J, Zhao Y, Xia L (2017a) Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Mol Plant 10(3):526–529

    Article  CAS  PubMed  Google Scholar 

  • Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, Fang J, Chu C, Yang J, Bu Q (2017b) High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. J Genet Genomics 44(3):175

    Article  PubMed  Google Scholar 

  • Li S, Li J, He Y, Xu M, Zhang J, Du W, Zhao Y, Xia L (2019) Precise gene replacement in rice by RNA transcript-templated homologous recombination. Nat Biotechnol 37(4):445–450

    Article  CAS  PubMed  Google Scholar 

  • Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun 8:14261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin CS, Hsu CT, Yang LH, Lee LY, Fu JY, Cheng QW, Wu FH, Hsiao HC, Zhang Y, Zhang R, Chang WJ (2018) Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnol J 16(7):1295–1310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lino CA, Harper JC, Carney JP, Timlin JA (2018) Delivering CRISPR: a review of the challenges and approaches. Drug Deliv 25(1):1234–1257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu D, Chen X, Liu J, Ye J, Guo Z (2012) The rice ERF transcription factor OsERF922 negatively regulates resistance to magnaporthe oryzae and salt tolerance. J Exp Bot 63(10):3899–3911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL (2017a) CRISPR-P 2.0: an improved CRISPR/Cas9 tool for genome editing in plants. Mol Plant 10(3):530–532

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Wu S, Xu J, Sui C, Wei J (2017b) Application of CRISPR/Cas9 in plant biology. Acta Pharm Sin B 7(3):292–302

    Article  PubMed  PubMed Central  Google Scholar 

  • Lloyd A, Plaisier CL, Carroll D, Drews GN (2005) Targeted mutagenesis using zinc-finger nucleases in arabidopsis. Proc Natl Acad Sci 102(6):2232–2237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lou D, Wang H, Liang G, Yu D (2017) OsSAPK2 confers abscisic acid sensitivity and tolerance to drought stress in rice. Front Plant Sci 8:993

    Article  PubMed  PubMed Central  Google Scholar 

  • Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 169(2):971–985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu Y, Zhu JK (2017) Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Mol Plant 10(3):523–525

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y, Xie Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8(8):1274–1284

    Article  CAS  PubMed  Google Scholar 

  • Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet-Loedin I, Čermák T, Voytas DF, Choi IR, Chadha-Mohanty P (2018) Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnol J 16(11):1918–1927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacPherson CR, Scherf A (2015) Flexible guide-RNA design for CRISPR applications using Protospacer workbench. Nat Biotechnol 33(8):805

    Article  CAS  PubMed  Google Scholar 

  • Mahas A, Ali Z, Tashkandi M, Mahfouz MM (2019) Virus-mediated genome editing in plants using the CRISPR/Cas9 system. In: Plant genome editing with CRISPR systems. Humana Press, New York, pp 311–326

    Chapter  Google Scholar 

  • Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, NagamangalaKanchiswamy C (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7:1904

    Article  PubMed  PubMed Central  Google Scholar 

  • Malzahn A, Lowder L, Qi Y (2017) Plant genome editing with TALEN and CRISPR. Cell Biosci 7(1):21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marco F, Bitrián M, Carrasco P, Rajam MV, Alcázar R, Tiburcio AF (2015) Genetic engineering strategies for abiotic stress tolerance in plants. In: Plant biology and biotechnology. Springer, New Delhi, pp 579–609

    Chapter  Google Scholar 

  • Martirosyan DM, Singh J (2015) A new definition of functional food by FFC: what makes a new definition unique? Funct Food Health Dis 5(6):209–223

    Article  Google Scholar 

  • Mehta S, Singh B, Dhakate P, Rahman M, Islam MA (2019a) Rice, marker-assisted breeding, and disease resistance. In: Disease resistance in crop plants. Springer, Cham, pp 83–111

    Chapter  Google Scholar 

  • Mehta S, James D, Reddy MK (2019b) Omics technologies for abiotic stress tolerance in plants: current status and prospects. In: Recent approaches in omics for plant resilience to climate change. Springer, Cham, pp 1–34

