Researchers have developed a method to boost protein content in crops using CRISPR-Cas9 gene editing, with applications ranging from staples like rice and soybeans to vegetables and fruits.
This innovation, which targets the NF-YC4 promoter, appears to improve disease resistance, boost protein content, and trigger early maturation in several crop varieties.
Fi Global Insights spoke with Dr Ling Li, associate professor at Mississippi State University and one of the authors of a paper published in New Phytology last month on a breakthrough finding on increased protein content in rice and soybean plants. Li and her team developed a technique that targets a key genetic pathway in crops, using the gene-editing technology CRISPR-Cas9 to modify the NF-YC-4 promoter.
“Our research is the first to discover that NF-YC is involved in regulation of primary metabolism and the regulation of carbon and nitrogen allocation,” explained Li. “When we deleted a motif sequence in the NF-YC-4 promoter, removing the brakes on NF-YC-4 expression, more carbon and more nitrogen is allocated to protein, and less to starch.”
The result is a protein content 10 to 20% higher than the original crops, without the introduction of any foreign DNA – as is the common method in previous generations of ‘transgenic’ genetic modification, where external genes are added to a plant genome.
Once cross-bred with other varieties, modified soybean crops could be commercially available within two to three years, with rice potentially hitting the market even sooner due to its shorter life cycle.
San Francisco-based biotechnology start-up Amfora – funded in part by German multinational pharmaceutical and biotechnology company Bayer’s so-called strategic impact investment unit, Leaps – has acquired several patents based on the NF-YC-4 editing. The company, established in 2022, is already partnering with an artificial intelligence (AI) company to scale up a high-protein soybean breeding program.
And while the immediate focus has been on staple crops like rice and soybean, Li’s research is also expanding into new territory – high-protein vegetables and fruits, including sweet potatoes, lettuce, and even strawberries.
The research originally focused on the Arabidopsis plant (or rockcress, a genus in the Brassicaceae family), where she discovered the role of the “orphan gene” ATQQS in increasing protein and reducing starch. The orphan gene is not found in crops like rice and soybean, but it could be introduced into those plants with the same effect. However, this is an expensive and highly regulated path. “A transgenic approach takes about seven to eight years and $1.1 billion to go through the safety evaluation process,” said Li.
The AtQQS research led to the identification of NF-YC-4, an interactor present in many plants including rice and soybean, but even organisms like yeast and algae. NF-YC-4 functions as a partner that can mimic AtQQS’s protein-boosting effects. Using the DNA editing technique, CRISPR-Cas9, to overexpress NF-YC-4 in soybean and rice significantly increased protein content and decreased starch without negatively impacting yield – a common problem in traditional breeding methods aimed at enhancing protein. Since researchers first discovered the effect, they have tested at least five generations of crops with boosted AtQQS and more than three generations of NY-FC-4.
In addition to raising protein levels, the CRISPR-edited plants have demonstrated improved disease resistance. Li and her team found that overexpressing NF-YC-4 boosts resistance to a variety of pathogens, including bacterial, viral, and fungal infections. This could reduce reliance on pesticides. According to Li, CRISPR technology is enabling more precise and faster research, making it possible to produce stress-resistant, high-protein crops in a matter of years rather than decades.
Li has also identified two isoforms of NF-YC-4 in soybeans—GM-NF-YC-4-1 and GM-NF-YC-4-2. The latter not only increases protein content, but also causes crops to mature faster. According to Li, “GM-NF-YC-4-2 matures at least three weeks earlier than other crops, allowing farmers to harvest before frost hits.”
Crossbreeding with currently available crops that have other beneficial properties could result in crops that are even more resilient. “Some commercial lines [have] desirable traits like drought resistance or high temperature resistance, but their protein content is not so high. With our approach, they could retain those traits, but also have a higher protein content,” said Li.
Because NFYC-4 is found in so many other plants, the method is not limited to staple grains. Li's team is now extending the use of CRISPR-Cas9 to enhance the protein content and improve the pest resistance of various vegetables and fruits. The team has seen success with crops like tobacco and yeast, and is broadening the scope to sweet potatoes, lettuce, and strawberries.
“With past experiments with tobacco plants, we saw that flowering tobacco buds attract no flies at all, unlike the regular variety,” said Li. “I would like to have a vegetable or fruit free from pests and bugs, where you would have to use less pesticide.”
And while vegetables and fruits are generally not seen as major protein sources, this could soon change, potentially reducing the need for reliance on meat-based protein sources.
Regulatory barriers differ across jurisdictions. In the US, the Department of Agriculture (USDA) has classified most CRISPR gene-edited plants as requiring less regulatory oversight than genetically modified organisms (GMOs). In effect, CRISPR-edited products have been treated like traditionally bred varieties under US regulations.
The EU has taken a very different approach to GMOs and new genomic techniques (NGT). The 2001 European GMO directive is a lot stricter than American legislation, including clear labelling requirements of any product defined as GMO. Unlike the US, the EU has until recently also taken a stronger stance on CRISPR-edited plants, covering them under the directive just like other GMOs.
However, in recent years there have been intense debates about the need to overhaul the blanket policy. In July 2023, the European Commission tabled a proposal that would update existing regulations in response to scientific developments and create two categories of NGT that would have less stringent labelling and other requirements.
Proponents of more flexible regulation on NGTs claim that the technology has a much lower risk profile and significantly different characteristics; many industry groups claim that the current legislation is therefore outdated and stifling important innovations. Opponents of the new approach, including organic food organisations, have raised concerns about organic food systems losing protection if the proposal were adopted.
While the legislation is not yet finalised, in 2024 a majority of MEPs on the EU Committee on Environment, Public Health and Food Safety voted in favour of the Commission’s proposal. An amendment banning the use of patents on NGT plants was also adopted by the Committee.
