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Review Articles

Vol. 12 No. 4 (2025)

Precision genome editing in agriculture: Tacking pathogens through CRISPR-Cas9

DOI
https://doi.org/10.14719/pst.7876
Submitted
22 February 2025
Published
18-11-2025 — Updated on 04-12-2025
Versions

Abstract

Precision genome-editing techniques, in particular CRISPR-Cas9, have revolutionised the management of agricultural diseases by allowing targeted modifications of resistance (R) genes, susceptibility (S) genes and targets of pathogen agents. This transformative approach provides unprecedented control of the interaction between plants and pathogens, enabling the development of crops with increased resistance to a variety of biotic stresses, including bacterial, viral and fungal pathogens. Recent advances have demonstrated the ability of CRISPR-Cas9 to precisely modify key genetic components, while integrating with multi-omics (transcriptomics, proteomics and metabolomics) technologies to identify new mechanisms of resistance and optimise the editing strategy. This development makes it easier to produce new, more stable crops under the pressure of climate change and to tackle critical food security challenges. However, the wide deployment of CRISPR-edited crops faces several obstacles, including regulatory uncertainty, potential unintended effects and public acceptance issues, which need careful consideration. Despite these challenges, CRISPR-Cas9 is a powerful tool for sustainable agriculture, offering precise manipulation of plant immunity and stress response, which contributes to building a more resilient and sustainable global food system. Continued innovation in genome editing, combined with responsible management and public involvement, will be crucial for realizing its full potential in meeting the complex challenges of modern farming.

References

  1. 1. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature. 2002;418:700-7. https://doi.org/10.1038/nature01019
  2. 2. Kalaitzandonakes N, Willig C, Zahringer K. The economics and policy of genome editing in crop improvement. Plant Genome. 2023;16. https://doi.org/10.1002/tpg2.20248
  3. 3. Lev-Yadun S, Gopher A, Abbo S. The cradle of agriculture. Science. 2000;288:1602-3. https://doi.org/10.1126/science.288.5471.1602
  4. 4. Lau S-E, Teo WFA, Teoh EY, Tan BC. Microbiome engineering and plant biostimulants for sustainable crop improvement and mitigation of biotic and abiotic stresses. Discover Food. 2022;2:9. https://doi.org/10.1007/s44187-022-00009-5
  5. 5. Hamdan MF, Mohd Noor SN, Abd-Aziz N, Pua T-L, Tan BC. Green revolution to gene revolution: technological advances in agriculture to feed the world. Plants. 2022;11:1297. https://doi.org/10.3390/plants11101297
  6. 6. Savary S, Willocquet L, Pethybridge SJ, Esker P, McRoberts N, Nelson A. The global burden of pathogens and pests on major food crops. Nat Ecol Evol. 2019;3:430-9. https://doi.org/10.1038/s41559-018-0793-y
  7. 7. Langner T, Kamoun S, Belhaj K. CRISPR crops: plant genome editing toward disease resistance. Annu Rev Phytopathol. 2018;56:479-512. https://doi.org/10.1146/annurev-phyto-080417-050158
  8. 8. Dong OX, Ronald PC. Genetic engineering for disease resistance in plants: recent progress and future perspectives. Plant Physiol. 2019;180:26-38. https://doi.org/10.1104/pp.18.01224
  9. 9. Nejat N, Rookes J, Mantri NL, Cahill DM. Plant-pathogen interactions: toward development of next-generation disease-resistant plants. Crit Rev Biotechnol. 2017;37:229-37. https://doi.org/10.3109/07388551.2015.1134437
