Success Story

In native plant diversity, scientists see a path to address food availability around the globe

Geneticists at 25:2 Solutions bring industrial innovations in agricultural technology to farming communities struggling with the harsh realities of global change 

25:2 Solutions

ChallengeAround 9% of the world population suffers from hunger and malnourishment. The challenge of global food availability is further exacerbated by environmental changes, as water-stressed farming communities struggle to produce an adequate harvest. Though highly nutritious crops exist, they lack drought tolerance and are often out of reach for lower-income populations due to intellectual property constraints. Scientists working to address this gap through the development of royalty-free agronomic crop varieties face a range of data challenges that limit the pace at which they make new seeds available.  
SolutionJMP® Genomics plays an important role in the development of new crop varieties because of its exploratory and model building data analysis tools. Scientists at 25:2 Solutions analyze phenotypic variables and combine the results with genotypic data to identify key allele states at specific loci that code for desired traits like drought resilience. 
Results“JMP Genomics has helped us to accelerate the development of breeding lines and varieties,” says geneticist and CTO of 25:2 Solutions Eric Jackson. Time savings, however, is not the only advantage. Jackson says the most important thing is the tool’s constant evolution as JMP software developers listen to the needs of users to design and develop new features. 

About 690 million people – roughly 9% of the world’s population – are undernourished according to the United Nations World Food Programme (WFP). Although this number has declined markedly since the early 2000s, food availability is an enduring humanitarian crisis, especially in farming communities affected by the confluence of climate change, displacement and conflict.

Access to food is further exacerbated in parts of the Middle East and Africa, where extreme drought may last for several years. In highly water-stressed regions of Morocco, a severe drought in 2019 caused all but one major crop to fail. The crop that survived was a fit-for-purpose oat variety developed by geneticist Dr. Eric Jackson.

“The Avena magna oat is both high in protein content and drought tolerance,” Jackson explains. After the crop was planted across a number of at-risk Moroccan farming communities in November 2018, there was no rain for an entire growing season. By harvest time the following June, though every other field lay barren – barley, wheat, potatoes – Avena magna had flourished. “The community matriarchs were overwhelmed,” he recalls. “We all were.” 


Eric Jackson, a former Research Geneticist for the United States Department of Agriculture and systems biologist at General Mills, now aims to build upon agricultural innovations developed in industry to address food availability around the world. 

 

Finding solutions in native diversity, removing barriers to access  

Jackson, a former Research Geneticist for the United States Department of Agriculture and systems biologist at General Mills, now aims to build upon agricultural innovations developed in industry to address food availability around the world. As co-founder and CTO of the Idaho-based agricultural technology company 25:2 Solutions, he and his wife work with a team of scientists and educators to take advantage of ancestral plant diversity in farming communities threatened by global change.

The organization’s goal is to distribute pioneering agricultural technologies like the Avena magna oat to all who need them – without imposing royalties or restrictions on their use. It’s a revolutionary approach for an industry where plant breeds and the resulting seed have historically been seen as proprietary technology.   

25:2 Solutions was born of the idea that breakthrough agricultural science could benefit communities facing food availability crisis. “We do meaningful work,” says Kim Jackson, the company’s co-founder and CEO. “We’re using augmented intelligence with genotyping to [develop heartier, more nutritious crops]” and, she says, removing the traditional financial barriers that limit who has access.

With combined expertise in agronomy, seed technology, mechanical and electrical engineering, molecular biology, statistics and bioinformatics, the team of researchers at 25:2 Solutions has developed a platform to support innovative breeding lines and varieties. “We’ve used our proprietary systems to build virtual breeding schemas and prescriptions which, when paired with our other technologies, have resulted in new lettuce, basil, cabbage, buckwheat and barley lines which improve agronomic and nutritional value,” Eric Jackson explains. “We’re using native diversity to impact food security.”

A major highlight is the team’s barley line, which offers complete protein in addition to pro- and prebiotic fiber. And the company is exploring a handful of barley varieties as a way of advancing basic food production in collaboration with WFP partners the Ethiopian Institute of Agricultural Research and the Hassan II Institute of Agronomy and Veterinary Sciences in Morocco. “To date, we’ve been successful in delivering some of our material into more nutritious [oat, barley, and wheat-based] couscous with small shareholder farming collectives,” he adds. “With disruptive techniques to plant breeding, we can provide both better nutrition and better economies to vulnerable communities.”             

