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How the CRISPR Tomato and Genome Editing is Shaping the Future of Agriculture

Updated: Jan 7, 2023

How the CRISPR Tomato and Genome Editing is Shaping the Future of Agriculture

One of the many applications of CRISPR-based genome editing is in agriculture, as it provides various benefits over conventional crop breeding strategies.

Traditionally, crop developers have grappled with costly, laborious, time-consuming, and complicated selective breeding workflows to identify advantageous traits, such as vitamin fortification, increased crop yields, and drought or disease resistance.

However, the agriculture sector has been tasked with nourishing the ever-expanding global population, currently projected to reach 9.8 billion in 2050, and addressing climate change. Speedy, streamlined, and low-cost solutions for increasing productivity, nutrition, and sustainability in food cultivation and commercialization are needed to ensure future food security.1

CRISPR-Cas systems offer a lower cost, more precise, and scalable path to crop improvement and have improved several crop characteristics, including yield, quality, and disease or herbicide resistance.2 CRISPR-edited produce can also quickly be brought to the plates of consumers worldwide as they are considered non-GMO by many scientists and regulatory bodies; through CRISPR, editing is possible without the introduction of any foreign genetic material.

Below, we discuss:

  • The First CRISPR-Edited Tomato to Hit Markets

  • What Other Foods is CRISPR Being Used on?

  • Optimizing Genome Editing Outcomes for Faster Crop Improvement

  • References

The First CRISPR-Edited Agricultural Product Hits Markets: Sicilian Rouge Tomatoes

A little over one year ago, in September 2021, the world’s first CRISPR-edited produce, Sanatech Seed’s Sicilian Rouge High GABA tomato, hit the markets.3 The genome-edited fruit contains five times more gamma-aminobutyric acid (GABA) than an average wild-type tomato.4

GABA is a popular, health-promoting compound added to many foods and beverages in Japan, where these tomatoes are primarily sold. Thus, the commercialization of the Sicilian Rouge marks a significant milestone, not only for being the first CRISPR-edited fruit on the market but also for meeting a precise consumer nutritional demand through genome editing.

What was the genetic improvement made to tomatoes using CRISPR?

Several research groups have focused on raising the concentration of endogenous GABA by engineering an increased flux through the GABA shunt, which bypasses the tricarboxylic acid (TCA) cycle and decarboxylates glutamate to make GABA.5,6 This reaction is catalyzed by an enzyme, glutamate decarboxylase (GAD), and three genes (SlGAD1–3) encode GAD enzymes, expressed by the tomato plant throughout development.5

GAD enzymes are autoinhibitory: A C-terminal calmodulin-binding domain (CaMBD) binds in its active site, blocking catalytic activity.5 Removal of the coding region for the CaMBD domain using CRISPR-Cas-based gene editing makes a constitutive GAD enzyme with increased enzymatic activity and higher concentrations of GABA in the leaves and fruit of engineered tomato plants.5

Santech Seed used this approach to create the Sicilian Rouge High GABA tomatoes.4 Other mutations in enzymes involved in the GABA shunt have also increased the GABA concentration in tomato plants and could be used to engineer next-generation, engineered tomato plants.6

Beyond Tomatoes: What Other Foods is CRISPR Being Used on?

With the plethora of different editing strategies, including base and prime editing, applying CRISPR-Cas systems to the vast array of commercially-important crops could be beneficial for the future of food production.

Increasing Yield

Studies focused on increasing yield have looked at rice (Oryza sativa), wheat (Triticum aestivum), and tomato (Solanum lycopersicum) plants.7

For instance, knocking out cytokinin oxidase/dehydrogenase in wheat creates a plant that generates higher yields. Edits in genes CLV and ENO in tomatoes are also associated with greater yields.8,9

Disease Resistance

CRISPR-Cas systems can also be used to engineer crops that are resistant to common bacteria or viruses, either through targeting the microbe directly or inactivating host susceptibility genes.7

Proof-of-concept experiments have been done in Nicotiana benthamiana and Arabidopsis, where Cas9 was used to inhibit the accumulation of geminivirus.11

Engineered rice lines that have broad-spectrum resistance to bacterial blight (caused by Xanthomonas oryzae, a global threat to rice production) have also been developed by introducing CRISPR-induced mutations in SWEET genes.12 These genes are induced during infection, promoting bacterial colonization.

Optimizing Genome Editing Outcomes for Faster Crop Improvement

Currently, all of us – scientists, researchers, entrepreneurs, and students – are exploring the seemingly limitless applications of CRISPR-Cas systems to improve lives, from the foods that we eat to the diseases that we treat.

As this expansion continues to boom, it’s important to keep optimization and quality control top-of-mind.

Our mission at CRISPR QC is to be the gold standard for planning and conducting genome editing in agriculture and medicine. We’re working to equip scientists with the data and insights they need to more effectively engineer the next wave of gene-edited crops and therapeutics.

Contact us to learn more about our CRISPR-focused analytics platform and to see it in action.


World population projected to reach 9.8 billion in 2050, and 11.2 billion in 2100. UN website: Accessed October 7, 2022.

Zhu H, Li C, Gao C. Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol. 2020;21(11):661-677. doi:10.1038/s41580-020-00288-9

First CRISPR food hits market: Sicilian Rouge tomato with blood pressure-lowering GABA available in Japan. Genetic Literacy Project website: Accessed October 7, 2022. Published January 11, 2022.

Waltz E. GABA-enriched tomato is first CRISPR-edited food to enter market. Nat Biotechnol. 2022;40(1):9-11. doi:10.1038/d41587-021-00026-2

Nonaka S, Arai C, Takayama M, Matsukura C, Ezura H. Efficient increase of ɣ-aminobutyric acid (GABA) content in tomato fruits by targeted mutagenesis. Sci Rep. 2017;7(1):7057. doi:10.1038/s41598-017-06400-y

Li R, Li R, Li X, et al. Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanum lycopersicum. Plant Biotechnol J. 2018;16(2):415-427. doi:10.1111/pbi.12781

Zhu H, Li C, Gao C. Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol. 2020;21(11):661-677. doi:10.1038/s41580-020-00288-9

Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. Cell. 2017;171(2):470-480.e8. doi:10.1016/j.cell.2017.08.030

Yuste-Lisbona FJ, Fernández-Lozano A, Pineda B, et al. ENO regulates tomato fruit size through the floral meristem development network. Proc Natl Acad Sci U S A. 2020;117(14):8187-8195. doi:10.1073/pnas.1913688117

Sánchez-León S, Gil-Humanes J, Ozuna CV, et al. Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol J. 2018;16(4):902-910. doi:10.1111/pbi.12837

Ji X, Si X, Zhang Y, Zhang H, Zhang F, Gao C. Conferring DNA virus resistance with high specificity in plants using virus-inducible genome-editing system. Genome Biol. 2018;19(1):197. Published 2018 Nov 15. doi:10.1186/s13059-018-1580-4

Oliva R, Ji C, Atienza-Grande G, et al. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol. 2019;37(11):1344-1350. doi:10.1038/s41587-019-0267-z

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