Abstract
Agriculture is experiencing a technological inflection point in its history, while also facing unprecedented challenges posed by human population growth and global climate changes. Key advancements in precise genome editing and new methods for rapid generation of bioengineered crops promise to both revolutionize the speed and breadth of breeding programmes and increase our ability to feed and sustain human population growth. Although genome editing enables targeted and specific modifications of DNA sequences, several existing barriers prevent the widespread adoption of editing technologies for basic and applied research in established and emerging crop species. Inefficient methods for the transformation and regeneration of recalcitrant species and the genotype dependency of the transformation process remain major hurdles. These limitations are frequent in monocotyledonous crops, which alone provide most of the calories consumed by human populations. Somatic embryogenesis and de novo induction of meristems — pluripotent groups of stem cells responsible for plant developmental plasticity — are essential strategies to quickly generate transformed plants. Here we review recent discoveries that are rapidly advancing nuclear transformation technologies and promise to overcome the obstacles that have so far impeded the widespread adoption of genome editing in crop species.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Phillips, R. L., Kaeppler, S. M. & Olhoft, P. Genetic instability of plant tissue cultures: breakdown of normal controls. Proc. Natl Acad. Sci. USA 91, 5222–5226 (1994).
Neelakandan, A. K. & Wang, K. Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. Plant Cell Rep. 31, 597–620 (2012).
Gordon-Kamm, B. et al. Using morphogenic genes to improve recovery and regeneration of transgenic plants. Plants (Basel) 8, 38 (2019).
Anami, S., Njuguna, E., Coussens, G., Aesaert, S. & Van Lijsebettens, M. Higher plant transformation: principles and molecular tools. Int. J. Dev. Biol. 57, 483–494 (2013).
Liu, J. et al. Genome-scale sequence disruption following biolistic transformation in rice and maize. Plant Cell 31, 368–383 (2019).
Clark, K. A. & Krysan, P. J. Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insertion lines. Plant J. 64, 990–1001 (2010).
Hu, Y., Chen, Z., Zhuang, C. & Huang, J. Cascade of chromosomal rearrangements caused by a heterogeneous T-DNA integration supports the double-stranded break repair model for T-DNA integration. Plant J. 90, 954–965 (2017).
Krispil, R. et al. The position and complex genomic architecture of plant T-DNA insertions revealed by 4SEE. Int. J. Mol. Sci. 21, 2373 (2020).
Pucker, B., Kleinbolting, N. & Weisshaar, B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics 22, 599 (2021).
Jupe, F. et al. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS Genet. 15, e1007819 (2019).
Woo, J. W. et al. DNA-free genome editing in plants with preassembled CRISPR–Cas9 ribonucleoproteins. Nat. Biotechnol. 33, 1162–1164 (2015).
Liang, Z. et al. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nat. Protoc. 13, 413–430 (2018).
Liang, Z. et al. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat. Commun. 8, 14261 (2017).
Svitashev, S., Schwartz, C., Lenderts, B., Young, J. K. & Mark Cigan, A. Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat. Commun. 7, 13274 (2016).
Hamilton, C. M., Frary, A., Lewis, C. & Tanksley, S. D. Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc. Natl Acad. Sci. USA 93, 9975–9979 (1996).
De Saeger, J. et al. Agrobacterium strains and strain improvement: present and outlook. Biotechnol. Adv. 53, 107677 (2021).
Lacroix, B. & Citovsky, V. Pathways of DNA transfer to plants from Agrobacterium tumefaciens and related bacterial species. Annu Rev. Phytopathol. 57, 231–251 (2019).
Yuan, Z. C. et al. The plant signal salicylic acid shuts down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium. Proc. Natl Acad. Sci. USA 104, 11790–11795 (2007).
Lee, C. W. et al. Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana. Plant Cell 21, 2948–2962 (2009).
Zhang, Q. et al. A novel ternary vector system united with morphogenic genes enhances CRISPR/Cas delivery in maize. Plant Physiol. 181, 1441–1448 (2019).
Anand, A. et al. An improved ternary vector system for Agrobacterium-mediated rapid maize transformation. Plant Mol. Biol. 97, 187–200 (2018).
Kang, M. et al. An improved Agrobacterium-mediated transformation and genome-editing method for maize inbred B104 using a ternary vector system and immature embryos. Front Plant Sci. 13, 860971 (2022).
Raman, V. et al. Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation. Nat. Commun. 13, 2581 (2022).
Lv, Z., Jiang, R., Chen, J. & Chen, W. Nanoparticle-mediated gene transformation strategies for plant genetic engineering. Plant J. 104, 880–891 (2020).
Vejlupkova, Z. et al. No evidence for transient transformation via pollen magnetofection in several monocot species. Nat. Plants 6, 1323–1324 (2020).
