Cultivated plants are the core of human nutrition. To ensure our food supply, plant breeders are in an ongoing race with newly emerging pests and diseases. Deterioration of growing conditions due to climate change and ever-increasing demand provide further challenges. Traditionally, plant breeders wait an unpredictable amount of time for a useful change to occur through random alterations that happen spontaneously to the plants’ genes. Such a change, known as mutation, might make the plant resistant against a new harmful fungus or help it use water more efficiently. To speed up this process, seeds can be exposed to radiation and chemicals. These treatments drastically increase the changes in genes, but in an untargeted manner. If breeders find a beneficial mutation, the plants also have a bunch of detrimental changes. To separate the beneficial mutation from the unwanted, it can take many generations of breeding with the original, unaltered plant and ages of time. Therefore, if mutations could be deliberately controlled, the pace of breeding improved plant varieties could be accelerated considerably. 

Shortly after the turn of the millennium, geneticists finally succeeded in developing good tools. Genes could be changed in a targeted manner, quickly and without creating a lot of unwanted mutations. This was possible by creating a gene scissor that among all the thousands of genes only cuts a single one at a pre-defined site. When plants’ cellular machinery repair these cuts, they on rare occasions make errors, thus creating the desired change. The first versions of these tools – including so-called TALENs – were labour-intensive to create, especially when setting them upon a new target gene. But then, CRISPR/Cas entered the stage. Because reprogramming CRISPR/Cas to new targets was extremely easy, it took over the scene and displaced the predecessor versions of gene-changing tools. However, despite its popularity, CRISPR/Cas has a tiny flaw. While it can easily reach the bulk of the genes that reside in the cell’s command centre, the nucleus, CRISPR/Cas cannot enter the plant’s powerhouses, the mitochondria. And mitochondria contain their own set of genes. These genes are few in numbers, but indispensable, as they are required to drive the processes in mitochondria. 

TALENs, our gene scissors, on the other hand can enter mitochondria. And this is why we decided to work with them. We wanted to see whether we might change mitochondrial genes after all. As we were set only upon a proof of principle and not yet upon agricultural application, we choose a plant that is easy to work with in the laboratory, the common tobacco. We selected a target gene that is not strictly necessary for plant survival. Thus we introduced our TALENs into tobacco plants and checked what would happen. Indeed, the TALENs cut our target gene. The more tricky part was to get these cuts to be converted into permanent changes in the target gene. Gene repair in mitochondria is extremely efficient, usually preventing any changes during the repair process. We thought to devise a trick using chemicals that can introduce damage in mitochondrial genes in a random way. Eureka! The combination of TALENs and chemical proved to be effective. How so? Put simply, if the chemical by pure chance creates a DNA change at the target site of the TALENs in the gene, the TALENs do not recognize this as a target any longer. The chemically changed version of the gene is not scissored anymore, but the unchanged version still is. This gives the changed version the crucial edge to take over, because it is not destroyed repeatedly. 

So, using a method that had been trashed, we paved the way for the targeted modification of genes in plant mitochondria. This should be a big asset for plant breeders, since altered mitochondrial genes are key to efficient hybrid breeding, a well-known way to boost yield. Having higher crop yields will be vital to meet the global food demand that is expected to double by 2050. Plant breeding by design can help produce crops meeting the challenges of feeding the world.