Oct. 30, 2019
Breeding: to improve the response to the changing climate
Climate change is outpacing evolution, and our crops desperately need to keep up. Some plants are able to cope with the increasingly extreme weather conditions, and research is being done to facilitate gene transfer from more resilient plants to important but vulnerable crop species. For example, researchers at the Plant Sciences Department in Cambridge, are working on engineering rice to use the more efficient form of photosynthesis found in cacti. However, this modern method of crop improvement does not fit within EU regulations for GM foods.
A more widely accepted form of crop improvement is selective breeding, which humans have been performing for thousands of years. The main problem with this method is that it can take decades, by which point the stresses of the environment will have changed again, and so the crop will be lagging behind. A new method is needed that is relatively fast while also complying with GMO regulations.
One solution lies in transposons, the “jumping genes” first discovered by Barbara McClintock in the 1950s, dismissed as junk DNA until recent decades. Transposons, or transposable elements, are short stretches of DNA that have the ability to copy and paste themselves throughout the genome they inhabit; this is possible because these either include the transposase gene, which carries out the copy-and-paste process of the whole element, or are integrated via an RNA intermediate by reverse transcription.
Insertion of a transposon into the genome can have various effects: it can change the expression level of a gene, it can introduce new or remove functions, or it can have no effect at all. It is for this reason that transposons are credited as the largest generator of genetic diversity in plants, and therefore why they provide a novel answer to the problem of crop improvement. They are used to grow a large number of plants containing transposons, under the conditions required to activate their copy-and-paste mechanism. From this wide variety of different phenotypes produced, the best-performing ones are selected to continue breeding.
This year, researchers at the Sainsbury Laboratory here in Cambridge have discovered that the Rider transposon, previously known to be responsible for altering the colour and shape of tomato fruits, is activated by drought stress. By quantifying the number of Rider copies, they found that the genome of drought-stressed plants contained 4.4 times more copies than plants under normal conditions.
To further substantiate their claims, they also quantified the number of copies of Rider in mutant tomato plants for the production of the main chemical signal for drought stress in plants, ABA. These ABA mutants have reduced copies of Rider compared to wild-type plants in stressed conditions, showing that if no drought is detected, then Rider is less active.
The newly discovered feature of Rider, to be activated by water deprivation, is important for two reasons: firstly, it allows one to grow the tomato plants under “positive selection”, ie putting them under drought stress to activate the transposon and then selecting the plants that grow the best under those stressful conditions. Secondly, Rider could be used to generate new pathways of gene control in tomato plants that allow them to better cope with low water levels. This is possible if Rider inserts into the region of DNA that controls the expression of a relevant set of genes; the transposon’s own control regions are then co-opted to regulate the genes in question in response to the environment.
The main problem from this point onwards is the stability of the transposon - once it has inserted into the desirable area, its copy-and-paste function must be inactivated so that it remains stable, and does not insert into an unwanted region of the genome. This inactivation can occur naturally. However, this is rare and thus it is likely that the transposase gene will be edited by researchers to become non-functional, allowing Rider to remain where it is.
The use of transposons provides multiple benefits over previous methods of crop improvement. The most important one is that they can be used to produce improved crop varieties at a much faster rate, for two reasons: they increase the rate of diversification and so significantly reduce breeding time, and they can be used even when the gene control pathway is poorly understood. This solves a major problem associated with both selective breeding and gene editing, namely, that the former takes several generations to gain the desired result, and the latter requires an exhaustive understanding of the genes in question, which can take too long to unravel. From a policy perspective, the use of transposons is in line with the EU’s regulation on GMOs, since it requires no insertion of genes that are not already in the plant - it simply involves activating a jumping gene that naturally resides in its genome.
The use of the Rider transposon to improve crops comes in a long line of many modern techniques used in biochemistry and crop improvement that have originally come from nature. From the Thermus aquaticus (Taq) polymerase used in PCR reactions, to the more recent CRISPR/Cas9 system for gene editing, it is obvious that the best solutions to the problems researchers have can often be found in nature. This example is no different, although it is being used to solve the different and more pressing problem of crop adaptation to the rapidly changing environment. Although the Rider transposon has been primarily studied in tomato plants, it is also present in many economically important crops such as rapeseed and beetroot. It is possible that other transposons are also activated by environmental stresses, even if not by drought stress. If this is the case, then they can be used in other plants to improve their response to the changing climate in the same way that Rider can with tomatoes.