    Google Scholar 

  • Merga IF, Tripathi L, Hvoslef-Eide AK, Gebre E (2019) Application of genetic engineering for control of bacterial wilt disease of Enset, Ethiopia’s sustainability crop. Front Plant Sci 10:133

    Article  PubMed  PubMed Central  Google Scholar 

  • Mew TW, Alvarez AM, Leach JE, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77(1):5–12

    Article  Google Scholar 

  • Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Wan J, Gu H, Qu LJ (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23(10):1233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miao C, Xiao L, Hua K, Zou C, Zhao Y, Bressan RA, Zhu JK (2018) Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity. Proc Natl Acad Sci 115(23):6058–6063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mikami M, Toki S, Endo M (2015a) Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice. Plant Mol Biol 88(6):561–572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mikami M, Toki S, Endo M (2015b) Parameters affecting frequency of CRISPR/Cas9 mediated targeted mutagenesis in rice. Plant Cell Rep 34(10):1807–1815

    Article  CAS  PubMed  Google Scholar 

  • Minkenberg B, Zhang J, Xie K, Yang Y (2019) CRISPR-PLANT v2: an online resource for highly specific guide RNA spacers based on improved off-target analysis. Plant Biotechnol J 17(1):5–8

    PubMed  Google Scholar 

  • Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42(W1):W401–W407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo. Nat Methods 12(10):982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morton LW, Roesch-McNally G, Wilke AK (2017) Upper Midwest farmer perceptions: too much uncertainty about impacts of climate change to justify changing current agricultural practices. J Soil Water Conserv 72(3):215–225

    Article  Google Scholar 

  • Muralidharan K, Krishnaveni D, Rajarajeswari NV, Prasad AS (2003) Tungro epidemics and yield losses in paddy fields in India. Curr Sci 85(8):1143–1147

    Google Scholar 

  • Naito Y, Hino K, Bono H, Ui-Tei K (2014) CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31(7):1120–1123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nielsen J, Keasling JD (2016) Engineering cellular metabolism. Cell 164(6):1185–1197

    Article  CAS  PubMed  Google Scholar 

  • Noman A, Aqeel M, He S (2016) CRISPR/Cas9: tool for qualitative and quantitative plant genome editing. Front Plant Sci 7:1740

    Article  PubMed  PubMed Central  Google Scholar 

  • Novak S (2019) Plant biotechnology applications of zinc finger technology. In: Transgenic plants. Humana Press, New York, pp 295–310

    Chapter  Google Scholar 

  • Oerke EC (2006) Crop losses to pests. J Agric Sci 144(1):31–43

    Article  Google Scholar 

  • Oldeman LR, Hakkeling RT, Sombroek WG (2017) World map of the status of human-induced soil degradation: an explanatory note. International Soil Reference and Information Centre, Wageningen

    Google Scholar 

  • Oliveros JC, Franch M, Tabas-Madrid D, San-León D, Montoliu L, Cubas P, Pazos F (2016) Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res 44(W1):W267–W271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osakabe Y, Watanabe T, Sugano SS, Ueta R, Ishihara R, Shinozaki K, Osakabe K (2016) Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci Rep 6:26685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osakabe Y, Liang Z, Ren C, Nishitani C, Osakabe K, Wada M, Komori S, Malnoy M, Velasco R, Poli M, Jung MH (2018) CRISPR–Cas9-mediated genome editing in apple and grapevine. Nat Protoc 13(12):2844

    Article  CAS  PubMed  Google Scholar 

  • Pacher M, Puchta H (2017) From classical mutagenesis to nuclease-based breeding–directing natural DNA repair for a natural end-product. Plant J 90(4):819–833

    Article  CAS  PubMed  Google Scholar 

  • Park J, Bae S (2017) Cpf1-database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. Bioinformatics 34(6):1077–1079

