Sometimes Less Is More – Silencing Genes in Plants

From Decaf Coffee Plants To Non-Browning Apples

Have you ever had a really good cup of decaf coffee?

Me neither.

This is likely because most decaf coffee results from chemical processing of normal coffee beans.

But why would anyone want coffee without caffeine? And why do plants make caffeine in the first place?

These questions have been addressed in a previous post, but suffice it to say here that there certainly is a very large potential market for coffee beans that naturally have very low or no caffeine.

Indeed, coffee plant breeders have been trying to develop such varieties for decades, with very little success.

In 2003, a more efficient gene-silencing technology was used in order to shut off caffeine production in coffee plants. (See Ref. 1 below.)

This approach is called RNA interference (RNAi).

The Benitec Biopharma website has provided a nice summary of this biological process:
RNA interference (RNAi) is a natural process that cells use to ‘turn off’ or silence unwanted or harmful genes. The initial discovery of this phenomenon was in 1991, by scientists trying to deepen the colour of petunias. Surprisingly, by introducing a gene for colour, they found that they had turned off the gene.
Several years after the petunia experiments, the mechanism of RNA interference was revealed: it is triggered by double-stranded RNA (dsRNA), not usually found in healthy cells, but needed to turn genes off, if the cell is threatened or damaged by invading viruses.

To learn more about how this technology may impact plant breeding, please see Ref. 2 below.

Back to decaf coffee plants….Unfortunately, it’s been difficult to produce coffee plants that don’t make caffeine because its biosynthesis involves a complex metabolic pathway. Thus, to develop “decaf” coffee plants has been especially challenging for plant genetic engineers, but they’re still trying. (e.g., see Ref. 3 below.)

There are, however, plant products produced using RNAi gene-silencing that you will likely soon encounter.

Arctic® Apples and Innate® Potatoes

According to the official Arctic® apples website: “Arctic® apples aren’t slow browning. They aren’t low browning. They’re nonbrowning! By silencing the enzyme that causes apples to brown when bitten, sliced or bruised popular apple varieties like Golden Delicious and Granny Smith can be enhanced with the Arctic Advantage™. Our goal? To help consumers eat more apples by making them more convenient, and reducing food waste while we’re at it!

What is the “Arctic Advantage™”?

Briefly, these apple plants were genetically modified using RNA interference to silence genes coding for the enzyme polyphenol oxidase, which is primarily responsible for the browning of apples and other fruits and vegetables.

These apple trees were approved for commercial planting by the USDA in 2015.

A year earlier, another crop plant with specific genes silenced by RNAi was USDA-approved, namely, the Innate® potato.

According to the official Innate® potato website:
“Innate® potatoes are less prone to bruising and black spots, which means consumers waste less and fewer potatoes end up in landfills. Innate potatoes also contain less asparagine. By producing less asparagine, Innate potatoes provide the potential for the formation of acrylamide to be reduced by 58-72% when potatoes are baked, fried or roasted at high temperatures.”

As I understand it, in the first generation of Innate® potatoes, RNAi gene-silencing was used to block the production of two enzymes, namely, polyphenol oxidase (see Arctic® apples, above) and asparagine synthetase.

The second generation of Innate® potatoes blocked the biosynthesis of these two enzymes, plus two more – starch-associated R1 and phosphorylase-L. These two enzymes are involved in converting starch into reducing sugars, such as glucose and fructose. By blocking the production of these two enzymes, this results in a decrease in reducing sugars in stored potatoes, which also contributes to the lowering of acrylamide in French fries, for example.

Online Resources: More thorough considerations of Innate® potatoes can be found at:

  • A look at the Innate Potato
  • Q&A with Haven Baker on Simplot’s Innate™ Potatoes
  • Recent News: Genetic improvement of tomato by targeted control of fruit softening


    1. Ogita, S., et al. (2003) “Producing decaffeinated coffee plants.” Nature, Vol. 243, p. 823. (Full Text)

    2. Younis, A., et al. (2014) “RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding.” International Journal of Biological Sciences, Vol. 10, pp. 1150–1158. (Full Text)

    3. Borrell, B. (2012) “Plant biotechnology: Make it a decaf.” Nature, Vol. 483, pp. 264–266. (Full Text + Extras)

    *Please Note: The subject of RNAi mediated gene-silencing has also popped up on this blog in a previous post, entitled “Spray and Pray? – Will Spraying RNA on Plants Revolutionize Agriculture?”.

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