Research Progress of CRISPR/Cas Gene Editing Technology in Herbicide-resistant Crop Breeding
TONG Chao-Yun1,*, HUANG Yu-Ting1,*, YANG Jing-Ru1, WANG Zhi-Rui1, LIU Xiao-Shuang1, LI Juan2,**, WEI Peng-Cheng1,**
1 College of Agronomy, Anhui Agricultural University, Hefei 230031, China; 2 Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
Abstract:The creation and selection of superior new germplasm resistant to herbicides is a highly cost-effective and environmentally friendly method of weed control. CRISPR/Cas gene editing technology, characterized by simplicity, efficiency, and precision, holds tremendous potential for application in crop breeding. This study summarizes the research progress of CRISPR/Cas gene editing technology in herbicide-resistant crop breeding, with a focus on the types of crop herbicides, the mutant sites of resistance gene targets, and the development of CRISPR/Cas-mediated precision editing technology. It also provides a detailed introduction to the application of gene editing technology in the creation of superior new herbicide-resistant crop germplasm. Finally, by elaborating on the existing challenges and future development directions of CRISPR/Cas gene editing technology, this study provides a theoretical basis and technical support for the creation of new herbicide-resistant crop germplasm.
[1] 董立尧, 高原, 房加鹏, 等. 2018. 我国水稻田杂草抗药性研究进展[J].植物保护, 44(5): 231-238. (Dong L Y, Gao Y, Fang J P, et al.2018. Research progress on weed resistance in paddy fields in our country[J]. Plant Protection, 44(5): 231-238.) [2] 李燕敏, 祁显涛, 刘昌林, 等. 2017. 除草剂抗性农作物育种研究进展[J]. 作物杂志, 1(2): 1-6. (Li Y M, Qi X T, Liu C L, et al.2017. Research progress of herbicide-resistant crop breeding[J]. Crop Journal, 1(2): 1-6.) [3] 马红, 王月超, 孙莹, 等. 2024. 杂草对9类常用不同作用机制除草剂的非靶标抗性机制研究进展[J]. 植物保护, 50(1): 15-23. (Ma H, Wang Y C, Sun Y, et al.2024. Research progress on the mechanisms of non-target site resistance of weeds to nine categories of commonly used herbicides with different modes of action[J]. Plant Protection, 50(1): 15-23.) [4] 王俊丽, 徐小博, 孙玥, 等. 2019, 乙酰辅酶A羧化酶抑制剂类除草剂的研究进展[J]. 植物学研究, 8(5): 410-415. (Wang J L, Xu X B, Sun Y, et al.2019. Research progress of acetyl-CoA carboxylase inhibitors herbicides[J]. Botanical Research, 8(5): 410-415.) [5] 杨丽, 张荣全, 叶非. 2003. 对羟苯基丙酮酸双氧化酶抑制剂的研究进展[J]. 现代农药, 2(5): 1-4. (Yang L, Zhang R Q, Ye F.2003. Research progress of p-hydroxyphenylpyruvate dioxidase inhibitors[J]. Modern Pesticides, 2(5): 1-4.) [6] 张红磊, 李军玲, 张融雪, 等. 2021. ALS以及ALS抑制剂类除草剂的研究进展[J]. 植物学研究, 10(6): 781-791. (Zhang H L, Li J L, Zhang R X, et al.2021. Research progress of ALS and ALS inhibitor herbicides[J]. Botanical Research, 10(6): 781-791.) [7] 张玲玲, 徐凡, 李嘉文, 等. 2024. 杂草对除草剂抗性机理研究进展[J]. 农药学学报, 26(4): 703-715. (Zhang L L, Xu F, Li J W, et al.2024. Research progress on the resistance mechanism of weeds to herbicides[J]. Journal of Pesticides, 26(4): 703-715.) [8] Achary V M M, Sheri V, Manna M, et al.2020. Overexpression of improved EPSPS gene results in field level glyphosate tolerance and higher grain yield in rice[J]. Plant Biotechnology Journal, 18: 2504-2519. [9] Ali Z, Shami A, Sedeek K, et al.2020. Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice[J]. Communications Biology, 3(1): 44-57. [10] An J, Shen X, Ma Q, et al.2014. Transcriptome profiling to discover putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.)