Biotech Crop Discovery Poised for Fast Growth Thanks to Big Data
Big agriculture companies have been using HPC techniques to understand and manipulate the genes of food staples like corn and soy for many years. Now, thanks to the big data revolution, that kind of fine-grained genetic control will soon be wielded by smaller firms targeting a much wider swath of biotech crops.
One of the companies on the cutting edge of biotech crops is Benson Hill Biosystems. The company, which came out of the Donald Danforth Plance Science Center in St. Louis, Missouri, today unveiled a new big data-powered platform called CropOS that’s designed to put powerful gene discovery techniques into the hands of small and midsize ag firms looking to take innovation from the lab into the field.
CropOS is a cloud-based platform that essentially enables biologists and food scientists to predict what will happen when they cross one plant with another (selective breeding) or a specific group of genes from one plant with those of another (genetic engineering). The company does this by combining the genetic sequences of plants (the genotype) with the known expression of genes (the phenotype), and then running the data through powerful machine learning algorithms that predict how the genes interact.
This general approach has been used for decades by big multi-national agricultural firms like Monsanto, DuPont, and Dow Chemical, which have the huge resources needed to fund this type of research. And it’s been very successful: According to the International Service for the Acquisition of Agri-Biotech Applications, more than 90 percent of sugar beets, of soybeans, cotton, and feed corn grown in the United States is genetically engineered, usually to be either herbicide or pest resistant.
But this technique is not widespread in the rest of the world. Globally, just 12 percent of cropland is planted with genetically modified organisms (GMOs), according to the ISAAA. But that could soon change, according to Benson Hill CEO Matthew Crisp, who says the global biotech food industry is on the cusp of huge advances thanks to the rapid maturation of big data tech and cloud computing.
“The data acquisition costs have just gone down orders of magnitude compared to 10 years ago,” Crisp tells Datanami. “Today we can sequence entire populations of plants and ascertain genetic diversity in a matter of weeks, whereas it would have taken years and 100 to 1,000 as much from a cost standpoint before.”
Better Living Through Genetic Engineering
Benson Hill, whose research was funded with $10 million in grants from the DoE, USDA, and the Bill and Melinda Gates Foundation, is already working with a handful of agricultural firms to help them explore new combinations of genes that will create crops with the desired characteristics. For example, one of the company’s clients is investigating the potential to combine the drought-resistant properties of sorghum with modern corn.
There are more than 10,000 different varieties of sorghum in the world, which makes even sequencing the genomes of the strains a major task. But thanks to breakthroughs in gene-sequencing and analysis from companies like Illumina and Pacific Biosciences, that genetic data is now readily accessible in a digital format.
However, once you have that data, figuring out what to do with it is a whole different story. That’s what Benson Hill looks to tackle with CropOS.
“If you took all 10,000 of those sorghum varieties and crossed them all, with every combination, that’s a nearly infinite amount of work, which nobody would ever begin to try,” Crisp says. “But if I can look at the genome of those in a high throughput manner, and say ‘Take line 637 and cross it with line 8,112,’ and you’re going to get something that, combined, is better than 99 percent of the possible crosses that you can make, that gets really powerful.”
The St. Louis-based company runs all of its data storage and processing systems on Amazon Web Services, which provides the necessarily elasticity to scale up for intense workloads and scale down to save money. The company uses RDS, DynamoDB, and RedShift managed services at AWS, as well as customized implementations of similar systems for targeted purposes, the company says.
Cassava, Chickpeas, and Quinoa, Oh My
To date, most of the genetic effort has been heaped upon major U.S. crops like corn, soybeans, and cotton. But there’s a whole slew of other crops around the world that could benefit from some big data-powered genetic tinkering, including sorghum, cassava, chickpeas, blueberries, quinoa, and potatoes.
“The consolidation of innovation into a few companies has limited the larger scale opportunity,” Crisp says. “But in developing countries, there’s a whole cadre of additional crops that haven’t received any innovation or investment in developing better varieties…Crops like cassava and sorghum are of immense importance for food security. Those are a couple where we’re eager to find somebody to partner with.”
In many cases, CropOS will be asked to work with the genes that already exist in the natural world, and which farmers could theoretically breed together to create a new crop that has the desired feature. “Our tagline is ‘Harness the global genetic potential of plants,'” Crisp says. “Often times the genetic potential is within the plant already.”
In other cases, CropOS may be asked to predict what will happen with more targeted breeding that involves snipping one group of genes from one species (like sorghum) and mixing them with another (like corn).
“We can identify those genes and enable our partners to isolate them and put them into, say, corn,” Crisp says. “Then ideally we have a corn plant that can produce the same amount of grain without as much water.”
No Silver Bullet
While Benson Hill is confident it can help shave the process of discovering novel genetic combination in plants by years and millions of dollars, it still requires years of field tests by the ag companies and farmers to prove that the novel creation is commercially viable. Whether or not there’s a regulatory component involved, the process of creating better food products still takes years.
“You can design all this stuff ’till the cows come home, but if you can’t take the intelligence from the system,” then it’s all for naught, Crisp says. “You’re shortening the discovery cycle from five years to one or two years….[but] you still have to go through years of field trials to be sure that you don’t have any unintended effects in the plant, that it doesn’t cause it to be more susceptible to a disease or cause it to be not able to withstand a drought.”
Benson Hill is benefiting from some good timing this week. On Tuesday, the National Academies of Science released a report that found genetically engineered crops and animals are safe to eat and that they have not caused increases in cancer, obesity, gastrointestinal illnesses, kidney disease, autism or allergies. The report concluded that genetically engineered crops helped to save money for U.S. farmers but didn’t increase crop yields. They’ve also lowered pest populations in some areas but increased the prevalence of weeds that are resistant to herbicides, like Round-Up.
The timing of CropOS’s launch was not tied to that study, Crisp says. While the study may help ease the fears of some consumers, he recognizes that GMOs and genetically engineered crops in general face a perception problem, not just in segments of the U.S. but in “anti-science” areas like Europe.
Crisp seems to understand that questions of food safety and ethics will likely persist for some time, but he sounds confident that reason will win in the long run. “Consumers who understand very much embrace the concept of creating more resource efficient plants, especially to the extent we’re already using genes that already exist in nature,” he says. “We’re confident that technology, whether it’s breeding technology or genetic engineering, has a place, and it will be required if we want to improve the sustainability of agriculture, which is something we’re passionate about.”