数据处理与分析

深度学习在作物基因编辑技术的应用与研究进展

  • 赵晓燕 ,
  • 周焕斌 ,
  • 周国民 ,
  • 张建华
展开
  • 1 中国农业科学院农业信息研究所/农业农村部农业大数据重点实验室北京 100081
    2 中国农业科学院国家南繁研究院海南三亚 572024
    3 中国农业科学院植物保护研究所北京 100193
    4 国家农业科学数据中心北京 100081
    5 农业农村部南京农业机械化研究所南京 210014
    6 中国农业科学院西部农业研究中心新疆昌吉 831100
赵晓燕,E-mail:2896216851@qq.com
张建华,E-mail:zhangjianhua@caas.cn
周国民,E-mail:zhouguomin@caas.cn

收稿日期: 2025-06-18

  录用日期: 2025-09-28

  网络出版日期: 2026-04-01

基金资助

国家重点研发计划(2022YFF0711805);国家重点研发计划(2022YFF0711801);海南省自然科学基金(325MS155);三亚崖州湾科技城科技专项资助(SCKJ-JYRC-2023-45);三亚中国农业科学院国家南繁研究院南繁专项(YBXM2409);三亚中国农业科学院国家南繁研究院南繁专项(YBXM2410);三亚中国农业科学院国家南繁研究院南繁专项(YBXM2508);三亚中国农业科学院国家南繁研究院南繁专项(YBXM2509);中央级公益性科研院所基本科研业务费专项(JBYW-AII-2024-05);中央级公益性科研院所基本科研业务费专项(JBYW-AII-2025-05);中央级公益性科研院所基本科研业务费专项(Y2025YC90);中国农业科学院科技创新工程(CAAS-ASTIP-2024-AII)

Application of Deep Learning in Crop Gene Editing Technology and Research Progress

  • ZHAO XiaoYan ,
  • ZHOU HuanBin ,
  • ZHOU GuoMin ,
  • ZHANG JianHua
Expand
  • 1 Agricultural Information Institute of CAAS/Key Laboratory of Agricultural Big Data, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
    2 Nation Nanfan Research Institute of CAAS, Sanya 572024, Hainan, China
    3 Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
    4 National Agricultural Science Data Center, Beijing 100081, China
    5 Nanjing Institute of Agricultural Mechanization, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
    6 Institute of Western Agriculture, Chinese Academy of Agricultural Sciences, Changji 831100, Xinjiang, China

Received date: 2025-06-18

  Accepted date: 2025-09-28

  Online published: 2026-04-01

摘要

近年来,基因编辑技术发展迅猛,已成为基础基因功能研究与生物育种的核心工具。并且随着计算机和大数据的增长推动了深度学习在基因编辑中的应用,深度学习技术在优化基因编辑过程,特别是在提升作物改良效率方面,正发挥着日益显著的作用。本文综述了深度学习在基因编辑优化方面的研究进展,重点介绍了深度学习在基因编辑效率和特异性增强方面的应用。此外,文章深入探讨了深度学习与基因编辑深度融合所面临的技术挑战,并展望了其未来发展前景。通过将先进的基因编辑技术与深度学习相结合,未来将进一步加快作物育种的进展。

本文引用格式

赵晓燕 , 周焕斌 , 周国民 , 张建华 . 深度学习在作物基因编辑技术的应用与研究进展[J]. 农业大数据学报, 2026 , 8(1) : 24 -35 . DOI: 10.19788/j.issn.2096-6369.000120

Abstract

In recent years, gene editing technology has developed rapidly and has become a core tool for basic gene function research and biological breeding. And with the growth of computers and big data driving the application of deep learning in gene editing, deep learning technology is playing an increasingly significant role in optimizing the gene editing process, especially in enhancing the efficiency of crop improvement. This article reviews the research progress of deep learning in gene editing optimization, focusing on the application of deep learning in gene editing efficiency and specificity enhancement. In addition, the article delves into the technical challenges facing the deep integration of deep learning and gene editing, and looks forward to its future development prospects. By combining advanced gene editing technology with deep learning, the progress of crop breeding will be further accelerated in the future.

