Precise genomic editing technology and its application in the improvement of woody plants

JIANG Bo, AN Xinmin

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (1) : 11-20.

PDF(1995 KB)
PDF(1995 KB)
JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (1) : 11-20. DOI: 10.12302/j.issn.1000-2006.202402006

Precise genomic editing technology and its application in the improvement of woody plants

Author information +
History +

Abstract

The rapid advancement of genome precision editing technologies has revolutionized our understanding of life’s mysteries. Central to these technologies is the capacity to precisely insert, delete, and substitute DNA sequences at designated genomic positions, facilitating the targeted modification of genetic information within living organisms. These technologies have become the cornerstone of research in the field of biology, from early explorations to the groundbreaking application of the CRISPR system, emphasizing the profound impact of scientific inquiry. The application of the CRISPR system has brought about a significant leap in genomic editing, catalyzing the emergence of more precise editing tools, such as base editors and prime editors, which have significantly enhanced the ability to edit genomes with precision. This milestone shift has already demonstrated tremendous potential in a wide range of fields, including agricultural improvement and disease treatment. The potential applications for gene editing technology are vast, especially in forestry and grass breeding. The CRISPR/Cas system can knock out multiple genes, offering high targeting efficiency, ease of design and operation, and low costs, making it widely applicable in crop genetic improvement. However, it is also associated with numerous limitations, which can be overcomed by new editing tools. As the technologies continues to advance, gene editing technology is expected to solve complex biological problems in the future, bringing more innovation and breakthroughs to human health and agricultural development.

Key words

CRISPR / Cas9 / cytosine base editor / adenine base editor / glycosylase base editor / dual base editor / prime editor

Cite this article

Download Citations
JIANG Bo , AN Xinmin. Precise genomic editing technology and its application in the improvement of woody plants[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2025, 49(1): 11-20 https://doi.org/10.12302/j.issn.1000-2006.202402006

