Prime-edited rice & CRISPR golden rice

Do you remember prime editing? It’s the new ‘search-and-replace’ genome editing technology that mediates targeted insertions, deletions, all 12 possible base-to-base conversions, and combinations thereof. The first good news is that David Liu et al. adapted prime editors for use in rice and wheat, so don’t miss their paper in Nature Biotechnology.

Sometimes, however, transgenes are the only way ahead. You need a super-high level of molecular understanding to be able to produce a novel gain of function trait by mutagenesis, as the inventors of golden rice told me a few years ago. Of course “it is possible to introduce a gene cassette through CRISPR. But this has some disadvantages, let alone the fact that [the resulting plants] would be as transgenic as those produced in the old-fashion way”, said Peter Beyer when asked about a hypothetical CRISPR golden rice. Here comes the other good news: a carotenoid-enriched rice generated through targeted gene insertion using CRISPR is now a reality; see the paper by Pamela Ronald et al. in Nature Communications

Their approach offers a couple of advantages in comparison with classic genetic engineering. First: CRISPR precisely targets the transgenes onto genetic safe harbors, instead than integrating them into random positions in the genome. Second: it allowed a marker-free insertion that might hopefully lower public concern and regulatory requirements. I asked the leading author to further compare the old and new approaches. Below you can read her reply. 

PAMELA RONALD (UC Davis) : The interview with Beyer and Potrykus on your blog is very good. I agree with the points they stated. The last point is interesting: “If you (or somebody else) could tell me which is the right position to intervene in the rice genome, I would certainly consider it. As you may know, the position of the cassette determines levels of expression. Moreover, somebody should tell me what the right expression level should look like”. 

In fact, that is exactly what we are doing. Oliver Dong showed that we can use CRISPR to insert the cassette into a precise location in the genome. He is also carrying out experiments now to assess other locations and the effect of those locations on expression level. At this point, I agree with Beyer that “Considering advantages and disadvantages of both methods of transgenic cassette integration I would still use Agrobacterium for integration.” Still, science is moving fast, so it may become more efficient to insert cassettes at precise locations using CRISPR. 

Using random mutagenesis (chemical or irradiation) is not a precise approach. This means that conventional mutagenesis methods are not a promising avenue to create new traits such as biofortification. Also, random mutagenesis introduces many more mutations than modern techniques. 

Scientifically, and from a humanitarian point of view, it makes sense to regulate a specific plant trait in light of its socio-economic and environmental effects (rather than the process in which the plant was made). Golden Rice was generated using Agrobacterium-mediated transformation to save the sight and lives of young children and has been approved as safe to eat by diverse regulatory agencies. The focus should be on the children, not the genetic process. 

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