  10. 10. Bhattacharya A, Parkhi V, Char B. Genome editing for crop improvement: a perspective from India. In vitro Cell Dev Biol Plant. 2021;57:565-73. https://doi.org/10.1007/s11627-021-10184-2
  11. 11. Goulet BE, Roda F, Hopkins R. Hybridization in plants: old ideas, new techniques. Plant Physiol. 2017;173:65-78. https://doi.org/10.1104/pp.16.01340
  12. 12. Hartung F, Schiemann J. Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. Plant J. 2014;78:742-52. https://doi.org/10.1111/tpj.12413
  13. 13. Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu Rev Plant Biol. 2019;70:667-97. https://doi.org/10.1146/annurev-arplant-050718-100049
  14. 14. Hickey LT, Hafeez AN, Robinson H, Jackson SA, Leal-Bertioli SCM, Tester M, et al. Breeding crops to feed 10 billion. Nat Biotechnol. 2019;37:744-54. https://doi.org/10.1038/s41587-019-0152-9
  15. 15. Gao C. Genome engineering for crop improvement and future agriculture. Cell. 2021;184:1621-35. https://doi.org/10.1016/j.cell.2021.01.005
  16. 16. Lyzenga WJ, Pozniak CJ, Kagale S. Advanced domestication: harnessing the precision of gene editing in crop breeding. Plant Biotechnol J. 2021;19:660-70. https://doi.org/10.1111/pbi.13576
  17. 17. Raman R. The impact of genetically modified (GM) crops in modern agriculture: a review. GM Crops Food. 2017;8:195-208. https://doi.org/10.1080/21645698.2017.1413522
  18. 18. Voytas DF. Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol. 2013;64:327-50. https://doi.org/10.1146/annurev-arplant-042811-105552
  19. 19. Voytas DF, Gao C. Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol. 2014;12:e1001877. https://doi.org/10.1371/journal.pbio.1001877
  20. 20. Anzalone AV, Koblan LW, Liu DR. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020;38:824-44. https://doi.org/10.1038/s41587-020-0561-9
  21. 21. Zaman QU, Li C, Cheng H, Hu Q. Genome editing opens a new era of genetic improvement in polyploid crops. Crop J. 2019;7:141-50. https://doi.org/10.1016/j.cj.2018.07.004
  22. 22. Christou P. Plant genetic engineering and agricultural biotechnology 1983-2013. Trends Biotechnol. 2013;31:125-7. https://doi.org/10.1016/j.tibtech.2013.01.006
  23. 23. Lorence A, Verpoorte R. Gene transfer and expression in plants. In: Recombinant gene expression. New Jersey: Humana Press; 2004. p. 329-50. https://doi.org/10.1385/1-59259-774-2:329
  24. 24. Turnbull C, Lillemo M, Hvoslef-Eide TAK. Global regulation of genetically modified crops amid the gene edited crop boom - a review. Front Plant Sci. 2021;12. https://doi.org/10.3389/fpls.2021.630396
  25. 25. Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016;34:933-41. https://doi.org/10.1038/nbt.3659
  26. 26. Lassoued R, Macall DM, Hesseln H, Phillips PWB, Smyth SJ. Benefits of genome-edited crops: expert opinion. Transgenic Res. 2019;28:247-56. https://doi.org/10.1007/s11248-019-00118-5
  27. 27. Abdallah NA, Prakash CS, McHughen AG. Genome editing for crop improvement: challenges and opportunities. GM Crops Food. 2015;6:183-205. https://doi.org/10.1080/21645698.2015.1129937
  28. 28. Carroll D. Genome engineering with targetable nucleases. Annu Rev Biochem. 2014;83:409-39. https://doi.org/10.1146/annurev-biochem-060713-035418
  29. 29. Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013;31:397-405. https://doi.org/10.1016/j.tibtech.2013.04.004
  30. 30. Wada N, Osakabe K, Osakabe Y. Expanding the plant genome editing toolbox with recently developed CRISPR-Cas systems. Plant Physiol. 2022;188:1825-37. https://doi.org/10.1093/plphys/kiac027