References

[1]
BARRANGOU R, FREMAUX C, DEVEAU H, et al. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 2007, 315(5819):1709-1712.DOI: 10.1126/science.1138140.
[2]
JINEK M, CHYLINSKI K, FONFARA I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821.DOI: 10.1126/science.1225829.
[3]
MOLLA K A, SRETENOVIC S, BANSAL K C, et al. Precise plant genome editing using base editors and prime editors[J]. Nat Plants, 2021, 7(9):1166-1187.DOI: 10.1038/s41477-021-00991-1.
[4]
MALI P, ESVELT K M, CHURCH G M. Cas9 as a versatile tool for engineering biology[J]. Nat Methods, 2013, 10(10):957-963.DOI: 10.1038/nmeth.2649.
[5]
QI L S, LARSON M H, GILBERT L A, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression[J]. Cell, 2013, 152(5):1173-1183.DOI: 10.1016/j.cell.2013.02.022.
[6]
STRECKER J, JONES S, KOOPAL B, et al. Engineering of CRISPR-Cas12b for human genome editing[J]. Nat Commun, 2019, 10(1):212.DOI: 10.1038/s41467-018-08224-4.
[7]
MA X L, ZHU Q L, CHEN Y L, et al. CRISPR/Cas9 platforms for genome editing in plants:developments and applications[J]. Mol Plant, 2016, 9(7):961-974.DOI: 10.1016/j.molp.2016.04.009.
[8]
SYMINGTON L S, GAUTIER J. Double-strand break end resection and repair pathway choice[J]. Annu Rev Genet, 2011, 45:247-271.DOI: 10.1146/annurev-genet-110410-132435.
[9]
CHANG L, GRAHAM P H, HAO J, et al. PI3K/Akt/mTOR pathway inhibitors enhance radiosensitivity in radioresistant prostate cancer cells through inducing apoptosis,reducing autophagy,suppressing NHEJ and HR repair pathways[J]. Cell Death Dis, 2014, 5(10):e1437.DOI: 10.1038/cddis.2014.415.
[10]
WANG G H, WANG C M, CHU T, et al. Deleting specific residues from the HNH linkers creates a CRISPR-SpCas9 variant with high fidelity and efficiency[J]. J Biotechnol, 2023, 368:42-52.DOI: 10.1016/j.jbiotec.2023.04.008.
[11]
GILBERT L A, LARSON M H, MORSUT L, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes[J]. Cell, 2013, 154(2):442-451.DOI: 10.1016/j.cell.2013.06.044.
[12]
HUANG S, YAN Y L, SU F, et al. Research progress in gene editing technology[J]. Front Biosci, 2021, 26(10):916-927.DOI: 10.52586/4997.
[13]
REES H A, LIU D R. Base editing:precision chemistry on the genome and transcriptome of living cells[J]. Nat Rev Genet, 2018, 19(12):770-788.DOI: 10.1038/s41576-018-0059-1.
[14]
KOMOR A C, KIM Y B, PACKER M S, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 2016, 533(7603):420-424.DOI: 10.1038/nature17946.
[15]
WANG X, DING C F, YU W X, et al. Cas12a base editors induce efficient and specific editing with low DNA damage response[J]. Cell Rep, 2020, 31(9):107723.DOI: 10.1016/j.celrep.2020.107723.
[16]
HU J C, SUN Y, LI B S, et al. Strand-preferred base editing of organellar and nuclear genomes using CyDENT[J]. Nat Biotechnol, 2024, 42:936-945.DOI: 10.1038/s41587-023-01910-9.
[17]
WANG X, LI J N, WANG Y, et al. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion[J]. Nat Biotechnol, 2018, 36(10):946-949.DOI: 10.1038/nbt.4198.
[18]
NISHIDA K, ARAZOE T, YACHIE N, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems[J]. Science, 2016, 353(6305):aaf8729.DOI: 10.1126/science.aaf8729.
[19]
HESS G T, FRÉSARD L, HAN K, et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells[J]. Nat Methods, 2016, 13(12):1036-1042.DOI: 10.1038/nmeth.4038.
[20]
KOBLAN L W, DOMAN J L, WILSON C, et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction[J]. Nat Biotechnol, 2018, 36(9):843-846.DOI: 10.1038/nbt.4172.
[21]
NISHIMASU H, SHI X, ISHIGURO S, et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space[J]. Science, 2018, 361(6408):1259-1262.DOI: 10.1126/science.aas9129.
[22]
KOMOR A C, ZHAO K T, PACKER M S, et al. Improved base excision repair inhibition and bacteriophage mu gam protein yields C:G-to-T:a base editors with higher efficiency and product purity[J]. Sci Adv, 2017, 3(8):eaao4774.DOI: 10.1126/sciadv.aao4774.
