Improving food security and genome editing

Professor Yu Hao (left) and research team member Dr Norman Teo Zhi Wei (right) holding the CRISPR-Cas9 modified bok choy.

The COVID-19 outbreak, as well as the resulting lockdowns to stop the coronavirus spread, has wrought disruptions to global food production capacities and supply chains. The effects are significant for a country like Singapore, which imports 90 percent of its food. 

While the island-state government’s foresight in stockpiling supplies, diversifying its food sources, and putting in place various contingency plans have proven effective in mitigating the impact, in the face of continued volatility, there is an urgent need to bolster local food production and strengthen Singapore’s own food security in the years to come. A promising way to contribute to this, according to Professor Yu Hao, Head of NUS Biological Sciences, is genome editing.

“Genome editing can contribute by increasing yield through generating new crop varieties that can grow faster and accumulate higher biomass under urban farming conditions. In addition, given that there is a lack of research in cultivating leafy vegetables, we can increase the fundamental knowledge of this field to enable relevant findings that could be commercialised in the near future,” he explained.

A marriage of food science and technology 

Since the beginning of agriculture, humans have been selecting crops with more desirable traits, mainly for higher yield, better nutritional values and improved resiliency. With scientific and technological advancements, farmers are currently using a combination of physical, chemical and biological methods to increase the production and generate better quality produce. 

“In using biological methods such as genome editing, we are mainly modifying certain genes that are known to influence particular characteristics such as biomass or disease resistance,” shared Prof Yu. “To date, there are many interesting modified crops developed by scientists around the world that have achieved proof of concept, such as decaffeinated coffee, fungi-resistant bananas and spicy tomatoes. This shows that application of genome editing offers a sustainable and limitless way to generate new elite crop varieties with enhanced or novel characteristics.” 

Bringing the example closer to home – in March 2019, the Singapore Food Agency announced its target of producing 30 per cent of Singapore’s nutritional needs domestically by 2030, among which 20 per cent consists of fruit and vegetables. This target has motivated the NUS team led by Prof Yu to look into establishing and optimising protocols for improving crops like rice, fruits and leafy vegetables. The research team’s long-term goal is to generate high-value vegetable and food varieties with higher biomass and better stress resistance. 

Prof Yu elaborated, “Singapore consumed more than 92,000 tonnes of leafy vegetables in 2018. Almost 87 per cent of that was imported. Such imports continue to be subject to severe fluctuations, as the ongoing coronavirus outbreak has shown us.” 

The science of genome editing

The research team currently leverages on CRISPR-Cas9 technology to genetically modify genes in different crops. CRISPR-Cas9 – short for Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9 – is a technology adapted from the natural function of a bacteria immune system. When the immune system is faced with an invading virus, bacteria captures snippets of DNA from the virus to create new DNA segments, known as CRISPR arrays. This allows bacteria to recognise the virus when it attacks again, and produce RNA segments for Cas9 enzymes to target the virus and disable it. 

Similarly, genome editing makes use of an RNA-directed DNA endonuclease to create small insertions or deletions (indels) in targeted DNA sequences. In other words, this allows genetic material to be added, removed, or altered at particular locations in the genome. The application of CRISPR/Cas9 facilitates the generation of heritable gene mutations for crop breeding. 

“Plants generated from CRISPR-Cas9 technology are indistinguishable at both phenotypic and genomic levels from those plants that acquired genetic mutations naturally through traditional selective breeding,” Prof Yu said. 

In addition, CRISPR-Cas9 technology has proven the ability to develop plants with the desired traits many years faster than traditional selective breeding. Among the modified food ready for market are white button mushrooms that are resistant to browning and low-gluten wheat.  

Towards a sustainable food system

The availability of a highly efficient genome editing system is a prerequisite of successful CRISPR/Cas9-mediated plant gene editing. Although Prof Yu and his team have gained insights about the genomes of leafy vegetables such as choy sum and bok choy over the years, they are on a quest to deepen their understanding of the functions of annotated genes in those vegetable varieties. 

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A regenerated CRISPR-edited choy sum plantlet growing under artificial lighting conditions.

“There is limited data in correlating between gene function and the corresponding plant characteristics. In most cases, more investigations which are specific to the species of leafy vegetables are needed. We will have to establish and optimise the method specifically to each species, and the process of which may take one to a few years depending on the species,” said Prof Yu. 

Despite the long wait to see the fruit of this technology, the team is confident that the application of genome editing will revolutionise agriculture to ensure food and nutritional security.

“Singapore is at the top of the global index ranking for food security in 2018 and actively plans to ensure Singaporeans continue to have access to safe and quality food at affordable prices in both the short and longer term,” reiterated Prof Yu. “Through a combination of food science and technology, the global shift to a more sustainable food system can ensure a better future for all of us.”