  31. 31. Cermak T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. High Frequency precise modification of the tomato genome. Genome Biol. 2015;16:232. https://doi.org/10.1186/s13059-015-0796-9
  32. 32. Fernández A, Josa S, Montoliu L. A history of genome editing in mammals. Mamm Genome. 2017;28:237-46. https://doi.org/10.1007/s00335-017-9699-2
  33. 33. Beyer HM, Iwaï H. Structural basis for the propagation of homing endonuclease-associated inteins. Front Mol Biosci. 2022;9. https://doi.org/10.3389/fmolb.2022.855511
  34. 34. Bijlani S, Pang KM, Sivanandam V, Singh A, Chatterjee S. The role of recombinant AAV in precise genome editing. Front Genome Ed. 2022;3. https://doi.org/10.3389/fgeed.2021.799722
  35. 35. Rebar EJ, Huang Y, Hickey R, Nath AK, Meoli D, Nath S, et al. Induction of angiogenesis in a mouse model using engineered transcription factors. Nat Med. 2002;8:1427-32. https://doi.org/10.1038/nm1202-795
  36. 36. Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci. 1996;93:1156-60. https://doi.org/10.1073/pnas.93.3.1156
  37. 37. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods. 2011;8:67-9. https://doi.org/10.1038/nmeth.1542
  38. 38. Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, et al. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods. 2008;5:374-5. https://doi.org/10.1038/nmeth0508-374
  39. 39. Lee JG, Sung YH, Baek I-J. Generation of genetically engineered animals using engineered endonucleases. Arch Pharm Res. 2018;41:885-97. https://doi.org/10.1007/s12272-018-1037-z
  40. 40. Puchta H, Hohn B. Breaking news: Plants mutate right on target. Proc Natl Acad Sci. 2010;107:11657-8. https://doi.org/10.1073/pnas.1006364107
  41. 41. Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, et al. A critical review: recent advancements in the use of CRISPR/Cas9 technology to enhance crops and alleviate global food crises. Curr Issues Mol Biol. 2021;43:1950-76. https://doi.org/10.3390/cimb43030135
  42. 42. Boch J, Bonas U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol. 2010;48:419-36. https://doi.org/10.1146/annurev-phyto-080508-081936
  43. 43. Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat Rev Genet. 2010;11:636-46. https://doi.org/10.1038/nrg2842
  44. 44. Iqbal Z, Iqbal MS, Ahmad A, Memon AG, Ansari MI. New prospects on the horizon: genome editing to engineer plants for desirable traits. Curr Plant Biol. 2020;24:100171. https://doi.org/10.1016/j.cpb.2020.100171
  45. 45. Miller JC, Zhang L, Xia DF, Campo JJ, Ankoudinova IV, Guschin DY, et al. Improved specificity of TALE-based genome editing using an expanded RVD repertoire. Nat Methods. 2015;12:465-71. https://doi.org/10.1038/nmeth.3330
  46. 46. Li T, Liu B, Spalding MH, Weeks DP, Yang B. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol. 2012;30:390-2. https://doi.org/10.1038/nbt.2199
  47. 47. Zhang H, Si X, Ji X, Fan R, Liu J, Chen K, et al. Genome editing of upstream open reading frames enables translational control in plants. Nat Biotechnol. 2018;36:894-8. https://doi.org/10.1038/nbt.4202
  48. 48. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli and identification of the gene product. J Bacteriol. 1987;169:5429-33. https://doi.org/10.1128/jb.169.12.5429-5433.1987
  49. 49. Mojica FJM, Ferrer C, Juez G, Rodríguez-Valera F. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol. 1995;17:85-93. https://doi.org/10.1111/j.1365-2958.1995.mmi_17010085.x