    Article  CAS  Google Scholar 

  • Park J, Kim JS, Bae S (2016) Cas-database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR/Cas9. Bioinformatics 32(13):2017–2023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, Ventura A (2017) GuideScan software for improved single and paired CRISPR guide RNA design. Nat Biotechnol 35(4):347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Philander SG (2018) Is the temperature rising?: the uncertain science of global warming. Princeton University Press, Princeton

    Book  Google Scholar 

  • Pliatsika V, Rigoutsos I (2015) “Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs. Biol Direct 10(1):4

    Article  PubMed  PubMed Central  Google Scholar 

  • Porteus MH, Carroll D (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol 23(8):967

    Article  CAS  PubMed  Google Scholar 

  • Pradinaud C, Northey S, Amor B, Bare J, Benini L, Berger M, Boulay AM, Junqua G, Lathuillière MJ, Margni M, Motoshita M (2019) Defining freshwater as a natural resource: a framework linking water use to the area of protection natural resources. Int J Life Cycle Assess 24(5):960–974

    Article  PubMed  PubMed Central  Google Scholar 

  • Pratim Roy M (2019) Malnutrition in children and its determinants: a study from east India. Tropical Doctor. 0049475518824825

    Google Scholar 

  • Pray C, Huang J, Hu R, Deng H, Yang J, Morin XK (2018) Prospects for cultivation of genetically engineered food crops in China. Glob Food Sec 16:133–137

    Article  Google Scholar 

  • Prykhozhij SV, Rajan V, Gaston D, Berman JN (2015) CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One 10(3):e0119372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Project, I.R.G.S, Sasaki T (2005) The map-based sequence of the rice genome. Nature 436(7052):793

    Google Scholar 

  • Puchta H, Fauser F (2014) Synthetic nucleases for genome engineering in plants: prospects for a bright future. Plant J 78(5):727–741

    Article  CAS  PubMed  Google Scholar 

  • Rahman M, Sultana S, Nath D, Kalita S, Chakravarty D, Mehta S, Wani SH, Islam MA (2019) Molecular breeding approaches for disease resistance in sugarcane. In: Disease resistance in crop plants. Springer, Cham, pp 131–155

    Chapter  Google Scholar 

  • Ricroch A, Clairand P, Harwood W (2017) Use of CRISPR systems in plant genome editing: toward new opportunities in agriculture. Emerg Top Life Sci 1(2):169–182

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamoto T, Matsuoka M (2008) Identifying and exploiting grain yield genes in rice. Curr Opin Plant Biol 11(2):209–214

    Article  CAS  PubMed  Google Scholar 

  • Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS (2013) A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497(7448):254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Savary S, Ficke A, Aubertot JN, Hollier C (2012) Crop losses due to diseases and their implications for global food production losses and food security. Food Sec 4:519–537

    Article  Google Scholar 

  • Scheben A, Wolter F, Batley J, Puchta H, Edwards D (2017) Towards CRISPR/Cas crops–bringing together genomics and genome editing. New Phytol 216(3):682–698

    Article  CAS  PubMed  Google Scholar 

  • Shah T, Andleeb T, Lateef S, Noor MA (2018) Genome editing in plants: advancing crop transformation and overview of tools. Plant Physiol Biochem 131:12–21

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Wang Y, Li J, Gao C (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9(10):2395

    Article  CAS  PubMed  Google Scholar 

  • Shao GN, Xie LH, Jiao GA, Wei XJ, Sheng ZH, Tang SQ, Hu PS (2017) CRISPR/CAS9-mediated editing of the fragrant gene Badh2 in rice. Chin J Rice Sci 31(2):216–222

    Google Scholar 

  • Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X, Skarnes WC (2014) Efficient genome modification by CRISPR/Cas9 nickase with minimal off-target effects. Nat Methods 11(4):399–402

    Article  CAS  PubMed  Google Scholar 

  • Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H (2017a) Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat Biotechnol 35(5):441–443

    Article  CAS  PubMed  Google Scholar 

  • Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H (2017b) Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat Biotechnol 35(5):441–443

