RESOLVING THE LEDGER
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Add as preferred source 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 domesticating wild, deep-rooted Silphium species native to North American prairies into perennial crops for food, fiber, forage and medicine.
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.
Highlighting the significance of this genomic milestone, David Van Tassel, lead scientist for the Perennial Oilseeds Program at The Land Institute, said: "Wild perennial species could help improve food security by contributing sustainability-enhancing traits such as deep roots. Genomics-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."
"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," said 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 of 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 the 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.
The research was conducted by a diverse group of institutions, including The Land Institute, HudsonAlpha Institute for Biotechnology, University of Minnesota, Donald Danforth Plant Science Center, USDA ARS, University of Iowa, Savanna Institute, Saint Louis University, University of Georgia and Clemson University. Seeds for multiple local Silphium species and genotypes were donated by the Missouri Botanical Garden and the Southeastern Grasslands Institute.
Renan S. Souza et al, Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding, Nature Communications (2026). DOI: 10.1038/s41467-026-75205-3
Journal information: Nature Communications
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