Research Progress in Herbicide-resistant Rice Created by Gene Editing

doi:10.13560/j.cnki.biotech.bull.1985.2025-1321

Abstract

Abstract:

Weeds are a major limiting factor in rice production, as they not only cause significant reductions in rice yield and quality but also escalate the costs of field management. The development of herbicide-resistant rice varieties is therefore a core strategy for efficient weed control in rice cultivation, as it can effectively extend the application scope and period of herbicides. Gene editing technology, endowed with efficient, precise, and rapid targeted modification capabilities, has overcome the inherent bottlenecks of traditional breeding approaches-including long breeding cycles, poor directional selectivity, and heavy reliance on elite germplasm resources-thus providing a revolutionary technical tool for the development of herbicide-resistant crops. This paper systematically reviews the latest research progress in the application of gene editing technology to herbicide-resistant rice breeding and briefly elaborates on the core working principles of the three most widely adopted gene editing systems to date: CRISPR/Cas-mediated NHEJ/HDR, base editing, and prime editing. It focuses on the applications of these three systems in the genetic improvement of key herbicide target genes in rice, including ALS, ACCase, EPSPS, GS, HPPD, and TubA2. Additionally, this study summarizes the mutation types induced by gene editing, along with the corresponding types and levels of herbicide resistance achieved in rice following the modification of these target genes. Finally, in light of the current challenges confronting the development and breeding of herbicide-resistant rice, prospects are proposed for the further optimization and advancement of gene editing technologies, the mining of novel functional genes, and the enhancement of environmental safety and sustainable development in this field. This review aims to provide a comprehensive reference for subsequent research and practical applications of new herbicide-resistant rice varieties.

Key words: rice, genome editing, base editing, prime editing, herbicide resistance

JIN Man, GONG Yi-hang, PAN Wen-bo, LUO Pei-run, GAO Wei, LI Ping-dong, TANG Xiao-yan. Research Progress in Herbicide-resistant Rice Created by Gene Editing[J]. Biotechnology Bulletin, 2026, 42(8): 8-21.

Figures/Tables 5

References 91

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编辑器类型 Editing class	编辑载体 Editing tools	突变位点 Mutation sites	除草剂抗性 Herbicide resistance	参考文献 Reference
NHEJ	pYLsgRNA-OsU3	Gly628Trp	甲咪唑烟酸，咪唑乙烟酸	［29］
HDR	pCXUN-Cas9， DNA donor	Trp548Leu， Ser627Ile	双草醚	［30］
HDR	pZH-MMCas9， pPZ-mALS	Trp548Leu， Ser627Ile	双草醚	［31］
HDR	Cas9-VirD2， DNAdonor	Trp548Leu	双草醚	［32］
HDR	pCXUN-LbCpf1，RNA donor	Trp548Leu， Ser627Ile	双草醚	［33-34］
HDR	LbCas12a， crRNA	Trp548Leu， Ser627Ile	双草醚	［35］
CBE	pHUE411-BE3-sgRNA-nCas9	Pro171Ser， Pro171Ala， Pro171Try， Pro171Phe	烟嘧磺隆	［36］
CBE	pHUE411-BE3-sgRNA-nCas9	Pro171Phe/Gly628Glu/Gly629Ser	甲咪唑烟酸	［36］
GBE	OsGTBE： nCas9-gMPGv6.3	Pro171Thr/Asn/His/Arg	氟唑磺隆	［37］
GBE	OsGTBE： nCas9-gMPGv6.3	Gly628Trp/Val/Leu	咪唑乙烟酸	［37］
ABE	rBE49b （TadA9）	Ser627Gly	咪唑啉酮	［38］
TadDE	TadDE	Arg190His， Gly628Glu， Gly629Ser， Gly628Glu/Gly629Ser	双草醚	［22］
BEMGE	pUbi：rBE9， pUbi：rBE14	Ala152Thr， Ala154Thr， Pro171Phe/Leu/Ser， Arg190His	双草醚	［39］
PE	PE2， PE3	Trp548Leu	双草醚	［40］
PE	ePPE： nCas9-NC-RT pegRNA	Trp542Leu， Ser621Ile， Pro165Ser	甲咪唑烟酸，烟嘧磺隆	［41］
PE	PE-P1，PE-P2	Thr548Leu， Pro171Ser	咪唑啉酮	［42］
PE	PE3-HS， PE3-AS， PE3-DS	Ser627Ile	双草醚	［43］
PE	Sp-PE2， Sp-PE3， Sa-PE3	Ser627Asn	咪唑啉酮	［44］