Zhao, X. et al. Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers. Nat. Plants 3, 956–964 (2017).
Wang, Z. P. et al. Efficient and genotype independent maize transformation using pollen transfected by DNA-coated magnetic nanoparticles. J. Integr. Plant Biol. 64, 1145–1156 (2022).
Ma, X., Zhang, X., Liu, H. & Li, Z. Highly efficient DNA-free plant genome editing using virally delivered CRISPR–Cas9. Nat. Plants 6, 773–779 (2020).
Hu, J. et al. A barley stripe mosaic virus-based guide RNA delivery system for targeted mutagenesis in wheat and maize. Mol. Plant Pathol. 20, 1463–1474 (2019).
Li, T. et al. Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture. Mol. Plant 14, 1787–1798 (2021).
Williams, L. E. Genetics of shoot meristem and shoot regeneration. Annu. Rev. Genet. 55, 661–681 (2021).
Ikeuchi, M. et al. Molecular mechanisms of plant regeneration. Annu. Rev. Plant Biol. 70, 377–406 (2019).
Motte, H., Vereecke, D., Geelen, D. & Werbrouck, S. The molecular path to in vitro shoot regeneration. Biotechnol. Adv. 32, 107–121 (2014).
Efroni, I. et al. Root regeneration triggers an embryo-like sequence guided by hormonal interactions. Cell 165, 1721–1733 (2016).
Verma, S., Attuluri, V. P. S. & Robert, H. S. An essential function for auxin in embryo development. Cold Spring Harb. Perspect. Biol. 13, a039966 (2021).
Cheng, Y., Dai, X. & Zhao, Y. Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. Plant Cell 19, 2430–2439 (2007).
Stepanova, A. N. et al. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell 133, 177–191 (2008).
Lardon, R., Wijnker, E., Keurentjes, J. & Geelen, D. The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors. Commun. Biol. 3, 549 (2020).
Lin, G. et al. Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome Biol. 22, 175 (2021).
Wang, F. X. et al. Chromatin accessibility dynamics and a hierarchical transcriptional regulatory network structure for plant somatic embryogenesis. Dev. Cell 54, 742–757e748 (2020).
Li, M. et al. Auxin biosynthesis maintains embryo identity and growth during BABY BOOM-induced somatic embryogenesis. Plant Physiol. 188, 1095–1110 (2022).
Uc-Chuc, M. A. et al. YUCCA-mediated biosynthesis of the auxin IAA is required during the somatic embryogenic induction process in Coffea canephora. Int. J. Mol. Sci. 21, 4751 (2020).
Wang, Y. et al. Genetic variations in ZmSAUR15 contribute to the formation of immature embryo-derived embryonic calluses in maize. Plant J. 109, 980–991 (2021).
Wojcikowska, B. et al. LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis. Planta 238, 425–440 (2013).
Lotan, T. et al. Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93, 1195–1205 (1998).
Zhang, T. Q. et al. A two-step model for de novo activation of WUSCHEL during plant shoot regeneration. Plant Cell 29, 1073–1087 (2017).
Wu, L. Y. et al. Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration. Dev. Cell 57, 526–542e527 (2022).
Matsuo, N., Makino, M. & Banno, H. Arabidopsis ENHANCER OF SHOOT REGENERATION (ESR)1 and ESR2 regulate in vitro shoot regeneration and their expressions are differentially regulated. Plant Sci. 181, 39–46 (2011).
Iwase, A. et al. WIND1 promotes shoot regeneration through transcriptional activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis. Plant Cell 29, 54–69 (2017).
Heyman, J. et al. The heterodimeric transcription factor complex ERF115–PAT1 grants regeneration competence. Nat. Plants 2, 16165 (2016).
Ikeuchi, M. et al. Wounding triggers callus formation via dynamic hormonal and transcriptional changes. Plant Physiol. 175, 1158–1174 (2017).
Sakamoto, Y. et al. Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells. Plant Cell 34, 4348–4365 (2022).
Hofhuis, H. et al. Phyllotaxis and rhizotaxis in Arabidopsis are modified by three PLETHORA transcription factors. Curr. Biol. 23, 956–962 (2013).
Kareem, A. et al. PLETHORA genes control regeneration by a two-step mechanism. Curr. Biol. 25, 1017–1030 (2015).
Lian, Z. et al. Application of developmental regulators to improve in planta or in vitro transformation in plants. Plant Biotechnol. J. 20, 1622–1635 (2022).
Hernandez-Coronado, M. et al. Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense. Dev. Cell 57, 451–465.e6 (2022).
Boutilier, K. et al. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14, 1737–1749 (2002).
Khanday, I., Skinner, D., Yang, B., Mercier, R. & Sundaresan, V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565, 91–95 (2019).
