Mapping a 16-billion-part genome? Give these Israelis a few weeks

An Israeli start-up, NRGene, is leading the way in genome mapping, DNA sequencing, and genetic analysis.

AUGUST 20, 2016 13:48

Durum wheat (illustrative) (photo credit: ILLUSTRATIVE/STEFANO RELLANDINI/REUTERS) — Durum wheat (illustrative)

(photo credit: ILLUSTRATIVE/STEFANO RELLANDINI/REUTERS)

When scientists around the world decided they wanted to map out the genetic makeup of a human being for the first time, launching the human genome project in 1990, it took them 13 years. With over 3 billion base pairs – units of the DNA code – in the 23 chromosome pairs of any given human, completing the monumental task was an extraordinary achievement, and kicked off a new era of genetic innovation.

Fast forward another 13 years, and an Israeli start-up, NRGene, is leading the way in genome mapping, DNA sequencing, and genetic analysis.

Its unlikely source of pride: mapping the wheat genome.

“It’s the most complex genome map ever assembled,” said NRGene CEO Gil Ronen.

Surprisingly, different varieties of wheat can have genomes that are several times larger than those of humans, containing as many as 12 billion base pairs. In June, an international consortium of scientists announced that, for the first time, they had mapped out the most difficult and complex strain of wheat, durum wheat, which is used in pastas and couscous. It has roughly 16 billion base pairs.

The rate of technological change portends a revolution in the field of agriculture. For example, mapping the first maize genome took five years and cost $25 billion in 2009. By 2014, NRGene did it in two days for $50,000.

“I hope one of these days people will think of us as part of the canon of legendary Israeli agricultural technology alongside drip irrigation and cherry tomatoes,” said Ronen.

IF THE world of agriculture genetic mapping doesn’t get your juices flowing, consider a few facts. The United Nations projects that the world’s population will increase from about 7.3 billion in 2015 to 9.7b. in 2050, meaning we’ll have almost a third more mouths to feed, but the same limited resources we’ve always had to feed them.

Over a third of all people rely on bread wheat as a staple of their diet, and it represents about 20% of all calories consumed by humans, according to the Cold Spring Harbor Laboratory.

The types of wheat used in pasta and couscous account for only 10% of the amount of wheat grown for food, but they are part of a larger process in making food better, cheaper and more nutritious.

“Considering that pasta is a staple for the world’s population and recognizing that industries are asking for more and higher quality durum grains despite many abiotic and biotic constraints, it’s critical to select new durum cultivars with greater yield potential as well as enhanced quality and nutritional properties,” said Dr. Luigi Cattivelli of Italy’s Council for Agricultural Research and Economics, who led the project in coordination with Tel Aviv University, the National Research Council of Italy, the Crop Development Center of the University of Saskatchewan in Canada, the University of Bologna in Italy, the IPK Gatersleben in Germany and Montana State University.

Here’s how genetic mapping helps all that happen.

When farmers and scientists breed new varieties of plants, they are trying to combine the best characteristics from existing ones. Say you want your wheat to have excellent resistance to a certain kind of disease, so you find the samples that have that resistance and breed them.

But that’s the simple version, because what if the disease-resistant wheat is flavorless, or less nutritious? The idea is to get not just one characteristic to shine, but a variety, such as protein content and color. That process can be very slow, taking as long as a decade before a new variety of wheat is fully developed.

“Breeding is like an art of improving some elements without affecting the others,” said Ronen.

Instead of the trial-and-error method of picking and breeding generation after generation of the wheat that seems to have the best of the desired characteristics, genome mapping provides a path forward.

“When you have the map, in three months you can actually find where it’s written in the genome that this plant had growth tolerance, and that plant has high protein,” Ronen continued. That roadmap can cut the development time from 10 years to just four or five.

The process of finding those markers, however, means doing a lot more than mapping out one plant’s genome. It means comparing a variety of specimens, figuring out the genes that vary between them, finding DNA markers and associating them with characteristics.

When each genome has 16 billion data points in it, that process becomes a computational nightmare.

That’s where NRGene comes in.

Ronen, a plant geneticist from the Hebrew University who worked for years at Israeli genetics company EvoGene, opened up his own business in 2010 with the goal of processing all that genetics information.

“It’s very easy to produce data, but we take the building blocks of 250 letters and build them into blocks with millions of letters,” he explained.

To do it, he hired a team of mathematician graduates of the IDF’s 8200 division to help crack codes and develop the right algorithms.

“Now they’re working on agriculture instead of cybersecurity. For them it’s just another code,” he said.

The software they developed, he said, is the only one in the world that can quickly sort through all the data, map the genome, and run comparisons.

Of course, even that is only part of the process, and Ronen credited the project’s partners for extraordinary contributions to the wheat project.

Tel Aviv University, he noted, is a world center for wheat studies, as is the University of Saskatchewan. The Canadian province, which provided most of the funding for the project, has been called the world’s breadbasket for its wheat production. Italy, the world’s pasta bowl, has obvious interest in better durum wheat. The durum genome map is open source, meaning it’s accessible to anyone.

For its part, NRGene has seen its revenues triple from its first to its second commercial year, and expects another tripling next year.

But with a giant genetic blueprint of food now readily available, maybe the next step will be simply using the instructions to assemble food from scratch, feeding the DNA code into a nano-printer that can build fully formed agriculture.

That’s not how Ronen sees it.

“When people are talking about building something from scratch, it’s usually bacteria or viruses, which have just 1 million letters.” With 16 billion data points in wheat, he said, there’s no economic justification for growing food in a lab.

“Even if you’re talking about meat, agriculture is still 10,000-fold cheaper,” he said, referencing recent attempts to grow meat in a lab.

“It’s a gimmick, about environment and not sacrificing animals, but economically I don’t see anyone actually producing food in the next 20 years in the lab. That’s the way I see it.”

In the meantime, the world will simply make do with faster, cheaper ways of breeding healthier and more nutritious food.

Given that the coming decades will see so many more guests coming to dinner globally, that’s very good news.