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Progress of targeted genome modification approaches in higher plants

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Abstract

Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.

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Acknowledgments

The support of the “GenHort” project (“Adding value to elite Campania horticultural crops by advanced genomic technologies,” the Italian Ministry of Research and University-MIUR PON02_00395_3215002) to TC is acknowledged. CNS thanks funding from a USDA HATCH grant, a USDA NIFA Biotechnology Risk Assessment grant, and funding from the Ivan Racheff endowment at the University of Tennessee. TC dedicates this work to Prof. Luigi Monti, University of Naples “Federico II,” on occasion of his 80th birthday.

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  1. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Centro di Ricerca per l’Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy

    Teodoro Cardi

  2. Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA

    C. Neal Stewart Jr.

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  1. Teodoro Cardi
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Cardi, T., Neal Stewart, C. Progress of targeted genome modification approaches in higher plants. Plant Cell Rep 35, 1401–1416 (2016). https://doi.org/10.1007/s00299-016-1975-1

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