Lowe, K. et al. Morphogenic regulators BABY BOOM and WUSCHEL improve monocot transformation. Plant Cell 28, 1998–2015 (2016).
Khanday, I., Santos-Medellin, C. & Sundaresan, V. Rice embryogenic trigger BABY BOOM1 promotes somatic embryogenesis by upregulation of auxin biosynthesis genes. Preprint at bioRxiv https://doi.org/10.1101/2020.08.24.265025 (2020).
Horstman, A. et al. The BABY BOOM transcription factor activates the LEC1–ABI3–FUS3–LEC2 network to induce somatic embryogenesis. Plant Physiol. 175, 848–857 (2017).
Underwood, C. J. et al. A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce. Nat. Genet. 54, 84–93 (2022).
Maren, N. A. et al. Genotype-independent plant transformation. Hortic. Res. 9, uhac047 (2022).
Salaun, C., Lepiniec, L. & Dubreucq, B. Genetic and molecular control of somatic embryogenesis. Plants (Basel) 10, 1467 (2021).
Kausch, A. P. et al. Edit at will: genotype independent plant transformation in the era of advanced genomics and genome editing. Plant Sci. 281, 186–205 (2019).
Maher, M. F. et al. Plant gene editing through de novo induction of meristems. Nat. Biotechnol. 38, 84–89 (2020).
Lowe, K. et al. Rapid genotype ‘independent’ Zea mays L. (maize) transformation via direct somatic embryogenesis. In Vitr. Cell. Dev. Biol. Plant 54, 240–252 (2018).
Hoerster, G. et al. Use of non-integrating Zm-Wus2 vectors to enhance maize transformation. In Vitr. Cell. Dev. Biol. Plant 56, 265–279 (2020).
Pan, C. et al. Boosting plant genome editing with a versatile CRISPR–Combo system. Nat. Plants 8, 513–525 (2022).
Wang, K. et al. The gene TaWOX5 overcomes genotype dependency in wheat genetic transformation. Nat. Plants 8, 110–117 (2022).
Debernardi, J. M. et al. A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat. Biotechnol. 38, 1274–1279 (2020).
Sarkar, A. K. et al. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature 446, 811–814 (2007).
Ortiz-Ramirez, C. et al. Ground tissue circuitry regulates organ complexity in maize and Setaria. Science 374, 1247–1252 (2021).
Forzani, C. et al. WOX5 suppresses CYCLIN D activity to establish quiescence at the center of the root stem cell niche. Curr. Biol. 24, 1939–1944 (2014).
Pi, L. et al. Organizer-derived WOX5 signal maintains root columella stem cells through chromatin-mediated repression of CDF4 expression. Dev. Cell 33, 576–588 (2015).
Zhai, N. & Xu, L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. Nat. Plants 7, 1453–1460 (2021).
Wang, K. et al. Author correction: the gene TaWOX5 overcomes genotype dependency in wheat genetic transformation. Nat. Plants 8, 717–720 (2022).
Li, S. et al. The OsmiR396c–OsGRF4–OsGIF1 regulatory module determines grain size and yield in rice. Plant Biotechnol. J. 14, 2134–2146 (2016).
Rodriguez, R. E. et al. MicroRNA miR396 regulates the switch between stem cells and transit-amplifying cells in Arabidopsis roots. Plant Cell 27, 3354–3366 (2015).
Liebsch, D. & Palatnik, J. F. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. Curr. Opin. Plant Biol. 53, 31–42 (2020).
Debernardi, J. M. et al. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. Plant J. 79, 413–426 (2014).
Luo, G. & Palmgren, M. GRF–GIF chimeras boost plant regeneration. Trends Plant Sci. 26, 201–204 (2021).
Zhang, X. et al. Establishment of an Agrobacterium-mediated genetic transformation and CRISPR/Cas9-mediated targeted mutagenesis in hemp (Cannabis sativa L.). Plant Biotechnol. J. 19, 1979–1987 (2021).
Kong, J. et al. Overexpression of the transcription factor GROWTH-REGULATING FACTOR5 improves transformation of dicot and monocot species. Front. Plant Sci. 11, 572319 (2020).
Gao, F. et al. Blocking miR396 increases rice yield by shaping inflorescence architecture. Nat. Plants 2, 15196 (2015).
Aesaert, S. et al. Optimized transformation and gene editing of the B104 public maize inbred by improved tissue culture and use of morphogenic regulators. Front. Plant Sci. 13, 883847 (2022).
Masters, A. et al. Agrobacterium-mediated immature embryo transformation of recalcitrant maize inbred lines using morphogenic genes. J. Vis. Exp. https://doi.org/10.3791/60782 (2020).