[23]
HU J H, MILLER S M, GEURTS M H, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity[J]. Nature, 2018, 556(7699):57-63.DOI: 10.1038/nature26155.
[24]
GAUDELLI N M, KOMOR A C, REES H A, et al. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage[J]. Nature, 2017, 551(7681):464-471.DOI: 10.1038/nature24644.
[25]
HUANG T P, ZHAO K T, MILLER S M, et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors[J]. Nat Biotechnol, 2019, 37(6):626-631.DOI: 10.1038/s41587-019-0134-y.
[26]
ZHAO D D, LI J, LI S W, et al. Glycosylase base editors enable C-to-A and C-to-G base changes[J]. Nat Biotechnol, 2021, 39(1):35-40.DOI: 10.1038/s41587-020-0592-2.
[27]
YE L J, ZHAO D D, LI J, et al. Glycosylase-based base editors for efficient T-to-G and C-to-G editing in mammalian cells[J]. Nat Biotechnol, 2024, 42(10):1538-1547.DOI: 10.1038/s41587-023-02050-w.
[28]
ZHANG X H, ZHU B Y, CHEN L, et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells[J]. Nat Biotechnol, 2020, 38(7):856-860.DOI: 10.1038/s41587-020-0527-y.
[29]
GRÜNEWALD J, ZHOU R H, LAREAU C A, et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing[J]. Nat Biotechnol, 2020, 38(7):861-864.DOI: 10.1038/s41587-020-0535-y.
[30]
LI C, ZHANG R, MENG X B, et al. Targeted,random mutagenesis of plant genes with dual cytosine and adenine base editors[J]. Nat Biotechnol, 2020, 38(7):875-882.DOI: 10.1038/s41587-019-0393-7.
[31]
SAKATA R C, ISHIGURO S, MORI H, et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations[J]. Nat Biotechnol, 2020, 38(7):865-869.DOI: 10.1038/s41587-020-0509-0.
[32]
YUAN T L, WU L L, LI S Y, et al. Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes[J]. Cell Discov, 2024, 10(1):20.DOI: 10.1038/s41421-023-00624-1.
[33]
ANZALONE A V, RANDOLPH P B, DAVIS J R, et al. Search-and-replace genome editing without double-strand breaks or donor DNA[J]. Nature, 2019, 576(7785):149-157.DOI: 10.1038/s41586-019-1711-4.
[34]
LIN Q P, ZONG Y, XUE C X, et al. Prime genome editing in rice and wheat[J]. Nat Biotechnol, 2020, 38(5):582-585.DOI: 10.1038/s41587-020-0455-x.
[35]
DOMAN J L, PANDEY S, NEUGEBAUER M E, et al. Phage-assisted evolution and protein engineering yield compact,efficient prime editors[J]. Cell, 2023, 186(18):3983-4002.e26.DOI: 10.1016/j.cell.2023.07.039.
[36]
CHADWICK A C, WANG X, MUSUNURU K. In vivo base editing of PCSK9 (proprotein convertase subtilisin/kexin type 9) as a therapeutic alternative to genome editing[J]. Arterioscler Thromb Vasc Biol, 2017, 37(9):1741-1747.DOI: 10.1161/ATVBAHA.117.309881.
[37]
MUSUNURU K, CHADWICK A C, MIZOGUCHI T, et al. In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in Primates[J]. Nature, 2021, 593(7859):429-434.DOI: 10.1038/s41586-021-03534-y.
[38]
CHEMELLO F, CHAI A C, LI H, et al. Precise correction of Duchenne muscular dystrophy exon deletion mutations by base and prime editing[J]. Sci Adv, 2021, 7(18):eabg4910.DOI: 10.1126/sciadv.abg4910.
[39]
HAN W Y, GAO B Q, ZHU J J, et al. Design and application of the transformer base editor in mammalian cells and mice[J]. Nat Protoc, 2023, 18(11):3194-3228.DOI: 10.1038/s41596-023-00877-w.
[40]
ZENG Y T, LI J N, LI G L, et al. Correction of the Marfan syndrome pathogenic FBN1 mutation by base editing in human cells and heterozygous embryos[J]. Mol Ther, 2018, 26(11):2631-2637.DOI: 10.1016/j.ymthe.2018.08.007.
[41]
KUANG Y J, LI S F, REN B, et al. Base-editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms[J]. Mol Plant, 2020, 13(4):565-572.DOI: 10.1016/j.molp.2020.01.010.
[42]
LI Y M, ZHU J J, WU H, et al. Precise base editing of non-allelic acetolactate synthase genes confers sulfonylurea herbicide resistance in maize[J]. Crop J, 2020, 8(3):449-456.DOI: 10.1016/j.cj.2019.10.001.
[43]
ZONG Y, SONG Q N, LI C, et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A[J]. Nat Biotechnol, 2018, 36: 950-95.DOI: 10.1038/nbt.4261.