    Article  CAS  PubMed  Google Scholar 

  • Shigaki T (2018) Application of biotechnologies in the conservation and utilization of plant genetic resources for food security. In: Food Security and Climate Change, pp 413–431

    Chapter  Google Scholar 

  • Singh B, Mehta S, Aggarwal SK, Tiwari M, Bhuyan SI, Bhatia S, Islam MA (2019) Barley, disease resistance, and molecular breeding approaches. In: Disease resistance in crop plants. Springer, Cham, pp 261–299

    Chapter  Google Scholar 

  • Siro I, Kápolna E, Kápolna B, Lugasi A (2008) Functional food. Product development, marketing and consumer acceptance—a review. Appetite 51(3):456–467

    Article  PubMed  Google Scholar 

  • Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC (2011) QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database 2011:bar037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soda N, Verma L, Giri J (2018) CRISPR/Cas9 based plant genome editing: significance, opportunities and recent advances. Plant Physiol Biochem 131:2–11

    Article  CAS  PubMed  Google Scholar 

  • Sprink T, Metje J, Hartung F (2015) Plant genome editing by novel tools: TALEN and other sequence specific nucleases. Curr Opin Biotechnol 32:47–53

    Article  CAS  PubMed  Google Scholar 

  • Stemmer M, Thumberger T, del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One 10(4):e0124633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sticklen MB (2008) Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol. Nat Rev Genet 9(6):433–443

    Article  CAS  PubMed  Google Scholar 

  • Subramanian KR (2018) The crisis of consumption of natural resources. Int J Rec Innov Acad Res 2(8–19):8–19

    Google Scholar 

  • Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, Guo X, Du W, Zhao Y, Xia L (2016) Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant 9(4):628–631

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Jiao G, Liu Z, Zhang X, Li J, Guo X, Du W, Du J, Francis F, Zhao Y, Xia L (2017) Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front Plant Sci 8:298

    PubMed  PubMed Central  Google Scholar 

  • Sun J, Liu H, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu HJ, Chen LL (2019) CRISPR-local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics 35(14):2501–2503

    Article  CAS  PubMed  Google Scholar 

  • Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169(2):931–945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takeda Y, Suzuki S, Tobimatsu Y, Osakabe K, Osakabe Y, Ragamustari SK, Sakamoto M, Umezawa T (2019) Lignin characterization of rice coniferaldehyde 5-hydroxylase loss-of-function mutants generated with the CRISPR/Cas9 system. Plant J 97(3):543–554

    Article  CAS  PubMed  Google Scholar 

  • Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER (2017a) A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 3(3):17018

    Article  CAS  PubMed  Google Scholar 

  • Tang L, Mao B, Li Y, Lv Q, Zhang L, Chen C, He H, Wang W, Zeng X, Shao Y, Pan Y (2017b) Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Sci Rep 7(1):14438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang X, Ren Q, Yang L, Bao Y, Zhong Z, He Y, Liu S, Qi C, Liu B, Wang Y, Sretenovic S (2019) Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas 12a mediated plant genome editing. Plant Biotechnol J 17(7):1431–1445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsutsui H, Higashiyama T (2017) pKAMA-ITACHI vectors for highly efficient CRISPR/Cas9-mediated gene knockout in Arabidopsis thaliana. Plant Cell Physiol 58(1):46–56

    CAS  PubMed  Google Scholar 

  • Upadhyay SK, Kumar J, Alok A, Tuli R (2013) RNA-guided genome editing for target gene mutations in wheat. G3 3(12):2233–2238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Valin H, Sands RD, Van der Mensbrugghe D, Nelson GC, Ahammad H, Blanc E, Bodirsky B, Fujimori S, Hasegawa T, Havlik P, Heyhoe E (2014) The future of food demand: understanding differences in global economic models. Agric Econ 45(1):51–67

    Article  Google Scholar 

  • Voytas DF (2013) Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64:327–350

    Article  CAS  PubMed  Google Scholar 

  • Waltz E (2018) With a free pass, CRISPR-edited plants reach market in record time. Nat Biotechnol 36(1):6–7

