Application of Genome Editing Technology: CRISPR-Cas9 in Agriculture

Updated: Aug 20, 2021

The advancement of molecular biology and gene editing technologies alter the DNA sequences and modify gene function inside living organisms. One of the most successful genome-editing technologies known as CRISPR-Cas9. Recently, CRISPR-Cas9 technology, which was developed in 2012 by scientists from the University of California, Berkeley has received a lot of attention because of its wide range of applications, including biological research, biotechnological products, biomedicine, development of agricultural crops, and healthcare.

The acronym CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, is a part of the bacterial defense, made up of short palindromic repeating DNA sequence with ‘’spacers’’ sitting in between foreign DNA sequences from organisms that have previously attacked the bacteria. The CRISPR also includes CRISPR-associated genes or Cas9 genes which encode proteins that unwind DNA (helicase) and acts as ‘’molecular scissors’’ that can cut into DNA at the target (nucleases). This is by far the most common use of CRISPR and it’s called genome editing.

Using CRISPR is easy to disrupt a targeted gene or insert a new sequence at the precisely desired spot and this technology reduces the time and expense.

As CRISPR-Cas9, a precise gene-editing tool can be used to modify organisms to achieve the desired traits. This game-changing technology and groundbreaking innovation have been expanded rapidly in a diverse field with agriculture to increase crop yield, improve quality, develop the disease and pest-resistant varieties, and accelerate crop domestication.

In comparison to traditional methods of breeding for crop production, CRISPR-Cas9 is more cost-effective, precise, highly efficient, and less time-consuming.

The power of the gene-editing tool like CRISPR-Cas9 opens the door for the improvement of food production to ensure global food security. This versatile technology is capable of gene regulation with protein engineering and has widespread applications in agriculture and crop improvement.

Improving crop yield and quality

The crop yields are significantly reduced and susceptible due to adverse climate changes. That’s why scientists have been trying for a long time to establish resistant plants against the unpredictable environments that can yield more. For doing this using CRISPR-Cas9 is one of the widely used technologies. To get the desired traits, scientists are trying to use these techniques. For example, in Cold Spring Harbor Laboratory, the researchers engineered tomato plant and make small changes in the promoter regions in genes that control different quantitative traits such as LOCULE NUMBER (control fruit shape and size), COMPOUND INFLORESCENCE (control flower proliferation), SELF PRUNING (control flowering time and hence growth habit) in the tomato. In this way, researchers have successfully used this technology to introduce novel variation in plants to improve crop yield.

Another experiment by Xu in 2016, showed that the seed size of rice increased significantly up to 30% by mutating three genes that negatively regulate the seed size (GN2; GW5, TGW6). According to Wang, the higher seed number with increased grain weight can be obtained in Brassica napus by CRISPR-Cas9 mediated mutation of CLVTA3 genes.

There are many other studies conducted to use this technology indicate that CRISPR-Cas9 has a high demand for the crop improvement of various traits of the crop.

Other than yield, CRISPR-Cas9 can be used to improve the quality of crops. Gluten protein in wheat grains can cause coeliac disease and these proteins are encoded by around 100 loci in the wheat genome. The low gluten wheat lines can be obtained by using CRISPR-Cas9 to target the specific region of gluten genes, while it traditionally is not possible to decrease gluten control in wheat.

In addition, the improvement of carotenoids in plants was gained by the application of CRISPR-Cas9 with a 59% success rate in Bananas.

Gao and co-workers applied CRISPR-mediate multiple mutations in cotton to several target functions which indicate a great advancement of CRISPR-Cas technology to improve crop quality.

One Biotech company named Yield 10 Bioscience in 2017, produced CRISPR-edited plant Camelina sativa, which has increased omega-3 oil in plants.

There are many companies like DuPont collaborating with Doudna’s, Caribou, Biosciences to grow corn and wheat strains edited for drought resistance by CRISPR-Cas9 technology.

Developing resistant varieties for emerging disease and pests

Crop diseases are one of the major problems to reduce crop yield remarkably which increases global food insecurity. Insect pests also cause severe damage to the yield. CRISPR-Cas9-mediated genome editing technology has created a new scope to develop disease-resistant crop varieties.

One of the most common diseases of the blast in rice which is caused by a fungus named Magnaporthe oryzae can cause tremendous yield losses worldwide and also spread to other cereal crops such as wheat, oat, barley. Wang and colleagues have established a mutagenized rice line to enhance blast resistance by using CRISPR-Cas9 technology. They targeted the rice OsERF922 gene and these edited lines significantly increased gene and these edited lines significantly increased blast resistance.

Furthermore, the wheat blast is a very dangerous fungal disease that causes a serious threat to wheat production. In Bangladesh, 2016, a wheat blast outbreak occurred in wider areas and destroyed more than 15, 000 hectares of wheat with 100% yield loss. The International Maize and Wheat Improvement Centre (CIMMYT) has reported that due to this devastating wheat blast posed 300 million undernourished people in South Asia. It may be possible, by mutating S-gene associated with blast disease susceptibility which increases the blast-resistance in wheat. We envisage that CRISPR-Cas9 edited this S-gene mutant for developing blast-resistant wheat varieties.

Moreover, researchers from China have developed citrus plants that are resistant to citrus canker, a serious disease caused by Xanthomonas citri by CRISPR-Cas9 technology.

The Innovative Genomics Institute (IGI) at the University of California, Berkeley, created disease-resistant cacao by applying CRISPR techniques to make it resistant to pathogens because growing cacao is very difficult in hotter and drier regions which make it more vulnerable to pathogens.


Many have arguments about this tool, the ‘’precision’’ and the expected outcome.

It may create some unexpected effects when new genes are added or there is no guarantee to get the desired outcome. In local environments with different climatic conditions, the CRISPR-Cas9 can not provide a complete solution for agriculture-related problems.


All of these examples are the indications of new crops that reach the market faster than previously thought.

CRISPR-Cas9 has emerged as a game-changing tool for plant research. This tool helps to develop many crop varieties to desired traits with improved agronomic performance and revolutionize breeding technologies. CRISPR-Cas9 technology was adapted to perform high-throughput and precise genome editing which can easily be used in a versatile field in agriculture and plant synthetic biology.

However, these tools have not yet fulfilled all the needs for plant genome manipulations, and the further development of the application of the CRISPR-Cas9 in plants is necessary to advance the genetic research in plants related to desirable agronomic traits.


Author: Sanzida Akhter Anee (Horticulturist and Ecologist-Co-founder of AgriBioTechX)

Source: Pinterest | Nature | Google

*Note that any firm mentioned above does not sponsor this blog.

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