“If you talked about genome editing 10 years ago, nobody knew what you meant,” says Prof. Jasper Rees. “If you talk about it today, people still don’t know what it means, but they know about it as a concept.” Rees is a Distinguished Professor in Agricultural Technologies at UNISA.
He was responsible for establishing advanced genomics facilities at the Agricultural Research Council (ARC) from 2010–14. From 2014–17, he was the ARC’s group executive for Research and Innovation Systems.
According to Rees, SA isn’t applying advanced genetics to plant breeding, due to our restrictive legislative environment.
But these technologies are gradually gaining traction internationally, and he believes it’s only a matter of time before genome editing becomes integral to new cultivar development. In the future, growers are increasingly likely to have the option of growing cultivars developed using new plant-breeding technologies. Knowing the basics will help them make informed choices.
Marker-assisted selection
Not all new plant-breeding technologies involve directly engineering a cultivar’s genome. Many just speed up cultivar development through more efficient and precise selection. “Conventional breeding programmes are extremely slow, especially for tree crops,” says Rees. “For many breeders, what you breed in mid-career, you’re only going to see in the supermarket by the time you retire.”
Traditionally, breeders performed controlled crosses and selected the best offspring for further crosses. This meant raising the offspring until their performance could be assessed. If breeders were interested in fruit quality, they might have to wait five to six years for a tree to grow from seed to maturity.
In addition, inferring a tree’s genetic makeup from its appearance and behaviour is an imperfect science. Marker-assisted selection has revolutionised plant breeding by allowing breeders to select based on genetic rather than visible characteristics. Molecular markers are sections of DNA associated with specific traits.
They’re not the actual genes affecting that trait – they’re more like signposts indicating the presence of desirable genes. Using marker-assisted selection requires identifying and developing markers for traits of interest. This involves a significant research effort, but the benefit is that breeders can precisely select plants to include in their programmes, and offspring without the desired genes can be culled early.
High-speed breeding
Imagine how much time breeders would save if they could assess fruit traits in the first year of a tree’s life. Turns out it’s possible. A group of researchers introduced a gene for early flowering from silver birch into apple trees. The genetically modified apple trees flowered within six months of being planted as seeds.
The early-flowering apples were crossed with fire blight-resistant wild apple species, and their offspring was backcrossed with apple scab and powdery mildew-resistant strains. Seedlings were screened for desirable traits using marker-assisted selection. In approximately two years, the researchers produced three seedlings resistant to apple scab and fire blight and three resistant to powdery mildew. You might wonder why they didn’t introduce the resistance genes through genetic engineering.
Why engineer early-flowering plants and then go to all the trouble of conventional crosses? The reason is that the researchers can remove the birch-tree early-flowering gene once they no longer need early-flowering apple trees for their selection programme. The resulting cultivars would not be considered genetically modified because their resistance genes were introduced through conventional breeding.
Editing existing genes
“Of all the so-called new plant-breeding technologies, genome editing is the one that really matters,” says Rees. “For example, in the future, we could see people taking existing cultivars and modifying them to make them have low chilling requirements, which would be a significant advantage in our warm winter environment.” Genetic manipulation is right up there with nuclear power and Donald Trump in the constellation of controversial topics. But the reality is that all domesticated plants are genetically manipulated.
The process might have involved hand pollination and taking advantage of natural mutations, but the plant genomes have nonetheless been deliberately changed through selective breeding. Modern genetic manipulation technologies fall into two categories: those that work with the organism’s existing genome and those that introduce foreign genes. Gene editing usually refers to the former and tends to be less contentious. Gene editing has surged due to CRISPR-Cas9, a precision tool for inserting, removing, and replacing genes.
Historically, the only way breeders could introduce a desirable gene into an existing cultivar was by controlled crosses. The problem was that the offspring inherited a grab bag of genes. Breeders would then have to conduct a series of time-consuming backcrosses to eliminate the unwanted genes while retaining the desirable ones.
Gene editing allows breeders to introduce desirable genes without adding undesirable ones. Breeders can also potentially tweak genes to obtain better traits. The first commercial gene-edited apple cultivars are already on supermarket shelves in North America.
Okanagan Speciality Fruits developed non-browning strains of Granny Smith, Golden Delicious, and Fuji. Unlike most apples, their fresh Arctic apples can be sold pre-sliced. Browning in cut or otherwise damaged apples is caused by polyphenol oxidase enzymes. Arctic apples don’t brown because their production of polyphenol oxidase enzymes have been turned off using RNA interference. This technology is being extensively explored in many fields, including treating viral infections and human cancer.
Transgenic organisms
Transgenic plants have been modified by introducing genes their species doesn’t naturally have. Research on crown galls launched the field of transgenic plants. Crown gall bacteria cause galls by transferring some of their own genes to host plants. Once researchers discovered this, they soon realised they could repurpose the crown gall bacteria’s ability to introduce foreign genes to plants.
One of the first examples of a transgenic crop was BT-cotton, which contains bacterial genes for producing proteins that kill specific insect pests. Herbicide-resistant field crops are other well-known examples of transgenic crops.
Despite its restrictive legislation on genetically modified crops, SA is among the top 10 countries in terms of adoption. It grows about 2.7 million hectares of genetically modified maize, soybeans, and cotton. This hectarage comprises around 20% of our cultivated land.
Other genetically modified crops, however, have not been introduced here, at least partly due to the cost of obtaining regulatory approval. Genetic modification can increase crop yields, reduce production costs, and reduce postharvest losses. It can also make crops more environmentally friendly.
For example, pest-resistant plants require fewer pesticide applications, and drought-tolerant plants consume less water. Given their benefits, Rees argues that the South African government should support adopting new plant-breeding technologies in our deciduous-fruit industry. Globally, the public already seems to be making the necessary mind shift.
“I think if we go a generation forward, we’ll find that many of these new technologies have been incorporated, and people have moved on and accepted them,” reflects Rees. “At least, I hope so.”