参考文献

[1] 赖郑诗雨, 黄赞唐, 孙洁婷, 等. CRISPR/Cas基因组编辑技术及其在农作物品种改良中的应用. 科学通报, 2022, 67: 1923-1937.
  LAI Z S Y, HUANG Z T, SUN J T, et al. The recent progress of CRISPR/Cas genome editing technology and its application in crop improvement. Chinese Science Bulletion, 2022, 67: 1923-1937.
[2] LI J, WU P, CAO Z, et al. Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing. Cell Reports, 2024, 43(2): 113765.
[3] CHEN K, WANG Y, ZHANG R, et al. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual Review of Plant Biology, 2019, 70: 667-697.
[4] ZHANG B. CRISPR/Cas9: A robust genome-editing tool withversatile functions and endless application. International Journal of Molecular Sciences, 2020, 21: 5111.
[5] WATERMAN D P, HABER J E, SMOLKA M B. Checkpoint responses to DNA double-strand breaks. Annual Review of Biochemistry, 2020, 89:103-133.
[6] MORTON J, DAVIS M W, JORGENSEN E M, et al. Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(44):16370-16375.
[7] CARROLL D. Genome engineering with zinc-finger nucleases. Genetics, 2011, 188:773-778.
[8] JOUNG J K, SANDER J D. TALENs: A widely applicable technology for targeted genome editing. Nature Reviews of Molecular Cell Biology, 2013, 14: 49-55.
[9] RICHTER C, CHANG J T, FINERAN P C. Function and regulation of clustered regularly interspaced short palindromic repeats(CRISPR) / CRISPR associated (Cas) systems. Viruses, 2012, 4: 2291-2311.
[10] ESVELT K M, MALI P, BRAFF J L, et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature Methods, 2013, 10: 1116-1121.
[11] ZHANG X, CHENG J, LIN Y, et al. Editing homologous copies of an essential gene affords crop resistance against two cosmopolitan necrotrophic pathogens. Plant Biotechnology Journal, 2021, 19(11): 2349-2361.
[12] ZHANG J, ZHOU Z, BAI J, et al. Disruption of MIR396e and MIR396f improves rice yield under nitrogen-deficient conditions. National Science Review, 2019, 7: 102-112.
[13] 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. Nature, 2016, 533: 420-424.
[14] DOM L, RAGURAM A, NEWBY G A, et al. Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors. Nature Biotechnology, 2020, 38:620-628.
[15] ZHAO D, LI J, LI S, et al. Glycosylase base editors enable C-to-a and C-to-G base changes. Nature Biotechnology, 2021, 39: 35-40.
[16] CHEN P J, LIU D R. Prime editing for precise and highly versatile genome manipulation. Nature Reviews Genetics, 2022, 24:161-177.
[17] SHAH M A, JIARUI K, RUOFU T, et al. CRISPR/Cas 9 mediated knockout of the OsbHLH024 transcription factor improves salt stress resistance in rice (Oryza sativa L.). Plants, 2022, 11(9):1184-1184.
[18] LI S, ZHANG Y, LIU Y, et al. The E3 ligase TaGW2 mediates transcription factor TaARR12 degradation to promote drought resistance in wheat. The Plant cell, 2024, 36(3):605-625.
[19] LIU L, GALLAGHER J, AREVALO E D, et al. Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. Nature plants, 2021, 7(3): 287-294.
[20] WANG Y X, LIU X Q, ZHENG X X, et al. Creation of aromatic maize by CRISPR/Cas. Journal of Integrative Plant Biology, 2021, 63(9):1664-1670.
[21] LI H L, WANG L B, DAI Y Z, et al. Synergetic interaction between neighbouring platinum monomers in CO2 hydrogenation. Nature Nanotechnology, 2018, 13(5):411-417.
[22] LIU T F, JI J, CHENG Y Y, et al. CRISPR/Cas9-mediated editing of GmTAP1 confers enhanced resistance to Phytophthora sojae in soybean. Journal of Integrative Plant Biology, 2023, 65(7):1609-1612.
[23] CHAO C W, CUI Y, LIN Y, et al. Identification of salt tolerance- associated presence-absence variations in the OsMADS56 gene through the integration of DEGs dataset and eQTL analysis. The New Phytologist, 2024, 243(3):833-838.
[24] WANG L, NIE R, YU Z, et al. An interpretable deep-learning architecture of capsule networks for identifying cell-type gene expression programs from single-cell RNA-sequencing data. Nature Machine Intelligence, 2020, 2(11):693-703.
[25] GUO J, ZENG L, CHEN H, et al. CRISPR/Cas9-Mediated targeted mutagenesis of BnaCOL9 advances the flowering time of Brassica napus L. International Journal of Molecular Sciences, 2022, 23(23): 14944-14944.
[26] 王远立, 啜国晖, 闫继芳, 等. 计算机辅助 CRISPR 向导 RNA 设计. 生物工程学报, 2017, 33(10): 1744-1756.
  WANG Y L, CHUAI G H, YAN J F, et al. In silico CRISPR-based sgRNA design. Chinese Journal of Biotechnology, 2017, 33(10): 1744-1756.
[27] JINEK M, CHYLINSKI K, FONFARA I, et al. A programmable Dual-RNA-Guided DNA endonuclease in adaptive bacterial immunity. Science, 2012, 337(6096):816-821.
[28] MEJíA-GUERRA M K, BUCKLER E S. A k-mer grammar analysis to uncover maize regulatory architecture. BMC Plant Biology, 2019, 19(1):1-17.
[29] FENG Z Y, ZHANG B T, DING W, et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Research, 2013, 23: 1229-1232.
