U genomics, computing helps PepsiCo supercharge crop research

Stevia leaves

PepsiCo is exploring new ways to improve the flavor of foods and beverages sweetened with stevia. Recently, the company needed genetic data for the all-natural sweetener, but generating it would have taken their research and development labs up to two months.

Instead, they got the data in a few days.

The food and beverage company behind brands like Frito-Lay, Quaker Oats and Tropicana has supercharged its research to develop better agriculturally sourced ingredients, like oats, potatoes and oranges through an ongoing partnership with the University of Minnesota.

“Many companies want to tackle big problems through their own research and development, but in some cases they lack the specialized equipment needed to push their discoveries forward,” said Claudia Neuhauser, the U’s director of Research Computing. “We want to make these resources available for industry partners so they can reach their full potential.”

PepsiCo’s Agro-Discovery Group crop development work begins at the U’s Genomics Center, which uses next-generation sequencing techniques to generate data on specific varieties of crops. The Genomics Center then sends the data to the Minnesota Supercomputing Institute, where PepsiCo researchers in their New York state labs or their offices in Borlaug Hall on the U’s St. Paul campus can connect to supercomputers and analyze the large genetic and metabolic datasets.

To PepsiCo, one of the benefits of working with the U of M is having the Genomics Center’s cutting-edge data generation in the same place as MSI’s specialized bioinformatics software and hardware. Genomics work involves huge quantities of data that can be difficult to transfer quickly and securely to another location. MSI’s specialized data transfer tools streamline the process, saving PepsiCo time and preventing data loss.

Veronica Vallejo, Ph.D., leads the Agro-Discovery Group’s computational sciences efforts and provides analytical support and computational resources for her team. Vallejo said the U’s research infrastructure helps accelerate data analyses and lowers the obstacles to better collaboration, both with the University’s and with PepsiCo’s research divisions focused on plant gene pathways, plant breeding and applied crop physiology.

“Computational biology works across all three of those areas,” said Vallejo. “We’re fortunate to leverage the resources that MSI and the Genomics Center provide to complement our existing computational infrastructure facilitating complex and large-scale data analysis towards trait discovery and crop improvement.”

An all-natural, healthy sweetener

Whether crop development is especially challenging depends entirely on the crop. Data for the more frequently researched crops is already available, while crops like oat or stevia, for example, have not received ample attention but have a very complex genome. That’s where the U’s sequencing abilities come in.

Stevia, the plant used to make the calorie-free sweetener of the same name, is the focus of one of PepsiCo’s ongoing projects, but improving the crop/ingredient posed a challenge from the start. There was no reference genome available for stevia.

The Genomics Center sequenced the stevia RNA for PepsiCo, and using the high performance computing resources at MSI, the company’s bioinformatics experts generated a reference transcriptome for the crop — a “snapshot” of the plant’s active genes that can help scientists understand how individual genes influence traits.

At a molecular level, stevia contains a broad range of compounds that create its sweet flavor. By studying the transcriptome, scientists can dig into the genetic pathways that create those compounds and use the findings to guide new lab experiments toward improving the crop.

What does it mean to make stevia a better ingredient? Vallejo said there are many ways to improve the crop, including by making the plant derivatives taste better in a wider variety of products, cutting the cost of producing them or even boosting the plant yield for the farmers who grow the crop.

A sustainable future

The genomics and computing collaboration builds off of an existing partnership between PepsiCo and the U, which includes an on-site team housed within the U’s Department of Agronomy and Plant Genetics led by Gabe Gusmini, Ph.D., research and development director of the Agro-Discovery Group and adjunct associate professor in the department.

At the core of their research and development efforts, both with stevia and their other agriculturally derived ingredients, PepsiCo scientists are aiming for greater social, economic and environmental sustainability — a goal that their expanding partnership with the U will help support.

“Sustainability, productivity, and consumer’s benefit are what really drive what we do,” Vallejo said. “Our partnership with the Genomics Center and MSI is a natural fit that builds on what was already there at the U. I think there are a lot of really great opportunities for us to work together.”