On the surface, the sunflower is a familiar plant — cheerful, towering, and iconic. But beneath those golden petals lies a genetic world far stranger and more complex than most of us ever imagined.
Loren Rieseberg, a biologist at the University of British Columbia who spoke this week at the National Association for Plant Breeding (NAPB) meeting in Kona, Hawai’i, has spent his career pulling back the curtain on that hidden world. His work has revealed that wild sunflowers — and their cultivated cousins — are genomic kaleidoscopes, shaped by structural variations so profound they’re redefining how we think about evolution, adaptation, and plant breeding.
Rieseberg took the stage at the NAPB meeting May 20 for the first plant breeding conference of his career. With decades of evolutionary biology behind him and a growing interest in applied genomics, he delivered a talk that made even veteran breeders rethink what they knew about their crops.
“Structural variants — like deletions, duplications, translocations, and inversions — are not the exception in plant genomes,” Rieseberg explains. “They’re the rule.”
Supergenes in a Sunflower’s Shadow
These structural changes don’t just affect a few stray base pairs. In fact, they account for more genomic variation than single nucleotide polymorphisms (SNPs), the traditional darlings of genetic studies.
In sunflowers, Rieseberg’s team found tens of thousands of copy number variants, thousands of translocations, and hundreds of inversions — all within a small group of cultivated genotypes. And these are not minor tweaks. Some of the inversions span over 100 megabases — two-thirds the size of the entire Arabidopsis genome.
The kicker? These rearrangements don’t just shuffle the genome — they reshape it. Many of them suppress recombination, affect hybrid fertility, and create what Rieseberg calls “supergenes”: regions of the genome that bundle together traits for local adaptation. They’re like nature’s own prepackaged trait kits — tuned to survive extremes of drought, heat, and nutrient-poor soils.
Take the wild Helianthus petiolaris, which survives on sand dunes along Texas’ coast. Its massive seeds help seedlings tap deep water reserves. Rieseberg’s team traced this adaptation — and many others, from flowering time to nutrient use — to large chromosomal inversions. The genomic message was clear: these structural changes were not only real but essential.
A Breeding Paradox
But here’s the catch. While these structural variants can offer adaptive superpowers, they come with serious baggage.
In cultivated sunflowers, for instance, introducing resistance genes from wild relatives — especially from more genetically distant species — often leads to reduced seed size, lower oil content, or smaller heads. That’s because the translocated or inverted regions frequently drag along other, unwanted traits.
“We saw consistent negative trade-offs,” says Rieseberg. “Introgressions from the secondary gene pool nearly always decreased performance in key agronomic traits.”
It’s a sobering insight for breeders who rely on wild relatives to diversify their crop genetics. You can get the disease resistance — but at a cost. Sometimes, a big one.
Can we Outsmart the Genome?
So, what’s the way forward?
One option is precision: choosing breeding lines that naturally complement deleterious introgressions. Another is innovation: flipping inversions back using CRISPR-based technologies. In Arabidopsis, researchers have already shown this can restore recombination in inverted regions.
But perhaps the most practical takeaway is deceptively simple — go back to the basics. Primary gene pools, Rieseberg emphasized, often hold the same valuable traits as more exotic species, minus the genomic chaos. You just have to look harder.
“There’s almost always a version of the trait you need in the primary germplasm,” he says. “It might not be obvious at first. But it’s there.”