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu YG, Zhao K (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11(4):e0154027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang M, Mao Y, Lu Y, Tao X, Zhu JK (2017) Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol Plant 10(7):1011–1013

    Article  CAS  PubMed  Google Scholar 

  • Wang P, Zhang J, Sun L, Ma Y, Xu J, Liang S, Deng J, Tan J, Zhang Q, Tu L, Daniell H (2018) High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system. Plant Biotechnol J 16(1):137–150

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Han Y, Feng X, Li YZ, Qin BX, Luo JJ, Wei Z, Qiu YF, Liu F, Li RB (2019) Breeding of Indica glutinous cytoplasmic male sterile line WX209A via CRISPR/Cas9 mediated genomic editing. Czech J Genet Plant Breed 55:93–100

    Article  Google Scholar 

  • Wingeyer A, Amado T, Pérez-Bidegain M, Studdert G, Varela C, Garcia F, Karlen D (2015) Soil quality impacts of current South American agricultural practices. Sustainability 7(2):2213–2242

    Article  Google Scholar 

  • Wong N, Liu W, Wang X (2015) WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 16(1):218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wright DA, Townsend JA, Winfrey RJ Jr, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 44(4):693–705

    Article  CAS  PubMed  Google Scholar 

  • Wu G, Yan Q, Jones JA, Tang YJ, Fong SS, Koffas MA (2016) Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications. Trends Biotechnol 34(8):652–664

    Article  CAS  PubMed  Google Scholar 

  • Wu R, Lucke M, Jang YT, Zhu W, Symeonidi E, Wang C, Fitz J, Xi W, Schwab R, Weigel D (2018) An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana. Plant Methods 14(1):65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR–Cas system. Mol Plant 6(6):1975–1983

    Article  CAS  PubMed  Google Scholar 

  • Xie X, Ma X, Zhu Q, Zeng D, Li G, Liu YG (2017) CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol Plant 10(9):1246–1249

    Article  CAS  PubMed  Google Scholar 

  • Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442

    Article  CAS  PubMed  Google Scholar 

  • Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14(1):327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu R, Li H, Qin R, Wang L, Li L, Wei P, Yang J (2014) Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice. Rice 7(1):5

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu R, Yang Y, Qin R, Li H, Qiu C, Li L, Wei P, Yang J (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J Genet Genomics 43(8):529

    Article  PubMed  Google Scholar 

  • Xu R, Qin R, Li H, Li D, Li L, Wei P, Yang J (2017) Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotechnol J 15(6):713–717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xuan TD, Anh TT, Tran HD, Khanh TD, Dat TD (2019) Mutation breeding of a N-methyl-N-nitrosourea (MNU)-induced Rice (Oryza sativa L. ssp. Indica) population for the yield attributing traits. Sustainability 11(4):1062

    Article  CAS  Google Scholar 

  • Yin K, Qiu JL (2019) Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc B 374(1767):20180322

    Article  CAS  Google Scholar 

  • Yin K, Han T, Liu G, Chen T, Wang Y, Yu AY, Liu Y (2015) A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Sci Rep 5:14926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin K, Gao C, Qiu JL (2017) Progress and prospects in plant genome editing. Nat Plants 3(8):17107

    Article  CAS  PubMed  Google Scholar 

  • Yin X, Anand A, Quick P, Bandyopadhyay A (2019) Editing a stomatal developmental gene in rice with CRISPR/Cpf1. In: Plant genome editing with CRISPR systems. Humana Press, New York, pp 257–268

    Chapter  Google Scholar 

  • Youssef D, Nihou A, Partier A, Tassy C, Paul W, Rogowsky PM, Beckert M, Barret P (2018) Induction of targeted deletions in transgenic bread wheat (Triticum aestivum L.) using customized meganuclease. Plant Mol Biol Report 36(1):71–81

    Article  CAS  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92

    Article  CAS  PubMed  Google Scholar 

  • Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, Van Der Oost J, Regev A, Koonin EV (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163(3):759–771

