Applications of (CRISPR) genome editing in crops

In a previous blog post, we discussed some of the fascinating applications of genome editing. We covered basic research, bioproduction, and healthcare. In this post, we switch focus to some of genome editing’s applications in crops (the plants we grow for food). These include:

• Improving nutritional characteristics
• Improving disease resistance
• Accelerating domestication

Improving crop nutritional value with genome editing

Nearly 11% of people in the world are undernourished. This is due, in part, to nutrient deficiencies in the crops grown in different regions of the world. To better nourish the world, researchers can use genome editing to boost the production of nutrients in crops.

Researchers have done this in the past using “transgenic” technologies. These technologies insert genes encoding nutrient production into crops. In transgenics, these genes are from other species and aren’t found in the crops naturally. While transgenic crops do produce the desired nutrients, many people do not like that they have “foreign” genes. As a result, it can be difficult to achieve wide adoption of transgenic crops.

“Golden Rice” is a great example of a transgenic crop. Golden Rice produces large amounts of vitamin A. Its developers hoped it would be grown in regions of the world where people are vitamin A deficient.

To create the first generation of Golden Rice, researchers identified genes for vitamin A production from Daffodil and Erwinia uredovora (a bacteria). Then, they inserted these genes into rice. As a result, the rice produced large amounts of vitamin A and their grains turned a golden color.

Unfortunately Golden Rice and many crops like it have not been adopted yet. A few reasons for this include:

• People do not like transgenic crops. Some simply don’t like the idea of eating crops containing “foreign” genes. Others believe supporting transgenic crops overlooks deeper problems causing poverty and food insecurity.
  
• Suspicion of biotech. Many do not trust the companies that create transgenic crops.
  
• The engineered crops are not the same species/subspecies as those planted by the people in the regions where they’re needed. Thus, these engineered crops may not grow well in these regions. They also may not have flavor and cooking properties that local people like.

Genome edited crops have the potential to mitigate all of these issues.

First, genome edited crops need not be transgenic. Researchers can use genome editing to increase some crops’ natural nutrient production pathways. This is possible thanks to the precise nature of genome editing (and particularly CRISPR genome editing).

Second, genome edited crops may be produced by new companies. Many of the traditional transgenic producers will likely create genome edited crops as well. However, there’s potential for innovative new companies to gain ground. These companies may use CRISPR technologies to move the field forward. They may also be able to establish more trust with the people who will farm their genome edited crops.

You’ll learn more about the third issue in the section of this post titled “Accelerating crop domestication.” For now, suffice to say that genome editing can give crops characteristics that make them easier to farm.

Improving crop disease resistance using genome editing

Like us, crops are susceptible to infections and parasites. These can cause devastating crop diseases that ruin yields. Genome editing can protect crops from these diseases.

For example, insects often eat crops and lower yields. Researchers have been making transgenic crops that are resistant to insect for many years. To do so, they generally give the crops a bacterial gene encoding production of a pesticide protein. Insects who eat these crops are killed by the pesticide. Such transgenic crops are widely grown in the US already. Genome editing may make it easier to create similar transgenic crops.

Fungi can also devastate crops. Indeed, one of the worst crop diseases plaguing the agricultural world is Fusarium of banana. It is caused by a fungus known as TR4. This fungus infects bananas and, because most bananas grown at industrial scales are sterile, it’s difficult to breed TR4 resistance into them. This is potentially devastating because TR4 has already spread to many banana-producing regions.

Thankfully, researchers are already looking for ways to use genome editing to protect the banana from TR4. Some of the things they hope to do include:

• Deleting genes that cause bananas to be susceptible to TR4
• Increasing expression of genes that protect bananas from TR4

Researchers hope to use similar tactics to protect crops from all kinds of pathogens. As with genome editing for increased nutrient production, the disease-protected crops don’t need to be transgenic.

Finally, some genome editing researchers are looking to design CRISPR systems to attack viral genomes. In this case, the researchers are using the CRISPR systems themselves to protect crops from viral infection. We’re sure to see many more creative uses of CRISPR and genome editing to protect crops in the future.

Using genome editing to accelerate crop domestication

Ideal crops have many characteristics that make them easy to farm. For example, farmers might want short plants that produce a lot of fruit. Shorter plants are less likely to break in a storm and boosting fruit production leads to higher yields of the edible portion of the plant.

Crop “domestication” is the process of making plants easier to farm. To create short crops with high fruit production, you might think that researchers could simply put a “short” gene and a “lots of fruit” gene into a crop. Unfortunately, many important plant traits are encoded in genetically complex ways. That is, many different genes affect these traits. Thus, one might have to alter many genes to create a short crop that produces a lot of fruit.

CRISPR genome editing makes it possible to alter many different genes at once. Researchers can therefore use CRISPR genome editing to alter many “domestication” genes at the same time. As a result, they can create crops with desirable farming characteristics more quickly than they could in the past.

Indeed, in one recent example, researchers used CRISPR genome editing to dramatically alter wild tomato and cherry species. Their goal was to make these crops more amenable to urban farming in cramped spaces. With their knowledge of tomato genetics and CRISPR’s effectiveness, they were able to make the plants shorter and they increased fruit production. The researchers hope that these and similarly compact crops will be useful for urban farming.

Many more applications of (CRISPR) genome editing in agriculture

This is just a small sampling of the many ways researchers and farmers can use genome editing to improve their crops. Beyond crops, researchers would like to use similar techniques to create livestock breeds with beneficial characteristics. While promising, genome editing in livestock may face more stringent regulatory hurdles.

Interestingly, CRISPR diagnostics can also accelerate the crop breeding process. To learn how, see our blog post called “CRISPR diagnostics in agriculture.” Combining CRISPR genome editing and diagnostics may give crop development even more of a boost!