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The CRISPR/Cas genome editing system and its application in potatoes

This article was prepared and written by Jorge Luis Alonso G.

Researchers from the College of Plant Protection at Shandong Agricultural University in Tai’an, China recently published a paper in Frontiers in Genetics. In the paper, the research team discusses the principles and applications of the CRISPR/Cas system in potatoes. It also highlights potential future uses of this technology to improve potato traits. The article below provides a brief overview of the scientific paper.

Introduction

CRISPR/Cas is a component of the CRISPR adaptive immune system and has emerged as a central genome-editing tool. In contrast to older technologies such as TALEN and ZFN, which are technically complex and less economical, CRISPR/Cas offers distinct advantages such as simplicity, adaptability, efficiency and affordability. As a result, CRISPR/Cas has solidified its position as the leading genetic tool for improving crop traits. To date, this technology has been successfully implemented in a variety of plants, most notably Arabidopsis thaliana and Oryza sativa.

Potatoes rank third in global food consumption, surpassed only by rice and wheat. Their genetic makeup, which is tetraploid and highly heterozygous, combined with their vegetative propagation, makes the traditional breeding of innovative potato varieties an extended endeavor.

However, the introduction of the CRISPR/Cas system into potato breeding offers a glimmer of hope. It has the potential not only to speed up the breeding process, but also to increase yield, improve quality, and enhance stress resistance. This discourse explores the profound implications of using CRISPR/Cas in potato breeding and projects its future contributions to the refinement of potato traits.

CRISPR-Cas structures and mechanisms

The CRISPR/Cas9 system is like genetic scissors. It uses a special RNA called guide RNA (gRNA) to find the right spot on the DNA. The Cas9 enzyme then acts as a pair of scissors, cutting the DNA at that site. After the cut, the cell tries to repair the break in one of two ways. One way, called NHEJ, sometimes adds or removes bits at random. The other way, called HR, is more precise but doesn’t work as often. An interesting part of this system is that it looks for a specific DNA pattern (5′-NGG-3′) to know where to cut. This feature is especially useful for modifying plant genes.

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CRISPR/Cas12a is considered an improved version of the earlier Cas9. It fixes some problems with Cas9, such as sometimes targeting the wrong places in DNA or being too specific about where it can work. Cas12a makes the process of editing genes smoother. It can prepare itself for editing and also make specific cuts in the DNA. What’s great is that Cas12a is more precise and less likely to make mistakes when targeting DNA.

The CRISPR/Cas13 system is specifically designed to work with RNA. It has two main parts called HEPN RNase domains. Upon closer inspection, there are four versions of the Cas13 protein: Cas13a, Cas13b, Cas13c and Cas13d. Of these, Cas13a turns on when it finds a matching piece of RNA, and then it can grab and cut RNA sequences.

Base editors are tools that can change certain parts of DNA without breaking it. The first version of these tools could change a piece of DNA called cytosine to another called uracil. But that didn’t work very well in human cells. So scientists made better versions. One of them, the third version, is now popular for modifying plants. There’s also another type of editor that works on a different part of DNA called adenine. It changes the DNA in a way that can lead to new pairings.

CRISPR/Cas applications in potato research

The CRISPR/Cas system offers advanced genome editing technology capable of modifying genes related to stress resistance and nutritional quality in tuber crops, specifically in potatoes. This is pivotal as potatoes are vital both as a food source and for the food processing industry. Through CRISPR/Cas, significant strides have been made in potato breeding:

Overcoming potato self-incompatibility

Researchers have turned to various biotechnology strategies to improve potato yields. At the forefront of these innovations is the CRISPR/Cas system. Some of the notable achievements using this technology include the optimization of photosynthate transport. This optimization ensures that the plant uses its energy efficiently. There’s also been success in increasing the levels of beneficial compounds in the tubers. One exciting development involves genetic modification to promote stolon branching. This particular modification is promising as it has the potential to directly increase yield.

Improving resistance to biotic and abiotic stresses in potatoes

Potatoes are susceptible to a number of challenges that can affect their growth and quality. First and foremost, they face abiotic stresses, including drought and salinity, which can drastically affect their cultivation. In addition, biotic stresses caused by diseases and pests can also result in significant economic losses for farmers.

However, there is a ray of hope in modern agricultural science. With the advent of the CRISPR/Cas system, remarkable breakthroughs have been achieved. In particular, this technology has been instrumental in strengthening the potato’s resistance to pervasive threats such as late blight. It’s also had the added benefit of improving their ability to withstand drought. An extension of this technology, the CRISPR/Cas13a system, shows great promise. Preliminary research suggests its potential to protect potatoes from the damaging effects of potato virus Y.

Improve potato tuber quality

The CRISPR/Cas system has been effectively used to improve the properties of potato tubers. One of the major achievements is the production of pure amylopectin starch. Another important advance is the minimization of anti-nutrients and toxins. Specifically, this includes the regulation of steroidal glycoalkaloids (SGAs). These compounds not only affect the taste of potatoes but can also be harmful when present in high concentrations. In addition, a pressing issue in potato quality, enzymatic browning, which affects organoleptic properties, can be addressed through this innovative technology. By improving nutritional quality, potatoes have the potential to become an even more important staple in the global diet.

Improve potato yield

To improve the productivity of this important crop, researchers have turned to various biotechnological strategies. Among these, the CRISPR/Cas system stands out for its potential for genetic modification. These advances have led to a number of successes. For example, scientists have optimized the transport of photosynthates, ensuring that the plant’s energy is efficiently directed to tuber growth.

There has also been a significant increase in the levels of beneficial compounds in the tubers. A particularly promising development is the modification of specific genes to promote stolon branching. This modification is significant because it paves the way for potentially higher yields in potato production.

Future prospects

Food crops have become increasingly important around the world, especially as the world’s population grows. Among these, the potato stands out. Not only is it a staple food, but it also offers advantages in terms of yield, cost and cultivation.

However, like any other crop, potato production faces its own set of challenges. A major concern is the difficulty in maintaining the best characteristics of potato clones. This challenge is due to the complex nature of the potato genome.

Recently, technological advances have provided potential solutions. The CRISPR/Cas system, a breakthrough genome editing tool, promises to revolutionize crop breeding. For the potato, this technology has been a game changer. It has been used to improve multiple aspects, from yield to quality and even stress resistance.

And now that the entire genome sequence of the potato is available, scientists can make informed decisions when designing specific improvements.

But with any solution comes challenges. One of the drawbacks of the CRISPR/Cas9 system is its potential imprecision, which can lead to unintended genetic changes. To address this, base editing technology has been introduced to provide a more targeted approach to improving potato traits.

Acceptance of gene editing varies around the world. Some countries are open to its potential, while others remain cautious. However, as the technology continues to advance, it’s expected that more countries will embrace the benefits of gene editing.

It’s clear that the CRISPR/Cas system has already had a significant impact on potato breeding. With advances in high-throughput sequencing and gene editing technologies, the future of potato genetic improvement looks promising.

Source: Hou, X., Guo, X., Zhang, Y., & Zhang, Q. (2023). CRISPR/Cas genome editing system and its application in potato. Frontiers in Genetics, 14, 1017388. https://doi.org/10.3389/fgene.2023.1017388
Cover image created by Jorge Luis Alonso G.

Editor & Publisher: Lukie Pieterse


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