  50. 50. Jansen R, van Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43:1565-75. https://doi.org/10.1046/j.1365-2958.2002.02839.x
  51. 51. Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol. 2014;32:347-55. https://doi.org/10.1038/nbt.2842
  52. 52. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V. Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol. 2015;32:76-84. https://doi.org/10.1016/j.copbio.2014.11.007
  53. 53. Yin K, Gao C, Qiu J-L. Progress and prospects in plant genome editing. Nat Plants. 2017;3:17107. https://doi.org/10.1038/nplants.2017.107
  54. 54. Ha D-I, Lee JM, Lee N-E, Kim D, Ko J-H, Kim Y-S. Highly efficient and safe genome editing by CRISPR-Cas12a using CRISPR RNA with a ribosyl-2′-O-methylated uridinylate-rich 3′-overhang in mouse zygotes. Exp Mol Med. 2020;52:1823-30. https://doi.org/10.1038/s12276-020-00521-7
  55. 55. Swarts DC, van der Oost J, Jinek M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Mol Cell. 2017;66:221-33.e4. https://doi.org/10.1016/j.molcel.2017.03.016
  56. 56. Bayoumi M, Munir M. Potential use of CRISPR/Cas13 machinery in understanding virus-host interaction. Front Microbiol. 2021;12. https://doi.org/10.3389/fmicb.2021.743580
  57. 57. Zhu H, Li C, Gao C. Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol. 2020;21:661-77. https://doi.org/10.1038/s41580-020-00288-9
  58. 58. Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J, et al. Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9. Nat Plants. 2016;2:16139. https://doi.org/10.1038/nplants.2016.139
  59. 59. Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol. 2014;32:947-51. https://doi.org/10.1038/nbt.2969
  60. 60. Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K, et al. Loss of function of a proline-containing protein confers durable disease resistance in rice. Science. 2009;325:998-1001. https://doi.org/10.1126/science.1175550
  61. 61. Jørgensen IH. Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley. Euphytica. 1992;63:141-52. https://doi.org/10.1007/BF00023919
  62. 62. Kusch S, Panstruga R. mlo-based resistance: an apparently universal “weapon” to defeat powdery mildew disease. Mol Plant Microbe Interact. 2017;30:179-89. https://doi.org/10.1094/MPMI-12-16-0255-CR
  63. 63. Bai Y, Pavan S, Zheng Z, Zappel NF, Reinstädler A, Lotti C, et al. Naturally occurring broad-spectrum powdery mildew resistance in a Central American tomato accession is caused by loss of Mlo function. Mol Plant Microbe Interact. 2008;21:30-9. https://doi.org/10.1094/MPMI-21-1-0030
  64. 64. Consonni C, Humphry ME, Hartmann HA, Livaja M, Durner J, Westphal L, et al. Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Nat Genet. 2006;38:716-20. https://doi.org/10.1038/ng1806
  65. 65. Dangl JL, Horvath DM, Staskawicz BJ. Pivoting the plant immune system from dissection to deployment. Science. 2013;341:746-51. https://doi.org/10.1126/science.1236011
  66. 66. Dodds PN, Rathjen JP. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet. 2010;11:539-48. https://doi.org/10.1038/nrg2812
  67. 67. Dong S, Raffaele S, Kamoun S. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev. 2015;35:57-65. https://doi.org/10.1016/j.gde.2015.09.001
  68. 68. Vleeshouwers VGAA, Raffaele S, Vossen JH, Champouret N, Oliva R, Segretin ME, et al. Understanding and exploiting late blight resistance in the age of effectors. Annu Rev Phytopathol. 2011;49:507-31. https://doi.org/10.1146/annurev-phyto-072910-095326