[44]
ZHANG R, LIU J X, CHAI Z Z, et al. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing[J]. Nat Plants, 2019, 5(5):480-485.DOI: 10.1038/s41477-019-0405-0.
[45]
KANG B C, WOO J W, KIM S T, et al. Guidelines for C to T base editing in plants:base-editing window,guide RNA length,and efficient promoter[J]. Plant Biotechnol Rep, 2019, 13(5):533-541.DOI: 10.1007/s11816-019-00572-x.
[46]
HUANG X E, WANG Y C, WANG N. Base editors for Citrus gene editing[J]. Front Genome Ed, 2022, 4:852867.DOI: 10.3389/fgeed.2022.852867.
[47]
YAO T, YUAN G L, LU H W, et al. CRISPR/Cas9-based gene activation and base editing in Populus[J]. Hortic Res, 2023, 10(6):uhad085.DOI: 10.1093/hr/uhad085.
[48]
KIM Y, HONG S A, YU J, et al. Adenine base editing and prime editing of chemically derived hepatic progenitors rescue genetic liver disease[J]. Cell Stem Cell, 2021, 28(9):1614-1624.e5.DOI: 10.1016/j.stem.2021.04.010.
[49]
BOSE S K, WHITE B M, KASHYAP M V, et al. In utero adenine base editing corrects multi-organ pathology in a lethal lysosomal storage disease[J]. Nat Commun, 2021, 12(1):4291.DOI: 10.1038/s41467-021-24443-8.
[50]
KOBLAN L W, ERDOS M R, WILSON C, et al. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice[J]. Nature, 2021, 589(7843):608-614.DOI: 10.1038/s41586-020-03086-7.
[51]
LIU X S, QIN R Y, LI J, et al. A CRISPR-Cas9-mediated domain-specific base-editing screen enables functional assessment of ACCase variants in rice[J]. Plant Biotechnol J, 2020, 18(9):1845-1847.DOI: 10.1111/pbi.13348.
[52]
TIAN Y F, SHEN R D, LI Z R, et al. Efficient C-to-G editing in rice using an optimized base editor[J]. Plant Biotechnol J, 2022, 20(7):1238-1240.DOI: 10.1111/pbi.13841.
[53]
JANG H, JO D H, CHO C S, et al. Application of prime editing to the correction of mutations and phenotypes in adult mice with liver and eye diseases[J]. Nat Biomed Eng, 2022, 6(2):181-194.DOI: 10.1038/s41551-021-00788-9.
[54]
XU W, ZHANG C W, YANG Y X, et al. Versatile nucleotides substitution in plant using an improved prime editing system[J]. Mol Plant, 2020, 13(5):675-678.DOI: 10.1016/j.molp.2020.03.012.
[55]
QIAO D X, WANG J Y, LU M H, et al. Optimized prime editing efficiently generates heritable mutations in maize[J]. J Integr Plant Biol, 2023, 65(4):900-906.DOI: 10.1111/jipb.13428.
[56]
HUANG J, LIN Q, QIU J L, et al. Discovery of deaminase functions by structure-based protein clustering[J/OL]. Cell, 2023. DOI:10.1016/j.cell2023.05.041.
[57]
ZONG Y, LIU Y J, XUE C X, et al. An engineered prime editor with enhanced editing efficiency in plants[J]. Nat Biotechnol, 2022, 40(9):1394-1402.DOI: 10.1038/s41587-022-01254-w.
[58]
NELSON J W, RANDOLPH P B, SHEN S P, et al. Engineered pegRNAs improve prime editing efficiency[J]. Nat Biotechnol, 2022, 40(3):402-410.DOI: 10.1038/s41587-021-01039-7.
[59]
SUN C, LEI Y, LI B S, et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors[J]. Nat Biotechnol, 2024, 42:316-327.DOI: 10.1038/s41587-023-01769-w.
[60]
HUA K, TAO X P, YUAN F T, et al. Precise A·T to G·C base editing in the rice genome[J]. Mol Plant, 2018, 11(4):627-630.DOI: 10.1016/j.molp.2018.02.007.
[61]
袁雪宁, 姚凤鸽, 安轶, 等. CRISPR/Cas基因组编辑在木本植物性状改良中的应用[J/OL]. 科学通报, 2024, 1-17.
YUAN X N, YAO F G, AN Y, et al. Application of CRISPR/Cas genome editing in woody plant trait improvement[J/OL]. Chin Sci Bull, 2024,1-17. DOI: 10.1360/TB-2023-1125. (in Chinese)
[62]
LI G, SRETENOVIC S, EISENSTEIN E, et al. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid[J]. Plant Biotechnol J, 2021, 19(6):1086-1088.DOI: 10.1111/pbi.13581.
PDF(1995 KB)

Accesses

Citation

Detail

Sections
Recommended
The full text is translated into English by AI, aiming to facilitate reading and comprehension. The core content is subject to the explanation in Chinese.

/