Next-generation disease resistance breeding

Crop plants with DNA deletions are not GMOs

by Sophien Kamoun and Eric Ward

In 2007, Sebastian Schornack, then a freshly minted Ph.D. student from the laboratories of Thomas Lahaye and Ulla Bonas at the Martin-Luther-University Halle-Wittenberg, was fastidiously carrying out follow-up experiments to his thesis work. For the past few years he had been studying how the bacterium Xanthomonas infects its plant hosts. Specifically, he was interested in a class of “effector” proteins, called transcription activator-like (TAL) effectors, that the bacterium delivers to the nuclei of host cells to alter plant gene expression.
Ever since their discovery in the late 1980s, the unusual structure of these effector proteins has intrigued plant microbiologists. TAL effectors contain many near-perfect repeats 34 amino acids in length with two hypervariable residues, but the biological meaning of this peculiar modular structure was unknown. At the time Schornack was finishing his thesis, TAL effectors had just been discovered to bind specific DNA sequences in the genomes of their host plants, where they activated expression of host genes thought to favour colonization by the pathogen. While comparing the identity of the hypervariable amino acids in the repeats of particular TAL effectors with the corresponding DNA sequence of their binding sites, Schornack experienced a flash of insight, and noticed a defining pattern [Schornack].
Following discussions with Jens Boch and experimental work with their colleagues at Halle University, it became evident that, indeed, a “code” built into the TAL effector proteins determines their DNA binding specificity [Boch]. Not long after that, across the Atlantic, another Ph.D. student Matt Moscou, working with Adam Bogdanove at Iowa State University, independently reached a similar conclusion using clever computational analyses of TAL effector-induced expression changes in rice plants [Moscou].
Both teams immediately grasped the impact of their discoveries – synthetic TAL effectors could be custom designed to bind any target DNA sequence. Such a technological breakthrough would have far reaching implications in biotechnology.
Fast forward to 2012: the reach of TAL effectors has gone beyond the study of plant-microbe interactions. TAL effectors are now ubiquitously used in biotechnology and the emerging field of synthetic biology [Bogdanove]. Scientists have also shown that by hooking TAL effectors to nucleases, enzymes that nick DNA, they can target an exact site in a genome to produce variations. For instance, one study revealed that injection of mouse embryos with TAL-nucleases yields adult mice that vary at specific, predicted positions in their genomes [Tesson]. The possibilities are immense for using TAL technology to induce targeted variations in the genomes of mammals, flies, worms and plants. Laboratories worldwide are putting the technology to creative use with numerous exciting applications certain to emerge.
A game-changing application of TAL technology to crop breeding is described in a recent paper in Nature Biotechnology by Bing Yang and colleagues [Li]. In this landmark study, the authors used TAL-nucleases to remove a small stretch of DNA from the genome of rice that rendered it susceptible to bacterial blight, an important disease that affects millions of hectares throughout Asia.
This study ushers in a new era in crop breeding. Plant geneticists will now be able to use TAL-nucleases to introduce precise, favorable modifications in any region of the genome. Remarkably, because Li and colleagues have bred out the TAL sequences, the resulting rice varieties lack any foreign DNA.

Instead of adding a sentence or two to the genome book, as is done by standard genetic modification (GM) approaches, they removed a few letters; the rice varieties they generated lack anywhere from 3 to 57 bases in their genomes (as in the Figure to the right from the Li paper). Thus, the rice plants generated by Li et al. do not contain extraneous DNA and cannot by any reasonable definition be considered “GMOs.”
Specific removal or replacement of a few letters of DNA can already be achieved by much more laborious, less directed methods, using chemical mutagens or treatments with radioactivity. So in principle Li et al. could have generated an identical result by blasting rice seed with a fast neutron beam or soaking them in diepoxybutane and screening a massive population (10s of thousands to millions) of their progeny for the exact deletion they achieved in one go using the TAL nuclease. Curiously, the random mutagenesis method, which requires highly toxic radiation or chemical treatment, is perfectly acceptable in the production of crop varieties that can be sold as “organic”!

One intriguing aspect of the methodology used in this study is that the rice variants can in fact be considered the exact opposite of transgenic plants given that DNA has been removed from their genomes. One could even use this logic to turn some of the arguments raised against GM crops on their heads. For instance, GM opponents often argue that insertion of extraneous DNA can cause new, unknown allergenicity. Should one then argue that crops with genome deletions could be unpredictably hypoallergenic? GM opponents argue that foreign DNA raises the specter of contamination of other plants and the environment. Do these new rice reduce the risk of DNA pollution? And so on, ad absurdum.
One hopes that groups traditionally opposed to GMO crops will understand and appreciate that the outputs generated by TAL-induced variations, are indistinguishable from mutations that arise by other, more “acceptable” means and that already pervade the genomes of the crops we eat.
Let’s work together to bring to fruition “next-generation plant breeding” and use novel technologies to help secure an adequate, sustainable food supply for our growing population. The quality of our lives and the future of our planet are at stake.

Links

• Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, & Bonas U (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science (New York, N.Y.), 326 (5959), 1509-12 PMID: 19933107
• Bogdanove AJ, & Voytas DF (2011). TAL effectors: customizable proteins for DNA targeting. Science (New York, N.Y.), 333(6051), 1843-6 PMID: 21960622
• Moscou MJ, & Bogdanove AJ (2009). A simple cipher governs DNA recognition by TAL effectors. Science (New York, N.Y.), 326 (5959) PMID: 19933106
• Li T, Liu B, Spalding MH, Weeks DP, & Yang B (2012). High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology, 30 (5), 390-2 PMID: 22565958
• Schornack, S & Boch, J (2010). Unraveling a 20-Year Enigma. MPMI Reporter.
• Tesson L, Usal C, Ménoret S, Leung E, Niles BJ, Remy S, Santiago Y, Vincent AI, Meng X, Zhang L, Gregory PD, Anegon I, & Cost GJ (2011). Knockout rats generated by embryo microinjection of TALENs. Nature biotechnology, 29 (8), 695-6 PMID: 21822240

Bios

Sophien is a senior scientist and Head of The Sainsbury Laboratory. He received his B.S. degree from Pierre and Marie Curie University, Paris, France, and his Ph.D. in Genetics from the University of California, Davis, USA. He held a faculty position at Ohio State University, USA, in the Department of Plant Pathology, Wooster campus, before joining The Sainsbury Laboratory in 2007. His recent research focuses on plant pathogenomics, filamentous pathogen effector biology and devising new approaches to breeding disease-resistant crops. Follow him on twitter @KamounLab
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Eric has worked in ag biotech (Ciba-Geigy, Novartis, Cropsolution) since his PhD at Washington University in St. Louis.  He is President of Two Blades Foundation and in that capacity is responsible for a research group at The Sainsbury Laboratory.  His group focuses on identifying novel resistances to major crop diseases.
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