  69. 69. Michelmore R, Coaker G, Bart R, Beattie G, Bent A, Bruce T, et al. Foundational and translational research opportunities to improve plant health. Mol Plant Microbe Interact. 2017;30:515-6. https://doi.org/10.1094/MPMI-01-17-0010-CR
  70. 70. Roane CW. Trends in breeding for disease resistance in crops. Annu Rev Phytopathol. 1973;11:463-86. https://doi.org/10.1146/annurev.py.11.090173.002335
  71. 71. Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, et al. Rapid open-source engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell. 2008;31:294-301. https://doi.org/10.1016/j.molcel.2008.06.016
  72. 72. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009;326:1509-12. https://doi.org/10.1126/science.1178811
  73. 73. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819-23. https://doi.org/10.1126/science.1231143
  74. 74. Puchta H. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J Exp Bot. 2004. https://doi.org/10.1093/jxb/eri025
  75. 75. Puchta H. Applying CRISPR/Cas for genome engineering in plants: the best is yet to come. Curr Opin Plant Biol. 2017;36:1-8. https://doi.org/10.1016/j.pbi.2016.11.011
  76. 76. Zhou Z, Tan H, Li Q, Chen J, Gao S, Wang Y, et al. CRISPR/Cas9-mediated efficient targeted mutagenesis of RAS in Salvia miltiorrhiza. Phytochemistry. 2018;148:63-70. https://doi.org/10.1016/j.phytochem.2018.01.015
  77. 77. Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz MM. CRISPR/Cas9-mediated viral interference in plants. Genome Biol. 2015;16:238. https://doi.org/10.1186/s13059-015-0799-6
  78. 78. Ji X, Zhang H, Zhang Y, Wang Y, Gao C. Establishing a CRISPR-Cas-like immune system conferring DNA virus resistance in plants. Nat Plants. 2015;1:15144. https://doi.org/10.1038/nplants.2015.144
  79. 79. Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, et al. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018;19:1. https://doi.org/10.1186/s13059-017-1381-1
  80. 80. Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M, et al. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol. 2016;17:1140-53. https://doi.org/10.1111/mpp.12375
  81. 81. Pyott DE, Sheehan E, Molnar A. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. Mol Plant Pathol .2016;17:1276-88. https://doi.org/10.1111/mpp.12417
  82. 82. Kerr A. Biological control of crown gall. Australas Plant Pathol. 2016;45:15-8. https://doi.org/10.1007/s13313-015-0389-9
  83. 83. Mew TW. Focus on bacterial blight of rice. Plant Dis. 1993;77:5. https://doi.org/10.1094/PD-77-0005
  84. 84. Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, et al. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol. 2019;37:1344-50. https://doi.org/10.1038/s41587-019-0267-z
  85. 85. Xu Z, Xu X, Gong Q, Li Z, Li Y, Wang S, et al. Engineering broad-spectrum bacterial blight resistance by simultaneously disrupting variable TALE-binding elements of multiple susceptibility genes in rice. Mol Plant. 2019;12:1434-46. https://doi.org/10.1016/j.molp.2019.08.006
  86. 86. Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, et al. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One. 2016;11:e0154027. https://doi.org/10.1371/journal.pone.0154027
  87. 87. Chen LQ, Hou BH, Lalonde S, Takanaga H, Hartung ML, Qu XQ, et al. Sugar transporters for intercellular exchange and nutrition of pathogens. Nature. 2010;468:527-32. https://doi.org/10.1038/nature09606
  88. 88. Streubel J, Pesce C, Hutin M, Koebnik R, Boch J, Szurek B. Five phylogenetically close rice SWEET genes confer TAL effector-mediated susceptibility to Xanthomonas oryzae pv. oryzae. New Phytol. 2013;200:808-19. https://doi.org/10.1111/nph.12411