[J]. PLOS ONE, 9(6): 1-14. [11] Anzalone A V, Randolph P B, Davis J R, et al.2019. Search-and-replace genome editing without double-strand breaks or donor DNA[J]. Nature, 576(1): 149-157. [12] Butt H, Eid A, Momin A A, et al.2019. CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors[J]. Genome Biology, 20(1): 73-82. [13] Chen L, Hong M, Luan C, et al.2024. Adenine transversion editors enable precise, efficient A•T-to-C•G base editing in mammalian cells and embryos[J]. Nature Biotechnology, 42(4): 638-650. [14] Chen P J, Hussmann J A, Yan J, et al.2021. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes[J]. Cell, 184(22): 5635-5652. [15] Cheng H, Hao M, Ding B, et al.2021. Base editing with high efficiency in allotetraploid oilseed rape by A3A-PBE system[J]. Plant Biotechnology Journal, 19(1): 87-97. [16] Cong L, Ran F A, Cox D, et al.2013. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 339(6121): 819-823. [17] Daliri K, Hescheler J, Pfannkuche K P.2024. Prime editing and DNA repair system: Balancing efficiency with safety[J]. Cells, 13(10): 858-872. [18] Deltcheva E, Chylinski K, Sharma C M, et al.2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase Ⅲ[J]. Nature, 471(7340): 602-607. [19] Délye C, Zhang X Q, Michel S, et al.2005. Molecular bases for sensitivity to acetyl-coenzyme A carboxylase inhibitors in black-grass[J]. Plant Physiology, 137(3): 794-806. [20] Devine M D, Shukla A J C P.2000. Altered target sites as a mechanism of herbicide resistance[J]. Crop Protection, 19(8-10): 881-889. [21] Doman J L, Pandey S, Neugebauer M E, et al.2023. Phage-assisted evolution and protein engineering yield compact, efficient prime editors[J]. Cell, 186(18): 3983-4002. [22] Duff S M G, Zhang M, Zinnel F, et al.2024. Structural and functional characterization of triketone dioxygenase from Oryza Sativa[J]. Biochimica et Biophysica Acta General Subjects, 1868(2): 130504-130516. [23] Duggleby R G, Mccourt J A, Guddat L W.2008. Structure and mechanism of inhibition of plant acetohydroxyacid synthase[J]. Plant Physiology and Biochemistry, 46(3): 309-324. [24] Dweikat I M, Gelli M, Bernards M, et al.2023. Mutations in the acetolactate synthase (ALS) enzyme affect shattercane (Sorghum bicolor) response to ALS-inhibiting herbicides[J]. Hereditas, 160(1): 28-36. [25] Endo M, Mikami M, Endo A, et al.2019. Genome editing in plants by engineered CRISPR-Cas9 recognizing NG PAM[J]. Nature Plants, 5(1): 14-17. [26] Endo M, Mikami M, Toki S.2016. Biallelic gene targeting in rice[J]. Plant Physiology, 170(2): 667-677. [27] Fan T, Cheng Y, Wu Y, et al.2024. High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants[J]. Nature Communications, 15(1): 5103-5118. [28] Funke T, Yang Y, Han H, et al.2009. Structural basis of glyphosate resistance resulting from the double mutation Thr97 → Ile and Pro101 → Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli[J]. The Journal of Biological Chemistry, 284(15): 9854-9860. [29] Gaines T A, Zhang W, Wang D, et al.2010. Gene amplification confers glyphosate resistance in Amaranthus palmeri[J]. Proceedings of the National Academy of Sciences of the USA, 107(3): 1029-1034. [30] Gaj T, Gersbach C A, Barbas C F.2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering[J]. Trends in Biotechnology, 31(7): 397-405. [31] Gaudelli N M, Komor A C, Rees H A, et al.2017. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage[J]. Nature, 551(7681): 464-471. [32] Guo Y, Wang T, Lu X, et al.2024. Comparative genome-wide analysis of circular RNAs in Brassica napus L.: Target-site versus non-target-site resistance to herbicide stress[J]. Theoretical and Applied Genetics, 137(7): 176-195. [33] Guo Y, Xu X, Lin J, et al.2023. The herbicide bensulfuron-methyl inhibits rice seedling development by blocking calcium ion flux in the OsCNGC12 channel[J]. The Plant Journal: for Cell and Molecular Biology, 116(5): 1218-1233. [34] Jiang Y, Chai Y, Qiao D, et al.2022. Optimized prime editing efficiently generates glyphosate-resistant rice plants carrying homozygous TAP-IVS mutation in EPSPS[J]. Molecular Plant, 15(11): 1646-1649. [35] Jiang Y Y, Chai Y P, Lu M H, et al.2020. Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize[J]. Genome Biology, 21(1): 257-267. [36] Jin S, Zong Y, Gao Q, et al.2019. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice[J]. Science, 364(6437): 292-295. [37] Jinek M, Chylinski K, Fonfara I, et al.2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 337(6096): 816-821. [38] Kaul T, Thangaraj A, Jain R, et al.2024. CRISPR/Cas9-mediated homology donor repair base editing system to confer herbicide resistance in maize (Zea mays L.)[J]. Plant Physiology and Biochemistry, 207(1): 108374-108386. [39] Komor A C, Kim Y B, Packer M S, et al.2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 533(7603): 420-424. [40] Kuang Y, Li S, Ren B, et al.2020. Base-editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms[J]. Molecular Plant, 13(4): 565-572. [41] Kumar V P K, Bellinder R R, Gupta R K, et al.2008. Role of herbicide-resistant rice in promoting resource conservation technologies in rice-wheat cropping systems of India: A review[J]. Crop Protection, 27(3): 290-301. [42] Kurt I C, Zhou R, Iyer S, et al.2021. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells[J]. Nature Biotechnology, 39(1): 41-46. [43] Li C, Zhang R, Meng X, et al.2020a. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors[J]. Nature Biotechnology, 38(7): 875-882. [44] Li J, Meng X, Zong Y, et al.2016. Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9[J]. Nature Plants, 2(16139): 1-6 [45] Li Y, Zhu J, Wu H, et al.2020b. Precise base editing of non-allelic acetolactate synthase genes confers sulfonylurea herbicide resistance in maize[J]. The Crop Journal, 8(1): 449-456. [46] Lian L, Wang H, Zhang F, et al.2023. Cypyrafluone, a 4-Hydroxyphenylpyruvate dioxygenase inhibitor to control weed in wheat fields[J]. Journal of Agricultural and Food Chemistry, 71(23): 8825-8833. [47] Liu L, Kuang Y, Yan F, et al.2021a. Developing a novel artificial rice germplasm for dinitroaniline herbicide resistance by base editing of OsTubA2[J]. Plant Biotechnology Journal, 19(1): 5-7. [48] Liu P, Liang S Q, Zheng C, et al.2021b. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice[J]. Nature Communications, 12(1): 2121-2133. [49] Liu X, Qin R, Li J, et al.2020. A CRISPR-Cas9-mediated domain-specific base-editing screen enables functional assessment of ACCase variants in rice[J]. Plant Biotechnology Journal, 18(9): 1845-1847. [50] Liu X, Wang Y, Wang H, et al.2024. Generating herbicide resistant and dwarf rice germplasms through precise sequence insertion or replacement[J]. Plant Biotechnology Journal, 22(2): 293-295. [51] Liu X, Xiang S, Zong T, et al.2019. Herbicide resistance in China: A quantitative review[J]. Weed Science, 67(6): 605-612. [52] Lu