编辑器类型 Editing class	编辑载体 Editing tools	突变位点 Mutation sites	除草剂抗性 Herbicide resistance	参考文献 Reference
NHEJ	pYLsgRNA-OsU3	Gly628Trp	甲咪唑烟酸，咪唑乙烟酸	［29］
HDR	pCXUN-Cas9， DNA donor	Trp548Leu， Ser627Ile	双草醚	［30］
HDR	pZH-MMCas9， pPZ-mALS	Trp548Leu， Ser627Ile	双草醚	［31］
HDR	Cas9-VirD2， DNAdonor	Trp548Leu	双草醚	［32］
HDR	pCXUN-LbCpf1，RNA donor	Trp548Leu， Ser627Ile	双草醚	［33-34］
HDR	LbCas12a， crRNA	Trp548Leu， Ser627Ile	双草醚	［35］
CBE	pHUE411-BE3-sgRNA-nCas9	Pro171Ser， Pro171Ala， Pro171Try， Pro171Phe	烟嘧磺隆	［36］
CBE	pHUE411-BE3-sgRNA-nCas9	Pro171Phe/Gly628Glu/Gly629Ser	甲咪唑烟酸	［36］
GBE	OsGTBE： nCas9-gMPGv6.3	Pro171Thr/Asn/His/Arg	氟唑磺隆	［37］
GBE	OsGTBE： nCas9-gMPGv6.3	Gly628Trp/Val/Leu	咪唑乙烟酸	［37］
ABE	rBE49b （TadA9）	Ser627Gly	咪唑啉酮	［38］
TadDE	TadDE	Arg190His， Gly628Glu， Gly629Ser， Gly628Glu/Gly629Ser	双草醚	［22］
BEMGE	pUbi：rBE9， pUbi：rBE14	Ala152Thr， Ala154Thr， Pro171Phe/Leu/Ser， Arg190His	双草醚	［39］
PE	PE2， PE3	Trp548Leu	双草醚	［40］
PE	ePPE： nCas9-NC-RT pegRNA	Trp542Leu， Ser621Ile， Pro165Ser	甲咪唑烟酸，烟嘧磺隆	［41］
PE	PE-P1，PE-P2	Thr548Leu， Pro171Ser	咪唑啉酮	［42］
PE	PE3-HS， PE3-AS， PE3-DS	Ser627Ile	双草醚	［43］
PE	Sp-PE2， Sp-PE3， Sa-PE3	Ser627Asn	咪唑啉酮	［44］