  89. 89. Antony G, Zhou J, Huang S, Li T, Liu B, White F, et al. Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell. 2010;22:3864-76. https://doi.org/10.1105/tpc.110.078964
  90. 90. Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol. 2013;23:390-8. https://doi.org/10.1016/j.tcb.2013.04.003
  91. 91. Makino S, Sugio A, White F, Bogdanove AJ. Inhibition of resistance gene-mediated defense in rice by Xanthomonas oryzae pv. oryzicola. Molecular Plant-Microbe Interactions. 2006;19:240-9. https://doi.org/10.1094/MPMI-19-0240
  92. 92. Yang B, Sugio A, White FF. Os8N3 is a host disease-susceptibility gene for bacterial blight of rice. Proceedings of the National Academy of Sciences. 2006;103:10503-8. https://doi.org/10.1073/pnas.0604088103
  93. 93. Chen LQ, Qu XQ, Hou BH, Sosso D, Osorio S, Fernie AR, et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science. 2012;335:207-11. https://doi.org/10.1126/science.1213351
  94. 94. Chandran D. Co-option of developmentally regulated plant SWEET transporters for pathogen nutrition and abiotic stress tolerance. IUBMB Life. 2015;67:461-71. https://doi.org/10.1002/iub.1394
  95. 95. Chen LQ, Lin IW, Qu XQ, Sosso D, McFarlane HE, Londoño A, et al. A cascade of sequentially expressed sucrose transporters in the seed coat and endosperm provides nutrition for the Arabidopsis embryo. Plant Cell. 2015;27:607-19. https://doi.org/10.1105/tpc.114.134585
  96. 96. Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Research. 2014;42:10903-14. https://doi.org/10.1093/nar/gku806
  97. 97. Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Research. 2013;41:e188. https://doi.org/10.1093/nar/gkt780
  98. 98. Blanvillain-Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, et al. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. Plant Biotechnology Journal. 2017;15:306-17. https://doi.org/10.1111/pbi.12613
  99. 99. Peng A, Chen S, Lei T, Xu L, He Y, Wu L, et al. Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnology Journal. 2017;15:1509-19. https://doi.org/10.1111/pbi.12733
  100. 100. Jia H, Zhang Y, Orbović V, Xu J, White FF, Jones JB, et al. Genome editing of the disease susceptibility gene CsLOB1 in citrus confers resistance to citrus canker. Plant Biotechnology Journal. 2017;15:817-23. https://doi.org/10.1111/pbi.12677
  101. 101. Van Damme M, Huibers RP, Panstruga R, Weisbeek PJ, Van den Ackerveken G. Identification of Arabidopsis loci required for susceptibility to the downy mildew pathogen Hyaloperonospora parasitica. Molecular Plant-Microbe Interactions. 2005;18:583-92. https://doi.org/10.1094/MPMI-18-0583
  102. 102. Van Damme M, Huibers RP, Elberse J, Van den Ackerveken G. Arabidopsis DMR6 encodes a putative 2OG-Fe(II) oxygenase that is defense-associated but required for susceptibility to downy mildew. The Plant Journal. 2008;54:785-93. https://doi.org/10.1111/j.1365-313X.2008.03427.x
  103. 103. Schwartz AR, Potnis N, Timilsina S, Wilson M, Patanã J, Martins J, et al. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Frontiers in Microbiology. 2015;6:535. https://doi.org/10.3389/fmicb.2015.00535
  104. 104. Zeilmaker T, Ludwig NR, Elberse J, Seidl MF, Berke L, Van Doorn A, et al. Downy mildew resistant 6 and DMR6-like oxygenase 1 are partially redundant but distinct suppressors of immunity in Arabidopsis. The Plant Journal. 2015;81:210-22. https://doi.org/10.1111/tpj.12719
  105. 105. Jupe J, Stam R, Howden AJ, Morris JA, Zhang R, Hedley PE, et al. Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle. Genome Biology. 2013;14:R63. https://doi.org/10.1186/gb-2013-14-6-r63
