Gene editing technologies such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems have been developed to create targeted DNA mutagenesis in many crop plants. This report describes application of the TALEN system to generate bialaphos resistance (bar)-knockout null segregants in herbicide-tolerant rice (Ba15) and microarray analysis on transcriptome changes of mutated lines, to identify unexpected effects resulting from off-targets. We generated 41 T₀ plants and identified TALEN-mediated bar sequence mutations in 14 of them. Non-target site single nucleotide polymorphisms (SNPs) and small insertion/deletions (InDels) accounted for a large proportion of the mutations. Segregations of phosphinothricin acetyltransferase (PAT) protein expression levels were observed in T₁ generations of two lines, R6 and R9. In addition, most T₁ offspring harbored the TALE-R expression cassette and acquired some de novo mutations that were not inherited from their T₀ parents. Three bar-knockout T₁ lines were tested for PAT protein expression in progeny seedlings, and their T₂ plants possessed inactive bar. We selected three bar-knockout T₂ plants that were TALE-DNA-free for microarray analysis, aiming to understand the transcriptome differences between mutated null segregants and their recipient line. Only 31 differentially expressed genes (DEGs) were identified in the bar-knockout rice lines, possibly resulting from somaclonal variations from the in vitro cell culture process. Taken together, TALEN-mediated bar mutations have little effect on the whole transcriptome profile of rice. We believe our results will be helpful to study unexpected consequences in gene-edited crops.

Citations

Citations to this article as recorded by  

• Advanced gene editing techniques for enhancing disease resistance and climate resilience in crops
  Zareen Sarfraz, Yusra Zarlashat, Alia Ambreen, Muhammad Mujahid, Muhammad Shahid Iqbal, Muhammad Nadeem
  Functional Plant Biology.2025;[Epub]     CrossRef
• Recent advances in site-specific transgene insertion into the maize genome using recombinases and genome editing endonucleases
  Marcos Fernando Basso, Maisa de Siqueira Pinto, Juliana Vieira Almeida Nonato, Ricardo Augusto Dante, Juliana Erika de Carvalho Teixeira Yassitepe
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• The Role of Membrane Transporters in the Biofortification of Zinc and Iron in Plants
  T. P. Ajeesh Krishna, T. Maharajan, S. Antony Ceasar
  Biological Trace Element Research.2023; 201(1): 464.     CrossRef