编辑器类型 Editing class	编辑载体 Editing tools	突变位点 Mutation sites	除草剂抗性 Herbicide resistance	参考文献 Reference
ABE	pHUE411-PABE-7-esgRNA	Cys2186Arg	氟吡甲禾灵	［47］
ABE	rBE49b （TadA9）	Cys2186Lys	氟吡甲禾灵	［38］
A/CBE	pHUC411-derived eBE3/eABE	Trp2125Ser， Ile1879Val， Cys2186Arg	氟吡甲禾灵	［48］
A/C/DBE	（STEME-NG）， APOBEC3A-ecTadA ecTadA7.10-pOsU3	Trp2125Cys， Pro1927Phe， Ser1866Phe， Ala1884Pro	氟吡甲禾灵	［18］
A/C/DBE	ACE5-nSpCas9	Ile1879Leu， Ile1879Val， Trp2125Leu， Trp2125Gln， Trp2125Cys， Trp2125Cys/Arg2126Lys， Trp2125Ser， Trp2125Ser/Arg， Trp2125Ser/Gln， Trp2125Ser/2126Lys， Trp2125Cys/2126Lys/Gly2127Ser Cys2186His， Cys2186Arg， Gly2194Ser	氟吡甲禾灵	［49］
A/C/DBE	（pH-MoBE）， PlantBE-CODE-TadA9 CDA1	Trp2125Cys， Ile2139Asn， Cys2186Arg	氟吡甲禾灵	［50］
PE	（pPE2）， SpCas9 derived eBE3 and eABE	Trp2125Cys	氟吡甲禾灵	［51］
PE	PE-P1， PE-P2	Asp2176Gly， Gly2201Ala	氟吡甲禾灵	［42］
PE	（pPE2）， SpCas9 derived eBE3 and eABE	Pro1927Tyr/Phe， Ile1879Ser/Thr/Leu/Val， Trp2097Leu/Gly， Ile2139Ser/Val/Asn， Asp2176Gly， Gly2194Ser	氟吡甲禾灵	［52］

编辑器类型 Editing class	编辑载体 Editing tools	突变位点 Mutation sites	除草剂抗性 Herbicide resistance	参考文献 Reference
ABE	pHUE411-PABE-7-esgRNA	Cys2186Arg	氟吡甲禾灵	［47］
ABE	rBE49b （TadA9）	Cys2186Lys	氟吡甲禾灵	［38］
A/CBE	pHUC411-derived eBE3/eABE	Trp2125Ser， Ile1879Val， Cys2186Arg	氟吡甲禾灵	［48］
A/C/DBE	（STEME-NG）， APOBEC3A-ecTadA ecTadA7.10-pOsU3	Trp2125Cys， Pro1927Phe， Ser1866Phe， Ala1884Pro	氟吡甲禾灵	［18］
A/C/DBE	ACE5-nSpCas9	Ile1879Leu， Ile1879Val， Trp2125Leu， Trp2125Gln， Trp2125Cys， Trp2125Cys/Arg2126Lys， Trp2125Ser， Trp2125Ser/Arg， Trp2125Ser/Gln， Trp2125Ser/2126Lys， Trp2125Cys/2126Lys/Gly2127Ser Cys2186His， Cys2186Arg， Gly2194Ser	氟吡甲禾灵	［49］
A/C/DBE	（pH-MoBE）， PlantBE-CODE-TadA9 CDA1	Trp2125Cys， Ile2139Asn， Cys2186Arg	氟吡甲禾灵	［50］
PE	（pPE2）， SpCas9 derived eBE3 and eABE	Trp2125Cys	氟吡甲禾灵	［51］
PE	PE-P1， PE-P2	Asp2176Gly， Gly2201Ala	氟吡甲禾灵	［42］
PE	（pPE2）， SpCas9 derived eBE3 and eABE	Pro1927Tyr/Phe， Ile1879Ser/Thr/Leu/Val， Trp2097Leu/Gly， Ile2139Ser/Val/Asn， Asp2176Gly， Gly2194Ser	氟吡甲禾灵	［52］

编辑器类型 Editing class	编辑载体 Editing tools	突变位点 Mutation sites	参考文献 Reference
NHEJ-Crispr/Cas9	pHUN411	Thr173Ile， Pro177Ser	［55］
HDR-Crispr/Cas9	SpCas9： NICTK-1 pCRISPR-Cas9， HDR OsEPSPS template	Gly172Ala， Thr173Ile， Pro177Ser	［56］
BE	STCBE-2： nCas9（D10A）-NG	Asp213Asn	［57］
PE	pCXUN-Ubi-nCas9 NLS-PolyA E9 vector	Thr169Ile， Ala170Val， Pro173Ser	［59］
PE	ePE5max	Thr173Ile， Ala174Val， Pro177Ser	［60］
PE	PE3max	Thr173Ile， Ala174Val， Pro177Ser	［61］