Y, Wang J, Chen B, et al.2021. A donor-DNA-free CRISPR/Cas-based approach to gene knock-up in rice[J]. Nature Plants, 7(11): 1445-1452. [53] Maeda H, Murata K, Sakuma N, et al.2019. A rice gene that confers broad-spectrum resistance to β-triketone herbicides[J]. Science, 365(6451): 393-396. [54] Matsoukas I G2018. Commentary: Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage[J]. Frontiers in Genetics, 9(1): 21-24. [55] Niu Q, Xie H, Cao X, et al.2024. Engineering soybean with high levels of herbicide resistance with a Cas12-SF01-based cytosine base editor[J]. Plant Biotechnology Journal, 22(9): 2435-2437. [56] Pan L, Yu Q, Wang J, et al.2021. An ABCC-type transporter endowing glyphosate resistance in plants[J]. Proceedings of the National Academy of Sciences of the USA, 118(16): :e2100136118. [57] Park H J, Kim M, Lee D, et al.2024. CRISPR-Cas9 and beyond: Identifying target genes for developing disease-resistant plants[J]. Plant Biology, 26(3): 369-377. [58] Patterson E L, Pettinga D J, Ravet K, et al.2018. Glyphosate resistance and EPSPS gene duplication: Convergent evolution in multiple plant species[J]. The Journal of Heredity, 109(2): 117-125. [59] Polyak S W, Abell A D, Wilce M C, et al.2012. Structure, function and selective inhibition of bacterial acetyl-coa carboxylase[J]. Applied Microbiology and Biotechnology, 93(3): 983-992. [60] Schütte G, Eckerstorfer M, Rastelli V, et al.2017. Herbicide resistance and biodiversity: Agronomic and environmental aspects of genetically modified herbicide-resistant plants[J]. Environmental Sciences Europe, 29(1): 5-5. [61] Shimatani Z, Fujikura U, Ishii H, et al.2018. Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice[J]. Data in Brief, 20(1): 1325-1331. [62] Shimatani Z, Kashojiya S, Takayama M, et al.2017. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion[J]. Nature Biotechnology, 35(5): 441-443. [63] Sun C, Lei Y, Li B, et al.2024a. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors[J]. Nature Biotechnology, 42(2): 316-327. [64] Sun H, Yu S, Huang T, et al.2024b. Physiological basis for the mechanism of selectivity of tripyrasulfone between rice (Oryza sativa) and barnyard grass (Echinochloa crusgalli)[J]. Journal of Agricultural and Food Chemistry, 72(25): 14402-14410. [65] Svitashev S, Young J K, Schwartz C, et al.2015. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA[J]. Plant Physiology, 169(2): 931-945. [66] Symington L S, Gautier J.2011. Double-strand break end resection and repair pathway choice[J]. Annual Review of Genetics, 45(1): 247-271. [67] Tian S, Jiang L, Cui X, et al.2018. Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing[J]. Plant Cell Reports, 37(9): 1353-1356. [68] Tian Y, Shen R, Li Z, et al.2022. Efficient C-to-G editing in rice using an optimized base editor[J]. Plant Biotechnology Journal, 20(7): 1238-1240. [69] Tong H, Liu N, Wei Y, et al.2023. Programmable deaminase-free base editors for G-to-Y conversion by engineered glycosylase[J]. National Science Review, 10(8): 1-10 [70] Tong H, Wang H, Wang X, et al.2024. Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase[J]. Nature Communications, 15(1): 4897-4908. [71] Vázquez-García J G, Alcántara-De La Cruz R, Palma-Bautista C, et al.2020. Accumulation of target gene mutations confers multiple resistance to ALS, ACCase, and EPSPS inhibitors in lolium species in chile[J]. Frontiers in Plant Science, 11(553948): 1-13. [72] Veillet F, Perrot L, Chauvin L, et al.2019. Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor[J]. International Journal of Molecular Sciences, 20(2): 402-412. [73] Wang H, He Y, Wang Y, et al.2022. Base editing-mediated targeted evolution of ACCase for herbicide-resistant rice mutants[J]. Journal of Integrative Plant Biology, 64(11): 2029-2032. [74] Wu J, Chen C, Xian G, et al.2020. Engineering herbicide-resistant oilseed rape by CRISPR/Cas9-mediated cytosine base-editing[J]. Plant Biotechnology Journal, 18(9): 1857-1859. [75] Wu Y, Xiao N, Cai Y, et al.2023. CRISPR-Cas9-mediated editing of the OsHPPD 3' UTR confers enhanced resistance to HPPD-inhibiting herbicides in rice[J]. Plant Communications, 4(5): 100605. [76] Xu R, Liu X, Li J, et al.2021. Identification of herbicide resistance OsACC1 mutations via in planta prime-editing-library screening in rice[J]. Nature Plants, 7(7): 888-892. [77] Yan J, Oyler-Castrillo P, Ravisankar P, et al.2024. Improving prime editing with an endogenous small RNA-binding protein[J]. Nature, 628(8008): 639-647. [78] Yao S, Yin H, Li Y, et al.2024. Cytochrome P450 CYP81A104 in Eleusine indica confers resistance to multiherbicide with different modes of action[J]. Pest Management Science, 80(11): 5791-5798. [79] Zetsche B, Gootenberg J S, Abudayyeh O O, et al.2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 163(3): 759-771. [80] Zhang A, Shan T, Sun Y, et al.2023. Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors[J]. Plant Biotechnology Journal, 21(12): 2597-2610. [81] Zhang C, Zhong X, Li S, et al.2023. Artificial evolution of OsEPSPS through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance[J]. Journal of Integrative Plant Biology, 65(9): 2194-2203. [82] Zhang L, Du Y, Deng Y, et al.2024. Mutations in target gene confers resistance to acetolactate synthase inhibitors in Echinochloa phyllopogon[J]. Plant Physiology and Biochemistry, 216: 109194. [83] Zhang P, Zhang Y, Chen X, et al.2020. Cross resistance patterns to acetyl-CoA carboxylase inhibiting herbicides associated with different mutations in Italian ryegrass from China[J]. Crop Protection, 143(1): 105479-105484. [84] Zhang R, Chen S, Meng X, et al.2021. Generating broad-spectrum tolerance to ALS-inhibiting herbicides in rice by base editing[J]. Science China Life sciences, 64(10): 1624-1633. [85] Zhang R, Liu J, Chai Z, et al.2019. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing[J]. Nature Plants, 5(5): 480-485. [86] Zhang X Q, Powles S B.2006. Six amino acid substitutions in the carboxyl-transferase domain of the plastidic acetyl-CoA carboxylase gene are linked with resistance to herbicides in a Lolium rigidum population[J]. The New Phytologist, 172(4): 636-645. [87] Zhou F Y, Han H, Han Y J, et al.2023. Aldo-keto reductase may contribute to glyphosate resistance in Lolium rigidum[J]. Pest Management Science, 79(4): 1528-1537. [88] Zhou H, Liu B, Weeks D P, et al.2014. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice[J]. Nucleic Acids Research, 42(17): 10903-10914. [89] Zhou Z, Jiang Q, Qiu Z, et al.2024. Differential resistance to Acetyl-CoA carboxylase inhibitors in rice: Insights from two distinct target-site mutations[J]. Journal of Agricultural and Food Chemistry, 72(21): 12029-12044. [90] Zong Y, Song Q, Li C, et al.2018. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A[J]. Nature Biotechnology, 36(10): 950-953.