Editing Nature: The rise of ‘smart plants’ and ‘smart seeds’

The recent discovery of a ‘supercharged’ CRISPR technique will allow scientists the opportunity to transform seeds, crops and foods in a way that ‘connects them to the environment’.

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A new world of production.
Photo: ALM
Transforming our food systems.

CRISPR-CAS9

The CRISPR revolution started only a decade ago, in April 2012, when UC Berkeley researchers discovered how to redesign a protein at the heart of bacteria to target and cut DNA in any organism, plant or animal. 

Since then, CRISPR has become a leading ‘innovation’ of new treatments for sickle cell disease, hereditary blindness and several cancers, and has been used to bulk up pigs and dogs, and prevent mosquitoes from transmitting malaria.

Importantly, it has changed the way scientists and engineers conduct their research.

In recent years, many countries have eased regulation processes for crops with edited genomes — provided that the editing is relatively simple, and creates a mutation that could also have occurred naturally.

Australia deregulated gene-editing techniques in late-2019.

Current selections of genetically-modified crops are made by inserting genes into plant genomes. Many of us are familiar with the controversial field of GMO research for many years now.

However, until recently, there were relatively few ways to use the kind of gene-editing you see in humans and animals, to boost the nutrient content of a crop or plant species.

That is until earlier this year when a breakthrough was made.

Now, we are ready to see the next step in the CRISPR evolution.

Scientists have re-designed a key component of the widely used CRISPR-based gene editing tool – the enzyme Cas9 that cuts DNA at a specific location – to be 4,000 times less likely to target the wrong stretch of DNA.

First beginning with a March 2022 study published in Nature, researchers were successful in their attempt at re-designing Cas9 to be more accurate while also not sacrificing the speed at which it does its job.

The results have proven ground-breaking and will have implications for the planet moving forward.

CRISPR-Cas9, combining existing techniques with a new-and-improved enzyme, is predicted to revolutionise biomedical research — promising to help “re-engineer crops” to ‘deal with climate change’.

Here is how it works: The technology acts like the cut-and-paste command on a computer.

Scientists now say this technique allows them to identify a gene in a particular crop and “cut it out”.

Then, with this technology, they can stitch the two ends of the gene back together or replace the old gene with a one that ‘codes for an improvement’, like longer shelf life.

CRISPR-Cas9 technology consists of crossing plants with the most desirable traits over and over again until the ideal plant is achieved. It also allows scientists to avoid futzing with plant breeding.

This will help farmers avoid degradation or destruction of their crops, improve plant life cycles and health, as well as navigate changing environments, proponents of the technology argue.

“The advent of CRISPR basically allowed us to create new molecular tools for potentially skipping the slow aspects of plant tissue culture and plant genetic engineering, which are large barriers to doing experiments in plants,” says the Howard Hughes Medical Institute.

Combining existing GMO practices with gene-editing to achieve truly ‘smart crops’, consumers may see CRISPR gene-edited produce in the market soon. 

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‘SMART PLANTS’

Since this supercharged gene-editing discovery, researchers across many fields have been working to find new ways to use CRISPR-Cas9 in a way that can improve the production of GMO food products.

Think of this discovery as a kick-start that will enhance existing bioresearch efforts since CRISPR’s launch.

One particular field this will benefit is emerging understandings of plant behaviour with technological influence. The 2019 Laureate Fellowship, for example, was about creating ‘smart plants’.

In many ways, plants are as smart as us anyway – they just don’t have a brain.

But a ‘smart plant’ will be one that does what we want it to do, so you can switch from one function to another.

It might switch from rapid growth to drought resilience, then back to rapid growth.

Ideally, this will be controllable, according to those pioneering the field.

“Sequencing the genomes of plants is straightforward, the same as we sequence the genomes of the COVID virus every other day, for example. DNA is DNA.”

‘Smart plants’ have become a new wing of agricultural research; a field now set to grow exponentially.

Work is even being taken out right here at home.

For example, the ARC Training Centre For Future Crops Development is an Australian partnership of more than 20 national and international institutions, aimed at training the next generation of agri-tech leaders. 

Participants of the program are placed with breeding companies, with other partners who work in the regulatory space, with those who work in policy, in export, and even in communication.

One innovation that has sparked interest comes from researchers at The University of Western Australia, who are building ‘synthetic gene circuits’ to control and customise where, when, and under what environmental conditions a gene is turned on or off in a plant.

Dr James Lloyd and Professor Ryan Lister, from UWA’s School of Molecular Sciences, are authors of the study, Synthetic memory circuits for stable cell reprogramming in plants, published in Nature Biotechnology.

Professor Lister, from UWA’s ARC Centre of Excellence in Plant Energy Biology and Head of the Genome Biology and Genetics program at the Harry Perkins Institute, said the new DNA-based gene circuit system could be used to program a plant to turn certain genes on or off when it perceived a desired combination of specific conditions, which could be internal, environmental, or even artificial cues.

By using CRISPR to ‘connect’ plants to the environment around them, like humans, they can be tracked better.

And it all starts with the base foundation – the seeds themselves.

‘SMART SEEDS’

The aim of this new innovation in gene-editing is to create a “communication networks within plants”, according to researchers. This obviously starts at the basis — the seed of any crop.

Science is pushing new grounds to give plants a voice, via what are known as ‘smart seeds’.

InnerPlant, a California-based startup, is currently bioengineering plant genes so that crops can “send messages” that farmers will be able to translate and understand via drones, smartphones, or satellites.

