New research confirms GM causes massive off-target damage to plant genomes

GMWatch concludes scalpel and scissors metaphors used to describe GM methods must be replaced by child with chainsaw



A new open-access paper (abstract below) by researchers at the Salk Institute in the US confirms that the GM transformation process in plants is extraordinarily damaging at a genetic and epigenetic level. The researchers found that inserting new genes into a plant using the bacterium Agrobacterium tumefaciens as a shuttle creates major unintended effects in the genome. The authors studied four different GM lines of the standard laboratory model plant Arabidopsis.



The GMO lobby promotes GM methods, especially the new gene editing methods, using the metaphors of scissors or a scalpel to imply that these methods are precise and targeted. But based on the evidence, we suggest an alternative more accurate metaphor – that of a chainsaw in the hands of a young child. Hence our banner image for this article.



In addition to identifying multiple complete and partial GM gene insertions, numerous large rearrangements of the plant genome were detected. Furthermore, epigenetic (gene regulatory) changes were also identified that could have a wide range of effects, from the silencing of the introduced GM gene to alterations in function of multiple host gene systems.



The authors of the new paper do not discuss the consequences of this damage at a genetic and epigenetic level of the genome. However, it will result in substantial alterations in overall gene expression and consequent changes in the biochemistry, composition and growth characteristics of the GM plants.



New gene editing techniques, which rely on tools such as CRISPR, often involve the use of Agrobacterium in order to deliver this system into plant cells and in some cases to insert new genetic material into the genome. Thus, new gene editing GM techniques will not solve the problems highlighted by this new study.



In addition, the tissue culture process that is an obligatory part of all GM processes, including gene editing, is already known to cause mutations on a vast scale. So the implications of the new paper from the Salk researchers are that the tissue culture-induced mutations will be piled on top of the damage caused by the Agrobacterium-mediated GM transformation process.

Desperate spin

It's noteworthy how the Salk's press release bends over backwards, forwards, and sideways to try to put a positive spin on the new paper’s findings. Titled, "New technologies enable better-than-ever details on genetically modified plants", the press release says the results "offer new ways to more effectively minimize potential off-target effects".



In reality, however, the paper only describes new DNA mapping and sequencing techniques that can better identify the true extent and nature of the damage created by the genetic manipulation, enabling genetic engineers to more efficiently discard the most badly damaged GM plant lines. As one of the researchers says, "Current methods require screening of hundreds of transgenic lines to find good performing ones, such as those without extra insertions, so this technology could provide a more efficient approach.”



In other words, the new findings won't enable genetic engineers to prevent DNA damage in the first place, but only to more easily spot the lines in which they have caused the most unintended damage.



However, increased efficiency in weeding out those GM plants with the most off-target genetic and/or epigenetic damage will not ensure good crop performance and food safety. This is because even small changes in gene function can bring about unpredictable major alterations in the biochemistry and hence composition of plants. Thus, generic testing for unexpected toxic effects from the GM process (both old-style transgenic and newer gene editing) will still be needed.

Report: Claire Robinson

---

The complex architecture and epigenomic impact of plant T-DNA insertions

Florian Jupe, Angeline C. Rivkin, Todd P. Michael, Mark Zander, S. Timothy Motley, Justin P. Sandoval, R. Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R. Nery, Joseph R. Ecker

PLOS Genetics

Published January 18, 2019 https://doi.org/10.1371/journal.pgen.1007819

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007819

(open access)



Abstract



The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant genome. Although these transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. Here we applied two single-molecule technologies and analyzed Arabidopsis thaliana lines from three widely used T-DNA insertion collections (SALK, SAIL and WISC). Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and the length of individual insertions from 27 to 236 kilobases. De novo nanopore sequencing-based assemblies for two segregating lines partially resolved T-DNA structures and revealed multiple translocations and exchange of chromosome arm ends. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. The unprecedented contiguous nucleotide-level resolution enabled an in-depth study of the epigenome at T-DNA insertion sites. SALK_059379 line T-DNA insertions were enriched for 24nt small interfering RNAs (siRNA) and dense cytosine DNA methylation, resulting in transgene silencing via the RNA-directed DNA methylation pathway. In contrast, SAIL_232 line T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. Additionally, we profiled the H3K4me3, H3K27me3 and H2A.Z chromatin environments around T-DNA insertions using ChIP-seq in SALK_059379, SAIL_232 and five additional T-DNA lines. We discovered various effects ranging from complete loss of chromatin marks to the de novo incorporation of H2A.Z and trimethylation of H3K4 and H3K27 around the T-DNA integration sites. This study provides new insights into the structural impact of inserting foreign fragments into plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.





