Researchers Map First Chromosome-Scale Genomes for Sustainable Prairie Crops

The Land Institute and HudsonAlpha Institute for Biotechnology, in collaboration with key partners, have assembled the first chromosome-scale, haplotype-phased genomes for Silphium integrifolium (rosinweed, silflower) and Silphium perfoliatum (cup plant, silphie). This landmark research promises to expand and accelerate the development of more climate-resilient, sustainable perennial crops.

These findings, published in the journal Nature Communications, provide foundational genomic data for the domestication of the wild, deep-rooted North American prairie Silphium species into perennial crops for food, fiber, forage, and medicines.

Currently, more than half of the world's human calories come from just five crops: rice, wheat, corn, sugarcane, and barley. Introducing perennial crops, such as Silphium species, that live for many years after planting, could boost crop diversity and productivity while supporting long-term ecosystem health

Wild perennial species could help improve food security by contributing sustainability-enhancing traits such as deep roots. Genomic-informed breeding will help generate new crop varieties more quickly than in the past, but many wild perennials have challenging genomes. We showed that newer, affordable approaches work even for a stubborn genus that previously resisted genome assembly."

David Van Tassel, Lead Scientist for the Perennial Oilseeds Program, The Land Institute

Key Discoveries and Impacts:

• Massive, Complex Genomes: The sequenced Silphium genomes are large-7.6 gigabases (Gb) for S. integrifolium and 7.5 Gb for S. perfoliatum. The individual chromosomes are among the largest known in plants. Researchers identified an unusual helical DNA structure that helps organize these giant chromosomes.
• Faster New Crop Development: By mapping genetic markers for traits like drought tolerance, heat adaptation, and seed yield, breeders can now use genomic tools to rapidly domesticate Silphium while preserving its wild resilience.
• Sustainable Oilseed Crop: Silphium integrifolium is emerging as a promising, drought-tolerant perennial oilseed crop for food and medicine. Its seeds yield 11.8-25.3% edible oil and also contain squalene, which is valued for its use in vaccines and cosmetics.
• Ecological Benefits: Silphium species support diverse prairie ecosystems and could also strengthen agricultural systems. Their roots, which reach depths of up to 4.5 meters, help stabilize soil, increase organic carbon, improve water absorption and infiltration, and ensure resilience in drought conditions.

"Given the growing instability of climate patterns and disruptions in global food supplies, there's an urgent need to develop tools to accelerate domestication and breeding of more stress-resilient and locally adapted food crops," says Renan Souza, applied genomics researcher at The Land Institute and HudsonAlpha. "This genomic framework will help speed up the improvement of not only Silphium, but also other wild species with agricultural potential."

During the research, scientists created a method for DNA fingerprinting individual plants. Breeders can use these fingerprints to make more accurate, faster selections, identifying which genes are important for disease resistance, larger seed heads, and other key traits. Breeders can also use these fingerprints to identify and help conserve Silphium genetic diversity hotspots, which are key to studying how genetic and species diversity help regulate the spread of infectious diseases in prairies and perennial grain fields. 

The next step for the authors is to scale up genotyping to enable fingerprinting thousands of plants each year, possibly by pooling efforts across institutions to achieve cost efficiency. The team will also follow up on finding that several of Silphium's chromosomes are gigantic and may have an unusual structure. These genomic anomalies may need to be considered to optimize breeding and genetic conservation efforts.

Species in the genus Silphium range across the eastern and central prairies, grasslands, and plains of the United States and southern Canada. These ecosystems have evolved with grazing and burning and feature landscapes known and tended by numerous Indigenous communities, who have long-standing relationships with Silphium. The Land Institute researchers and collaborators are investigating the cultural dynamics of crop domestication and ethical approaches to data governance, including initial ethnobotanical research and engagement, development of educational materials, and testing of participatory civic science methods.