[30] ZHANG H, YAN J F, LU Z K, et al. Deep sampling of gRNA in the human genome and deep-learning-informed prediction of gRNA activities. Cell Discovery, 2023, 9(1):48-48.
[31] WANG D Q, ZHANG C D, WANG B, et al. Optimized CRISPR guide RNA design for two high-fidelity Cas 9 variants by deep learning. Nature Communications, 2019, 10(1):4284.
[32] CHUAI G, MA H, YAN J, et al. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biology, 2018, 19(1): 1-18.
[33] LIN J C, Zhang Z L, ZHANG S, et al. CRISPR-net: a recurrent convolutional network quantifies off-target with activities CRISPR mismatches and indels. Advanced Science, 2020, 7(13): 1903562.
[34] JASPER Z, FRéDERIC G, MIJUNG K, et al. SpliceRover: interpretable convolutional neural networks for improved splice site prediction. Bioinformatics, 2018, 34(24):4180-4188.
[35] SCHOONENBERG V A C, COLE M A, YAO Q M, et al. CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. Genome Biology, 2018, 19(1):169.
[36] KWON H K, GOOSANG Y, JINMAN P, et al. Predicting the efficiency of prime editing guide RNAs in human cells. Nature Biotechnology, 2020, 39(2):198-206.
[37] KIM H K, KIM Y, LEE S, et al. SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance. Science Advances, 2019, 5(11): eaax9249.
[38] CHEN Q C, CHUAI G, ZHANG H H, et al. Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints. Nature Communications, 2023, 14(1):7521-7521.
[39] 康里奇, 谈攀, 洪亮. 人工智能时代下的酶工程. 合成生物学, 2023, 4(3): 524-534.
  KANG L Q, TAN P, HONG L. Enzyme engineering in the age of artificial intelligence. Synthetic Biology Journal, 2023, 4(3): 524-534.
[40] THEAN D G L, CHU H Y, FONG J H C, et al. Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities. Nature Communications, 2022, 13(1): 2219.
[41] KIM N, KIM H K, LEE S, et al. Prediction of the sequence-specific cleavage activity of Cas9 variants. Nature Biotechnol, 2020, 38: 1328-1336.
[42] CONCORDET J P, HAEUSSLER M. CRISPOR: Intuitive guide selection for CRIsPR/Cas9 genome editing experiments and screens. Nucleic Acids Research, 2018, 46 (W1):W242-W2 45.
[43] NAYFACH S, BHATNAGAR A, NOVICHKOV A, et al. Engineer- ing of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data. BioRxiv: the preprint server for biology, 2025.
[44] JIANG F, LI M, DONG J, et al. A general temperature-guided language model to design proteins of enhanced stability and activity. Science Advances, 2024, 29;10(48).
[45] SINGH R, LANCHANTIN J, ROBINS G, et al. DeepChroene: deep- learning for predicting gene expressionfromhistone podifications. Bioinformatics, 2016. 32(17): i639-i648.
[46] YIN Q, WU M, LIU Q, et al. DeepHiatone: a deep leaming approach topredictinghistone modications. BMC Geomics, 2019, 20: 11-23.
[47] HOFFMAN G E, BENDL J, GIRDHAR K, et al. Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification. Nucleic Acids Research, 2019, 47 (20): 10597-10611.
[48] PARK H M, WON J, PARK Y, et al. CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins. BMC Bioinformatics, 2023, 24(1): 167.
[49] NETHERY M A, KORVINK M, MAKAROVA K S, et al. CRISPRclassify: repeat-based classification of CRISPR loci. The CRISPR Journal, 2021, 4(4): 558-574.
[50] YANG S S, HUANG J, HE B F. CASPredict: a web service for identifying Cas proteins. PeerJ, 2021, 9: e11887.
[51] ZHANG T J, JIA Y R, LI H F, et al. CRISPRCasStack: a stacking strategy-based ensemble learning identification of framework for accurate Cas proteins. Briefings in Bioinformatics, 2022, 23(5): bbac335.
[52] ALKHNBASHI O S, MITROFANOV A, BONIDIA R, et al. CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. Nucleic Acids Research, 2021, 49(W1): W125-W130.
[53] NAHYE K, SUNGCHUL C, SUNGJAE K, et al. Deep learning models to predict the editing efficiencies and outcomes of diverse base editors. Nature Biotechnology, 2023, 42(3):484-497.
[54] YUAN T, WU L, LI S, et al. Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes. Cell Discovery, 2024, 10(1):20-20.
[55] ALEX H, FLORENCE D, SEBASTIEN B, et al. Generating functional protein variants with variational autoencoders. Plos Computational Biology, 2021, 17(2):e1008736-e1008736.
[56] DAWID G, SIMON M, IRENE R G, et al. LATE-a novel sensitive cell-based assay for the study of CRISPR/Cas9-related long-term adverse treatment effects. Molecular Therapy - Methods & Clinical Development, 2021, 22 249-262.
[57] TAN Y Y, CHU A H Y, BAO S Y, et al. Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(42):20969-20976.
[58] TIEU V, SOTILLO E, BJELAJAC R J, et al. A versatile CRISPR- Cas13d platform for multiplexed transcriptomic regulation and metabolic engineering in primary human T cells. Cell, 2024, 187(5): 1278-1295.e20.
文章导航

/