Towards a Thousand New Crops
HudsonAlpha’s work to democratize plant genomics is unlocking the genetic potential of the world’s overlooked species, turning wild diversity into sustainable food security.
By: Sarah Sharman, PhD
“We are not on track to meet future food needs. Not even close.”
This stark warning, issued by more than 150 Nobel and World Food Prize Laureates, captures the scale of the world’s food challenge. Today, around 700 million people go hungry, and by 2050, we’ll need to feed 1.5 billion more. Meeting that demand will require not only improving existing crops, but also discovering or creating entirely new ones.
At the HudsonAlpha Institute for Biotechnology, plant genomics researchers are meeting that challenge head-on by decoding the DNA of wild plants to help breeders create new, climate-resilient crops.
Looking Beyond the Big Four
Wheat, rice, corn, and soybeans currently supply more than 50 percent of the global diet. Their intensive annual cultivation leaves them vulnerable to shifting weather patterns, pests, and disease, while overall crop biodiversity continues to decline. Yet researchers estimate that nearly 35,000 edible plant species exist on Earth that are not part of our everyday diet. Could even a fraction of these species be domesticated to help feed the world? The answer can be found in genomics, which aims to bring these underutilized plants into the mainstream.
From Ancient Breeding to Genomic Acceleration
It took our ancestors thousands of years to transform wild grasses like teosinte into modern corn. Today, DNA sequencing allows scientists to pinpoint the genes responsible for desirable traits and use that information to breed new crops in a fraction of the time.
“Historically, crop domestication was a lengthy process of repeatedly breeding plants with desirable traits until a hardy, nutritious crop emerged,” says HudsonAlpha Faculty Investigator Josh Clevenger, PhD. “Now, DNA sequencing technology allows us to pinpoint genetic regions underlying those traits and use that information to more efficiently breed or develop the plants we need.”
Partnering for Perennial Progress
HudsonAlpha’s genomic expertise makes it a valuable collaborator in efforts to domesticate new crops, especially perennials. Several HudsonAlpha labs have formed a key alliance with The Land Institute, a Kansas-based nonprofit organization recognized worldwide for its pioneering work in perennial agriculture.
The Land Institute’s field and breeding knowledge pairs naturally with HudsonAlpha’s molecular and genetic insights. Together, the two organizations, along with many other collaborators, are advancing three leading candidates for sustainable perennial crops: Kernza® perennial grain, the perennial legume sainfoin (perennial Baki™ bean), and the perennial oilseed silflower. By linking field performance with genetic markers, they can identify the most promising plants years earlier than traditional methods allow.
Kernza is already finding markets as an ingredient in bread and beer, while sainfoin and silflower are at earlier stages of improvement. Across these projects, HudsonAlpha’s genomic data and analytic pipelines guide every breeding cycle, transforming what was once trial-and-error field selection into a data-driven process.
Case Study: Silphium, a Promising Perennial Oilseed
Silphium integrifolium, commonly called silflower, is native to North America. It thrives in dry environments and produces large seeds, making it a strong candidate for domestication and downstream use for cooking oil and bioproducts. At The Land Institute, the lead perennial oilseed scientist, David Van Tassel, PhD, began collecting wild silflower seeds in 2001 and formally integrated it into the institute’s perennial grain research program two years later. With deep roots and drought tolerance, silflower can access groundwater up to six feet below the surface, reducing the need for irrigation and offering greater resilience to drought than many annual crops.
Although rugged and resilient in the wild, Silphium wasn’t ready for the farm. Its seeds vary wildly in size, many plants produce few seeds at all, and harvesting them is inefficient, all traits that make commercialization nearly impossible. Turning it into a reliable oilseed requires increasing yield, uniformity, and harvestability while preserving the drought tolerance that makes the species so valuable. HudsonAlpha’s genomic tools are helping breeders pinpoint the genes behind those key characteristics and accelerate improvement.
Building genetic resources for a perennial oilseed
Because perennials grow more slowly than annuals, breeders often wait three to four years before they can measure yield, making domestication both time- and cost-intensive. At HudsonAlpha, Faculty Investigators Josh Clevenger, PhD, and Alex Harkess, PhD, along with their teams, are addressing this challenge by creating low-cost genotyping strategies that identify valuable traits early, long before full field trials are complete.
“Reducing costs is central to the mission,” explains Postdoctoral Associate Renan Souza, PhD, who leads the silflower project for HudsonAlpha. “Many public breeding programs simply can’t maintain thousands of plants through multi‑year field testing, which can cost hundreds of dollars per plant each season.” By replacing years of observation with a single round of DNA sampling, HudsonAlpha’s workflows cut both time and expense, making genomic selection feasible for small, decentralized programs globally.
Using Silphium integrifolium as a proving ground, Souza and colleagues design and test these genotyping workflows in close collaboration with The Land Institute’s breeders. HudsonAlpha performs the sequencing and data analysis, while The Land Institute conducts extensive field evaluations. Together, they can rapidly link genetic variation to real-world agronomic performance.
The result is a replicable model for accelerating the domestication of underutilized crops. The same genomic tools refined for silflower can be readily adapted to other wild perennials poised for cultivation.
HudsonAlpha’s goal is to develop affordable and easy-to-use methods that enable public universities, small labs, and breeders worldwide to participate in the discovery process.
“When we make genomic tools affordable and simple to use, we give every breeder the chance to discover something new. There are thousands of wild plants with the potential to feed people and protect the environment. Our job is to make those possibilities reachable for everyone.
Looking Ahead: Scaling Sustainable Domestication
The HudsonAlpha-Land Institute collaboration shows how genomics can transform crop domestication. What once took centuries can now happen within a decade, guided by affordable DNA data and analytical tools that reveal a plant’s potential long before harvest. Building on the success of projects such as Kernza, sainfoin, and silflower, HudsonAlpha is expanding these frameworks to a broader range of species, from climate-tolerant grains to regionally important crops worldwide.
As global hunger intensifies and agricultural landscapes shift, HudsonAlpha’s work demonstrates what is possible when genomics meets sustainability. By equipping breeders and farmers with accessible genomic insight, we’re helping cultivate a future where biodiversity, productivity, and food security grow together.
To learn more about their crop domestication efforts, read this review article.
