The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants

Semin Cell Dev Biol. 2019 Dec;96:77-90. doi: 10.1016/j.semcdb.2019.03.010. Epub 2019 Apr 7.


Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.

Keywords: Arabidopsis thaliana (Arabidopsis); CRISPR off-targets; CRISPR-Cas9; Engineered Cas9 variants; Genetically modified (GM) crops; Oryza sativa (rice); Phosphate (Pi) deficiency; Transcription factor interaction maps.

Publication types

  • Review

MeSH terms

  • CRISPR-Cas Systems / genetics*
  • Gene Editing*
  • Genetic Variation / genetics
  • Homeostasis / genetics*
  • Models, Biological*
  • Phosphates / metabolism*
  • Plants / genetics*
  • Plants / metabolism
  • Plants, Genetically Modified / genetics
  • Plants, Genetically Modified / metabolism
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism*


  • Phosphates
  • Transcription Factors