  106. 106. Yang YX, Wang MM, Yin YL, Onac E, Zhou GF, Peng S, et al. RNA-seq analysis reveals the role of red light in resistance against Pseudomonas syringae pv. tomato DC3000 in tomato plants. BMC Genomics. 2015;16:120. https://doi.org/10.1186/s12864-015-1228-7
  107. 107. Doehlemann G, Ökmen B, Zhu W, Sharon A. Plant pathogenic fungi. In: The Fungal Kingdom. Washington, DC: ASM Press; 2017. p. 701-26. https://doi.org/10.1128/9781555819583.ch34
  108. 108. Lyngkjær MF, Newton AC, Atzema JL, Baker SJ. The barley mlo gene: an important powdery mildew resistance source. Agronomie. 2000;20:745-56. https://doi.org/10.1051/agro:2000173
  109. 109. Humphry M, Consonni C, Panstruga R. mlo-based powdery mildew immunity: silver bullet or simply non-host resistance? Molecular Plant Pathology. 2006;7:605-10. https://doi.org/10.1111/j.1364-3703.2006.00362.x
  110. 110. Kim MC, Panstruga R, Elliott C, Müller J, Devoto A, Yoon HW, et al. Calmodulin interacts with MLO protein to regulate defence against mildew in barley. Nature. 2002;416:447-51. https://doi.org/10.1038/416447a
  111. 111. Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S. Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Scientific Reports. 2017;7:482. https://doi.org/10.1038/s41598-017-00578-x
  112. 112. Zhang Y, Bai Y, Wu G, Zou S, Chen Y, Gao C, et al. Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. The Plant Journal. 2017;91:714-24. https://doi.org/10.1111/tpj.13599
  113. 113. Berrocal-Lobo M, Molina A, Solano R. Constitutive expression of ETHYLENE-RESPONSE-FACTOR1 in Arabidopsis confers resistance to several necrotrophic fungi. Plant J. 2002;29:23-32. https://doi.org/10.1046/j.1365-313x.2002.01191.x
  114. 114. Cao Y, Wu Y, Zheng Z, Song F. Overexpression of the rice EREBP-like gene OsBIERF3 enhances disease resistance and salt tolerance in transgenic tobacco. Physiol Mol Plant Pathol. 2005;67:202-11. https://doi.org/10.1016/j.pmpp.2006.01.004
  115. 115. Zhu X, Qi L, Liu X, Cai S, Xu H, Huang R, et al. The wheat ethylene response factor transcription factor PATHOGEN-INDUCED ERF1 mediates host responses to both the necrotrophic pathogen Rhizoctonia cerealis and freezing stresses. Plant Physiol. 2014;164:1499-514. https://doi.org/10.1104/pp.113.229575
  116. 116. Liu D, Chen X, Liu J, Ye J, Guo Z. The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. J Exp Bot. 2012;63:3899-911. https://doi.org/10.1093/jxb/ers079
  117. 117. Wang W, Pan Q, He F, Akhunova A, Chao S, Trick H, et al. Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. CRISPR J. 2018;1:65-74. https://doi.org/10.1089/crispr.2017.0010
  118. 118. D’Halluin K, Vanderstraeten C, Van Hulle J, Rosolowska J, Van Den Brande I, Pennewaert A, et al. Targeted molecular trait stacking in cotton through targeted double-strand break induction. Plant Biotechnol J. 2013;11:933-41. https://doi.org/10.1111/pbi.12085
  119. 119. Yin K, Qiu J-L. Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc B Biol Sci. 2019;374:20180322. https://doi.org/10.1098/rstb.2018.0322
  120. 120. Ahmad S, Wei X, Sheng Z, Hu P, Tang S. CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Brief Funct Genomics. 2020;19:26-39. https://doi.org/10.1093/bfgp/elz041
  121. 121. Erdoğan İ, Cevher-Keskin B, Bilir Ö, Hong Y, Tör M. Recent developments in CRISPR/Cas9 genome-editing technology related to plant disease resistance and abiotic stress tolerance. Biology. 2023;12:1037. https://doi.org/10.3390/biology12071037
