Plant DNA Repair Pathways and Their Applications in Genome Engineering

  • Qiudeng QueEmail author
  • Zhongying Chen
  • Tim Kelliher
  • David Skibbe
  • Shujie Dong
  • Mary-Dell Chilton
Part of the Methods in Molecular Biology book series (MIMB, volume 1917)


Remarkable progress in the development of technologies for sequence-specific modification of primary DNA sequences has enabled the precise engineering of crops with novel characteristics. These programmable sequence-specific modifiers include site-directed nucleases (SDNs) and base editors (BEs). Currently, these genome editing machineries can be targeted to specific chromosomal locations to induce sequence changes. However, the sequence mutation outcomes are often greatly influenced by the type of DNA damage being generated, the status of host DNA repair machinery, and the presence and structure of DNA repair donor molecule. The outcome of sequence modification from repair of DNA double-strand breaks (DSBs) is often uncontrollable, resulting in unpredictable sequence insertions or deletions of various sizes. For base editing, the precision of intended edits is much higher, but the efficiency can vary greatly depending on the type of BE used or the activity of the endogenous DNA repair systems. This article will briefly review the possible DNA repair pathways present in the plant cells commonly used for generating edited variants for genome engineering applications. We will discuss the potential use of DNA repair mechanisms for developing and improving methodologies to enhance genome engineering efficiency and to direct DNA repair processes toward the desired outcomes.

Key words

DNA repair Genome engineering Site-directed nuclease (SDN) Base editor (BE) Single-strand break (SSB) Double-strand break (DSB) Nonhomologous end joining (NHEJ) Alternative end joining (altEJ) Homology-directed repair (HDR) 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Qiudeng Que
    • 1
    Email author
  • Zhongying Chen
    • 1
  • Tim Kelliher
    • 1
  • David Skibbe
    • 1
  • Shujie Dong
    • 1
  • Mary-Dell Chilton
    • 1
  1. 1.Seeds Research, Syngenta Crop Protection, LLCResearch Triangle ParkUSA

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