The endeavour hopes to develop a “Google Translate for plants”:

“The way that we get them to communicate back is by engineering the code of the crops. So as they’re reacting to the stress, they can also generate a protein in their leaves that they don’t otherwise create … and that protein happens to fluoresce,” InnerPlant CEO Shely Aronov told the TechFirst podcast. 

The florescence that the plants create isn’t in a visible spectrum for humans, so farmers at present are not able to see deterioration with their naked eyes.

However, it is easily visible via a common smartphone with a filter, or with a multi-spectral camera, according to those working on the project.

Famers don’t have to walk through thousands of acres of fields holding up their phones to their crops, however: a drone can do the work, or a sensor attached to a tractor, or for very large farms, satellite imagery.

“One of the interesting trials that we just completed in a greenhouse was a drought trial between the biosensors and regular crops,” Aronov says.

Aronov says they will soon be able to provide that to farmers at precisely the existing cost they currently pay for seed, thanks to so many common GMO traits coming off-patent soon.

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PRODUCTS IN THE WORKS

Let’s take a look at the crops already being edited by CRISPR-Cas9 to become ‘smarter’.

Strawberries

The J.R. Simplot Company and Plant Sciences Inc. plan to edit the DNA of strawberries and make these new-and-improved fruits available on the commercial market, reports Keith Ridler for the Associated Press.

The companies will use CRISPR-Cas9 to edit the strawberries’ genes.

“At Simplot, we’re excited to participate in a project that may help growers achieve higher yields on less land, resulting in fewer pesticides and reduced water and labour needs, all while extending the quality of a consumer’s favourite foods,” Vice President of Simplot Plant Sciences Susan Collinge told The Hill.  

The goal is to modify the strawberries’ genes in a way that improves their shelf life, extends the growing season and reduces consumer waste.

Potatoes

Simplot has also shown success with this methodology on potatoes, reports Gretchen Parsons for BoiseDev. 

The company developed two potato varieties that have fewer black spots, less sugar and increased resistance to pathogens, and both of those are widely sold on the commercial market.

Two articles outlining how CRISPR can improve potatoes were recently published in the International Journal of Molecular Sciences and the Plant Cell, Tissue and Organ Culture journal.

Developing potato cultivars with modified starch could open new opportunities.

Potatoes with high amylopectin and low amylose, like the gene-edited Yukon Gold strain she described in the International Journal of Molecular Sciences, have industrial applications beyond traditional uses.

Rice and Wheat

Brian Staskawicz, a UC Berkeley Professor of Plant and Microbial Biology, is working with his colleagues to edit rice and wheat with CRISPR-Cas9 to increase its drought tolerance, among other things.

According to reports, the team inspecting how to improve immature grains of a wheat plant.

man in white lab coat inspecting rice plant

“What we’ve built at the IGI is an amazing infrastructure for plant gene editing and crop transformation and DNA delivery methods,” said Staskawicz.

“We probably have one of the most extensive and robust plant transformation facilities anywhere in academia.”

Utilising optimal transformation and heat treatment parameters greatly increases mutation efficiency and can help advance research efforts in wheat genomics, according to researchers.

Tomatoes

One last major crop that is set to gain a new life with enhanced gene-editing techniques are tomato’s.

Researchers recently reported editing a tomato with CRISPR-Cas9 to increase vitamin D production.

When the gene-edited tomatoes are exposed to ultraviolet light in the laboratory, some of the precursor, called provitamin D3, is converted to vitamin D3.

Researchers have already been given permission to grow their gene-edited tomatoes in fields

If the tomatoes perform well in field studies, they could eventually join a limited list of ‘nutritionally enhanced’ CRISPR-Cas9 crops that will soon become available to consumers.

And not only is the food itself become more tech-based, but those managing the food are as well. 

ROBOTIC FUTURE

AI will completely revolutionise farming, even beyond the progression of ‘smart plants’ and crops.

It will also be used to detect plant diseases, pests and weeds, and decide which and how much herbicides, insecticides and fungicides to use.

It will give farmers precise dates to sow seeds in order to maintain maximum yields, give insights into soil health, provide recommendations on the application of fertilizers, provide weather forecasts and determine water usage from irrigation. 

Agriculture is slowly becoming digital and AI in agriculture is emerging in three categories, (i) agricultural robots, (ii) soil and crop monitoring, and (iii) predictive analytics.

Farmers are increasingly using sensors and soil sampling to gather data and this data is stored on farm management systems that allows for better processing and analysis.

And soon they may be replaced all together.

Farms of the future will rely more on robots. In conjunction with AI, robots will pick fruits and vegetables, sow seeds and help to pack fruits and vegetables into boxes for shipment.

This is already happening in Australia with our first fully-automated farm launching in Wagga Wagga:

What are your thoughts on the radical transformation of food over the last few decades?

Will CRISPR-Cas9 be a positive addition to our food systems, or is it designed to disrupt them?

Make sure to leave your thoughts below!


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3 comments on “Editing Nature: The rise of ‘smart plants’ and ‘smart seeds’”

  1. No mention as to weather or not gene-edited plants will be safe for consumption especially in the long term. Then there is also the issue of patenting of gene-edited plants and the effect it will have on independent farmers.

  2. And beware, using this method, “they” will try to insert vaxxes into food crops,which would be a particularly unhealthy development. inking corporatised agriculture (“Big Food”) with Big pHARMa…what’s not to like?

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