Mookkan, M., Nelson-Vasilchik, K., Hague, J., Zhang, Z. J. & Kausch, A. P. Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2. Plant Cell Rep. 36, 1477–1491 (2017).
Chen, Z., Debernardi, J. M., Dubcovsky, J. & Gallavotti, A. The combination of morphogenic regulators BABY BOOM and GRF–GIF improves maize transformation efficiency. Preprint at bioRxiv https://doi.org/10.1101/2022.09.02.506370 (2022).
Reed, K. M. & Bargmann, B. O. R. Protoplast regeneration and its use in new plant breeding technologies. Front. Genome Ed. 3, 734951 (2021).
Cho, H. J. et al. Development of an efficient marker-free soybean transformation method using the novel bacterium Ochrobactrum haywardense H1. Plant Biotechnol. J. 20, 977–990 (2022).
Zobrist, J. D. et al. Transformation of teosinte (Zea mays ssp. parviglumis) via biolistic bombardment of seedling-derived callus tissues. Front. Plant Sci. 12, 773419 (2021).
Hufford, M. B. et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373, 655–662 (2021).
Thakare, D., Tang, W., Hill, K. & Perry, S. E. The MADS-domain transcriptional regulator AGAMOUS-LIKE15 promotes somatic embryo development in Arabidopsis and soybean. Plant Physiol. 146, 1663–1672 (2008).
Arroyo-Herrera, A. et al. Expression of WUSCHEL in Coffea canephora causes ectopic morphogenesis and increases somatic embryogenesis. Plant Cell Tissue Organ Cult. 94, 171–180 (2008).
Che, P. et al. Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum. Commun. Biol. 5, 344 (2022).
Liu, Y. et al. Establishment of Agrobacterium-mediated genetic transformation and application of CRISPR/Cas9 genome-editing system to Brassica rapa var. rapa. Plant Methods 18, 98 (2022).
Hu, W. et al. Kn1 gene overexpression drastically improves genetic transformation efficiencies of citrus cultivars. Plant Cell Tissue Organ Cult. 125, 81–91 (2016).
Elhiti, M., Tahir, M., Gulden, R. H., Khamiss, K. & Stasolla, C. Modulation of embryo-forming capacity in culture through the expression of Brassica genes involved in the regulation of the shoot apical meristem. J. Exp. Bot. 61, 4069–4085 (2010).
Heidmann, I., de Lange, B., Lambalk, J., Angenent, G. C. & Boutilier, K. Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor. Plant Cell Rep. 30, 1107–1115 (2011).
Deng, W., Luo, K., Li, Z. & Yang, Y. A novel method for induction of plant regeneration via somatic embryogenesis. Plant Sci. 177, 43–48 (2009).
Zhou, Z. et al. Boosting transformation in wheat by BBM–WUS. Preprint at bioRxiv https://doi.org/10.1101/2022.03.13.483388 (2022).
Feng, Q. et al. Highly efficient, genotype-independent transformation and gene editing in watermelon (Citrullus lanatus) using a chimeric ClGRF4–GIF1 gene. J. Integr. Plant Biol. 63, 2038–2042 (2021).
Acknowledgements
Research in the Gallavotti lab is supported by grants from the National Science Foundation (IOS nos 1546873, 1916804 and 2026561). Research in the Dubcovsky lab is supported by grants no. 2022-68013-36439 and no. 2022-67013-36209 from the USDA National Institute of Food and Agriculture and by the Howard Hughes Medical Institute.
Author information
Authors and Affiliations
Contributions
Z.C., J.M.D., J.D. and A.G. conceived the manuscript, contributed to writing and editing, and approved the manuscript.
Corresponding author
Ethics declarations
Competing interests
J.M.D. is co-inventor in patent no. US2017/0362601A1, which describes the use of chimaeric GRF–GIF proteins with enhanced effects on plant growth (Universidad Nacional de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas). J.D. and J.M.D. are co-inventors in UC Davis patent application no. WO2021007284A2, which describes the use of GRF–GIF chimaeras to enhance regeneration efficiency in plants.
Peer review
Peer review information
Nature Plants thanks David Jackson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Chen, Z., Debernardi, J.M., Dubcovsky, J. et al. Recent advances in crop transformation technologies. Nat. Plants 8, 1343–1351 (2022). https://doi.org/10.1038/s41477-022-01295-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41477-022-01295-8
This article is cited by
-
Genome-edited foods
Nature Reviews Bioengineering (2023)
-
Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects
Planta (2023)
-
Optimization of the regeneration and Agrobacterium-mediated transformation in pear
Horticulture Advances (2023)
-
GRF-GIF duo and GRF-GIF-BBM: novel transformation methodologies for enhancing regeneration efficiency of genome-edited recalcitrant crops
Planta (2023)