Advancing agriculture, according to C. S. Prakash

The evolution of maize

Presentation given by Prof. Prakash at the Virtual Workshop on Innovative Biotechnologies and Regulatory Approaches organized by the United States Department of Agriculture and the US Embassy in Rome (June 8, 2021).

I would like to start by reminding you that all our food crops were once growing wild in their native habitats. Teosinte, for example, gave rise to the maize we know today. It was through a slow genetic selection that our ancestral farmers modified these weeds, fundamentally unfit for agriculture, into the food crops that we grow nowadays. And especially in the past 100 years, we have used a variety of tools to modify plants using more scientific methods.

We have used, for instance, traditional breeding, which is primarily crossing plants A and B, to bring the best of two varieties into one. We have also employed mutagenesis, exposing seeds to chemicals or radiation, to create variation in the crop plants. And in the last 30 years, with the advent of biotechnology, we have had at our disposal many tools that are relatively more precise.

Credit: C.S. Prakash

RNA interference is a good technology when you want to turn off certain genes. It’s kind of very similar to the RNA vaccines that are being now used against Covid-19. In plants, it is used to turn off the production of certain proteins. Then there is the transgenic technology, where a foreign gene is introduced into the genome of the crop plant, or even the livestock. And finally, the focus of today’s topic is going to be on gene editing.

So, when you look at how many changes a crop undergoes naturally if you take a grain of wheat and sow it and look at all the mutations that come along, even if you do nothing, about 238 mutations have been observed, and is probably more. So 32 in maize, 16 in soybean, 13 in tomato: these are natural mutants that come without any radiation or chemicals.

Credit: C.S. Prakash

But if you try to use radiation, you get about 600 mutations and most of them are unknown. And yet this technique of mutagenesis has been used for the last 100 years widely, especially in Europe, because the International Atomic Energy Agency (located in Vienna) provides a lot of scientific guide for the use of this technique. Many new varieties, in fact 2300 new varieties, have been developed in food crops around the world using mutagenesis.

Now compare that to the mutation introduced by CRISPR/Cas, just one mutation. And so, gene editing involves a very subtle change of just one or two, or very minimal, but very directed change in the DNA of the organisms that we are working with, and this is one of the reasons why this has provoked a lot of excitement within the plant breeding and agricultural community.

Because here we have an opportunity to improve on the traditional breeding, especially mutagenesis, and bring about a small change in our food crops, without having to introduce foreign genes, unlike GMOs. And that way, a lot of us think this is an extension of the traditional techniques, but with more science, more precision, more speed.

Gene editing is at its best in deleting the genes or turning up the expression of genes. By gene editing we can remove unwanted traits, but also introduce new traits through gene modulation. Plant breeding has traditionally been used to remove seed color changes, to bring about seed size changes, to bring about quality of the oil. And all of those were primarily using natural mutations, or mutagenesis or genetic engineering.

But now we can do the same in genome editing much more precisely, much more rapidly. When you compare gene editing to mutagenesis, it’s kinda like using a scalpel compared to using a huge pickaxe. The big problem with traditional mutagenesis it’s completely random, when you expose the seeds of tomato or rice to gamma radiation, you get hundreds and hundreds of mutations, and many of them may be undesirable.

And if your trait is multiple copies, then you won’t be very good at changing that. Those quantitatively inherited traits, polygenic traits, for instance. So the mutations per million, as you can see, are quite high when we use traditional mutagenesis, but if you use gene editing, it removes many of these limitations. So let me give you some examples of what’s going on with gene editing.

By editing just a couple of nucleotides, scientists at the Sainsbury Laboratory, in Norwich, were able to make tomatoes resistant to a deadly disease called powdery mildew. Another example is to increase the shelf life of tomato. Considering that 50% of the fruits and vegetables produced today in the world are lost due to rotting, increasing the shelf life is more and more attractive to breeders, especially in developing countries. And that could be done in a variety of ways. By slowing down fruit ripening you can harvest tomatoes late and yet retain flavor and taste unlike some of the current tomatoes you see on the market.

And we can also increase the lycopene content in tomatoes by gene editing. This is healthier, especially of importance to men because it is known that high lycopene content reduces the incidence of prostate cancer. One other research is also aimed at altering plant architecture and making dwarf plants. Consider that all the Green Revolution was driven by the discovery of two dwarf genes, one in wheat, and another in rice, but it took 15 years for us to develop that. We can do the same with gene editing in practically any crop in a matter of months now, and also make it healthier.

This is a gene-edited tomato that is already released for commercial cultivation in Japan, it contains five times the compound called GABA, and it is known to reduce blood pressure. And talking about healthier stuff, gene editing has also been used to develop more diabetes-friendly rice, with a low glycemic index, especially of value to people who have type two diabetes. And we can also increase the grain size, resulting in higher grain yield.

And also, if you like beer, one day, you’re going to be thanking this research coming out of Australia, where the CRISPR technology is used to increase the levels of beta-glucan and to essentially improve the malting quality in beer.

Coming back to the nutritional qualities again, by gene editing scientists in India have introduced pro-vitamin A into bananas. And also you may have heard of golden rice that was developed earlier in Switzerland. Now using gene editing, we can also turn on some of the pro-vitamin A genes, and then improve the nutritional quality. This is just to give you an overview of so many things that are happening in using genome editing. Technically, there is a tremendous variety of options that scientists have in what we could do with CRISPR/Cas and similar technologies.

Credit: C.S. Prakash

Unlike GMOs, which tend to require a lot of regulation, gene editing at least in the USA and other countries is not as much regulated because this is primarily an extension of traditional breeding where there is no introduction of foreign genes involved. That also means that smaller entities like universities, and smaller companies would be able to bring out the products. And again, the list goes on and on, with a growing pipeline and thousands of papers coming out on what gene editing can do.

Almost every day, we get applications into the USDA website that you can check out to see how many new products, literally hundreds and hundreds of new products, are being done using gene editing. So in summary, gene editing is very popular among plant breeders, because it can delete, edit or replace genes. And there are many, many benefits. As I mentioned, better nutrition, longer shelf life, disease resistance, drought tolerance, and a reduced time to bring your product to the market.

Conventional breeding takes about eight to 12 years, and GMOs take even longer, but gene editing, you know, between three to four years can be enough. And this is why I talked briefly about regulation. The European Court of Justice ruled that genome-edited crops are the same as GMOs, but now there is a lot of talk going on that the European Union needs to modify the rules.

Already the United Kingdom has come about saying that they are going to be looking at treating gene editing differently from GMOs with reduced regulatory scrutiny. That’s one of the few good things to come out of Brexit I will say, because the UK was able to move forward quickly, without a large bureaucracy that is that we see in the EU.

Literally our imagination is the limit on what crop qualities we can improve by using gene editing, to cut down the use of chemicals like pesticides, improve food quality, extend the shelf life of fruits, vegetables and flowers, improve oil quality, and most importantly, to tailor our crops for climate resilience.

We have huge droughts going on here in California, for instance, the last four or five years, and this year has been the worst. So it has been in southern Africa, and we saw huge fires in Australia last year. And so much of this is due to the chaotic global changes. And gene editing is one powerful tool we have in our hands, to make our crops more resilient to some of these unknown factors, that farming is always exposed to.

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