  122. 122. Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, et al. Genome engineering technology for durable disease resistance: recent progress and future outlooks for sustainable agriculture. Front Plant Sci. 2022;13:860281. https://doi.org/10.3389/fpls.2022.860281
  123. 123. Zafar K, Noureen A, Awan MJA, Anjum N, Aslam MQ, Khan MZ, et al. Genome editing to develop disease resistance in crops. In: Genome engineering for crop improvement. Wiley; 2021. p. 224-52. https://doi.org/10.1002/9781119672425.ch14
  124. 124. Arora L, Narula A. Gene editing and crop improvement using CRISPR-Cas9 system. Front Plant Sci. 2017;8:1932. https://doi.org/10.3389/fpls.2017.01932
  125. 125. Gao Z, Liu Q, Zhang Y, Chen D, Zhan X, Deng C, et al. OsCUL3a-associated molecular switches have functions in cell metabolism, cell death and disease resistance. J Agric Food Chem. 2020;68:5471-82. https://doi.org/10.1021/acs.jafc.9b07426
  126. 126. Jaganathan D, Ramasamy K, Sellamuthu G, Jayabalan S, Venkataraman G. CRISPR for crop improvement: an update review. Front Plant Sci. 2018;9:985. https://doi.org/10.3389/fpls.2018.00985
  127. 127. Zaidi SS-A, Mukhtar MS, Mansoor S. Genome editing: targeting susceptibility genes for plant disease resistance. Trends Biotechnol. 2018;36:898-906. https://doi.org/10.1016/j.tibtech.2018.04.005
  128. 128. Ortigosa A, Gimenez-Ibanez S, Leonhardt N, Solano R. Design of a bacterial speck resistant tomato by CRISPR/Cas9-mediated editing of SlJAZ2. Plant Biotechnol J. 2019;17:665-73. https://doi.org/10.1111/pbi.13006
  129. 129. Santillán Martínez MI, Bracuto V, Koseoglou E, Appiano M, Jacobsen E, Visser RGF, et al. CRISPR/Cas9-targeted mutagenesis of the tomato susceptibility gene PMR4 for resistance against powdery mildew. BMC Plant Biol. 2020;20:284. https://doi.org/10.1186/s12870-020-02497-y
  130. 130. Tripathi JN, Ntui VO, Ron M, Muiruri SK, Britt A, Tripathi L. CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. overcomes a major challenge in banana breeding. Commun Biol. 2019;2:46. https://doi.org/10.1038/s42003-019-0288-7
  131. 131. Zaidi SS-A, Mahas A, Vanderschuren H, Mahfouz MM. Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biol. 2020;21:289. https://doi.org/10.1186/s13059-020-02204-y
  132. 132. Fister AS, Landherr L, Maximova SN, Guiltinan MJ. Transient expression of CRISPR/Cas9 machinery targeting TcNPR3 enhances defense response in Theobroma cacao. Front Plant Sci. 2018;9:268. https://doi.org/10.3389/fpls.2018.00268
  133. 133. Gumtow R, Wu D, Uchida J, Tian M. A Phytophthora palmivora extracellular cystatin-like protease inhibitor targets papain to contribute to virulence on papaya. Mol Plant Microbe Interact. 2018;31:363-73. https://doi.org/10.1094/MPMI-06-17-0131-FI
  134. 134. Mishra R, Mohanty JN, Mahanty B, Joshi RK. A single transcript CRISPR/Cas9 mediated mutagenesis of CaERF28 confers anthracnose resistance in chilli pepper (Capsicum annuum L.). Planta. 2021;254:5. https://doi.org/10.1007/s00425-021-03660-x
  135. 135. Sprink T, Wilhelm R. Genome editing in biotech regulations worldwide. In: Ricroch et al, editors. A roadmap for plant genome editing. 2024. p. 425-36. https://doi.org/10.1007/978-3-031-46150-7_25
  136. 136. Sharma N, Thakur K, Zinta R, Mangal V, Tiwari JK, Sood S, et al. Genome editing research initiatives and regulatory landscape of genome edited crops in India. Transgenic Res. 2025;34(1):1-8. https://doi.org/10.1007/s11248-025-00432-1

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