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H (2019) Genetically modified organisms (GMOs) as the new hope. In: Securing the ‘rice bowl’. Palgrave Macmillan, Singapore, pp 95–123

    Chapter  Google Scholar 

  • Zhang H, Wu Z, Wang C, Li Y, Xu JR (2014) Germination and infectivity of microconidia in the rice blast fungus Magnaporthe oryzae. Nat Commun 5:4518

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Zang Q, Xu B, Zheng W, Ban R, Zhang H, Yang Y, Hao Q, Iqbal F, Li A, Shi Q (2016) IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 32(13):2069–2071

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Zhang H, Botella JR, Zhu JK (2018) Generation of new glutinous rice by CRISPR/Cas9-targeted mutagenesis of the Waxy gene in elite rice varieties. J Integr Plant Biol 60(5):369–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Liang J, Wang M, Li D, Liu Y, Chen TH, Yang X (2019) Genetic engineering of the biosynthesis of glycine betaine enhances the fruit development and size of tomato. Plant Sci 280:355–366

    Article  CAS  PubMed  Google Scholar 

  • Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W (2014) RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res 43(D1):D1018–D1022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng Y, Zhang N, Martin GB, Fei Z (2019) Plant genome editing database (PGED): a call for submission of information about genome-edited plant mutants. Mol Plant 12(2):127–129

    Article  CAS  PubMed  Google Scholar 

  • Zhong Z, Zhang Y, You Q, Tang X, Ren Q, Liu S, Yang L, Wang Y, Liu X, Liu B, Zhang T (2018) Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Mol Plant 11(7):999–1002

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Peng Z, Long J, Sosso D, Liu B, Eom JS, Huang S, Liu S, Vera Cruz C, Frommer WB, White FF (2015) Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice. Plant J 82(4):632–643

    Article  CAS  PubMed  Google Scholar 

  • Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014) CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR/Cas9 genome-editing systems. PLoS One 9(9):e108424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zischewski J, Fischer R, Bortesi L (2017) Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv 35(1):95–104

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India

    Sahil Mehta, Shambhu Krishan Lal, Ajay Kumar Venkatapuram, Vijay Sheri, Panditi Varakumar, Renu Yadav, Miraj Ali, V. Mohan M. Achary & Malireddy K. Reddy

  2. Division of Plant Pathology, ICAR-Indian Agriculture Research Institute, New Delhi, India

    Kuleshwar Prasad Sahu & Mukesh Kumar

  3. Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi, India

    Chandrapal Vishwakarma

  4. Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia University, New Delhi, India

    M. Rizwan Jameel

Authors
  1. Sahil Mehta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shambhu Krishan Lal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kuleshwar Prasad Sahu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ajay Kumar Venkatapuram
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mukesh Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vijay Sheri
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Panditi Varakumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chandrapal Vishwakarma
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Renu Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. M. Rizwan Jameel
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Miraj Ali
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. V. Mohan M. Achary
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Malireddy K. Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Soil Science and Agricultural Chemistry, IAR, Banaras Hindu University, Varanasi, Uttar Pradesh, India

    Amitava Rakshit

  2. Department of Soil Science and Agricultural Chemistry, IAR, Banaras Hindu University, Varanasi, Uttar Pradesh, India

    Harikesh Bahadur Singh

  3. Indian Council of Agricultural Research, New Delhi, Delhi, India

    Anand Kumar Singh

  4. Center (ISARC), Director of IRRI South Asia Regional, New Delhi, Delhi, India

    Uma Shankar Singh

  5. Department of Environmental Engineering, São Paulo State University, Sorocaba, Brazil

    Leonardo Fraceto

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mehta, S. et al. (2020). CRISPR/Cas9-Edited Rice: A New Frontier for Sustainable Agriculture. In: Rakshit, A., Singh, H., Singh, A., Singh, U., Fraceto, L. (eds) New Frontiers in Stress Management for Durable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-15-1322-0_23

Download citation

Publish with us

Policies and ethics

Search

Navigation