Genomic consequences associated with Agrobacterium‐mediated transformation of plants

Abstract

SUMMARYAttenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium‐mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant‐microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long‐read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium‐mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large‐scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.

Disproportion among reticulon-like 16 (RTNLB16) splice variants disrupts growth and decreases sensitivity to ABA and senescence in Arabidopsis

“…Inversion of chromosomal fragments due to inter-chromosomal rearrangement leads to the suppression of recombination during homologous chromosomal pairing in Meiosis, resulting in resulted in gamete aneuploidy (Curtis et al, 2009). Multiple T-DNA insertions and concatenation of copies are common in plant transformation experiments, often leading to complex mutations, including flanking filler sequences and large-scale genomic rearrangements (Thomson et al, 2023). Translocation frequency surveyed in a collection of 64 independent Arabidopsis Salk lines detected chromosomal translocations in nearly 20% of the mutants, which in most cases led to abnormal pollen phenotype (Clark and Krysan, 2010).…”

Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 20: Suitability of taxonomic units notified to EFSA until March 2024

“…R. radiobacter contains also strains which are not pathogenic for plants. Extensive literature reports A. tumefaciens for its ability to transfer DNA into plant cells, a capacity intensively exploited to deliver recombinant DNA into plants (Azizi‐Dargahlou & Pouresmaeil, 2024; Thomson et al., 2024). R. radiobacter was detected as a food contaminant (Casalinuovo et al., 2015; Williams et al., 2023).…”