Sophisticated genomics tools and approachable data preparation rolled into one

As with geneticists working in industry, the platforms that form the basis of Jackson’s work combine standardized phenotypic data with image processing, genomic analysis and text mining. The company’s pioneering JAIS system uses input layers to discover allele states at key loci controlling specific traits. In the digital age, the speed at which raw data can be transformed into practical insights is a key determinant for success, however, and Jackson and his team face a number of data challenges in utilizing JAIS to its full potential.

JMP® Genomics, an advanced genomic data analysis software, provides a uniquely integrated solution for biological experimentation. The tool enables users to discover reliable biomarker profiles, detect differential expression patterns, perform single-cell sequencing analysis, find signals in next-generation sequencing data and increase genetic diversity for plant traits in silico.

JMP Genomics, Jackson says, is the key companion tool for validating the team’s JAIS neural network and overall knowledge base. “JMP Genomics makes validation possible with regards to the genetic output layers… and is our go-to to cross-check findings and train the system,” he adds. “From the start [with Avena magna in Morocco], I used JMP Genomics to accelerate the development of breeding lines and varieties. One of the key traits we modeled, for example, was improved drought tolerance.”  

“We're integrating [genotypic and phenotypic data] in JMP Genomics to run different types of linear models and analysis,” explains bioinformatician and 25:2 Solutions Principal Data Scientist Richard Linchangco. “Our goal is to come up with a specific set of genetic markers that are important for the traits we’re studying,” he says, and from there, make decisions about how to engineer new crop varieties with more nutritious value or weather resilience.

A key advantage of JMP Genomics, Jackson and Linchangco agree, is the ability to consolidate data workflows into one platform, from simpler data cleaning and exploration to sophisticated gene expression studies. The tool’s dynamic visualization capabilities alone streamline the data preparation steps that could otherwise be quite time consuming.

“We can find outliers really easily just by loading the data and looking at simple visualizations right away,” Linchangco says. “It's important to be able to clean up the data before we actually run any modeling.”

Furthermore, the ability to use the graphical interface in JMP makes analysis “a lot more accessible to those who don't have an understanding of how to use any of the programming languages,” he says, adding that even for data scientists who do enjoy coding, the ability to create a custom workflow in JMP speeds repeat analyses. “JMP makes [our analytical workflow] easier in terms of time savings. You can use some of the pipelines that already exist, or you can generate pipelines by clicking buttons instead of actually having to code it out.” Moreover, he notes, even though JMP is easy to use, it does not sacrifice power or flexibility; the software includes an array of analytical tools that perform robust data analyses.

“The number one thing we love about JMP Genomics is stability,” Jackson adds. “We’ve tried open source options, but they are not stable and have not produced reliable results.” The key advantage to JMP, he explains, is that there’s “actual support behind it” in the form of a team of deeply knowledgeable software developers working to continually improve the software. Even more importantly, that team listens to customers via the JMP New Features Wish List and a variety of Meet the Developer events to understand the new functionalities that are most needed by users. “The people at JMP are true professionals, he says, “and the results show.”

In humanitarianism and environmental stewardship, shared values

Like many who have used JMP for years, Jackson says that in some ways the software and his relationship to its chief architect, SAS co-founder and Executive Vice President John Sall, have helped shape the course of his career as a geneticist. “John once said to me that true innovation comes when logic and creativity meet. That [confluence] results in new ideas that can change the world.’” JMP is logic-driven, he explains; “and I’m a creative person, so if what we do together changes the world, John’s impression was correct, and our story is one of the many beneficiaries of his life’s work.”    

This alignment in values is a keen reminder that in a year marred by global crises unprecedented in modern times – climate change, the COVID-19 pandemic, the rise of extremism, violence and displacement – there is an equally unprecedented opportunity to do something about it. “John Sall is a doer,” Jackson says. “[Even after 30 years], he still codes! And that ethos runs through the whole organization – it’s the noble and pure founder effect.”

But the real vision comes from Kim and Eric Jackson and 25:2 Solutions’ scientists who have devoted their careers to creating access to innovation for those who most need it. In their model, industry and business partnerships created through shared values, can make all the difference – from a handful of farming communities in Morocco to all those who experience food around the world. Fortunately, it’s a model that has been proven to work.

 

The results illustrated in this article are specific to the particular situations, business models, data input and computing environments described herein. Each SAS customer’s experience is unique, based on business and technical variables, and all statements must be considered nontypical. Actual savings, results and performance characteristics will vary depending on individual customer configurations and conditions. SAS does not guarantee or represent that every customer will achieve similar results. The only warranties for SAS products and services are those that are set forth in the express warranty statements in the written agreement for such products and services. Nothing herein should be construed as constituting an additional warranty. Customers have shared their successes with SAS as part of an agreed-upon contractual exchange or project success summarization following a successful implementation of SAS software.