b'GIANT VIEWSOVERLOOKED MUTATIONS ARE WHY YOURHYBRID ISNT PERFORMINGI DIDNT EXPECTto end up here. Among all SVs, inversions are the When I began my career as an evolutionary biologist, Imost insidiousand the most fascinat-imagined fieldwork, maybe some molecular bench work, anding. Because they dont always harm a quiet academic life. I didnt anticipate talking to geneticists,fertility, they tend to go undetected. breeders, and data scientists about why their most frustratingYet they quietly suppress recombination obstacles arent about yield or resistance, but hidden deep insideacross vast genomic regions, effectively the structure of plant genomes. locking together adaptive alleles into But here I ambecause theres something weve missed. what we call supergenes.The real game-changer of the genomic era hasnt beenIt sounds elegantnature bundling single nucleotide polymorphisms (SNPs). Sure, SNPs gave ususeful traits into single, inheritable By Loren Rieseberg,fine-scale resolution and neat genome-wide association studyblocks. But those bundles often come Professor,(GWAS) signals. But the real beasts the hidden forces steer- with a catch. One inversion might boost Department ofing everything from trait inheritance to hybrid sterilityareseed size, surebut it may also reduce BotanyUniversity of British Columbia structural variants. oil content or delay flowering. Thats the Im talking about deletions, duplications, inversions anddouble-edged sword breeders live with.translocations. This isnt just a sunflower story. These are not minor anomalies. Theyre massive. They affectSimilar patterns are now emerging in far more of the genome than SNPs ever will. And theyre notmaize, barley and more. Structural varia-just commontheyre consequential. tion is turning out to be a near-universal Sunflowers, as it turns out, are the perfect model for thislanguage for local adaptation in plants.structural complexity, even though theyre terrible in manySo, whats the breeding takeaway?other ways. Theyre large, hard to transform, and slow toYes, you can harness these supergenes work with. But their genome? Its like a structural variationfor stress tolerance and climate adapta-theme park. tion. But you have to understand the When we sequenced 10 cultivated sunflower genomes, wetrade-offs. found ~12 million SNPs. Not bad. But alongside those wereSo where does this leave us?~40,000 copy number variants, 10,000 translocations, and sev- Structural variation isnt a nuisance eral hundred inversions. This isnt just messy. Its foundationallyto be managedits the architecture of different from what we expected. evolution. These rearrangements define And it matters. how traits move (or dont move) through When breeders try to bring in traits from wild relatives breeding populations. They create oppor-say, resistance to broomrape or Sclerotiniathey often runtunity and constraint, simultaneously. into a wall. That wall isnt the trait itself. Its the structural rear- We cant ignore them anymore.rangements. These changes suppress recombination and make itIf we want to future-proof our crops nearly impossible to cleanly integrate new alleles without drag- for climate, disease, and demand, we ging along a mess of unwanted genetic baggage. Worse, someneed to build tools and strategies that rearrangements trigger hybrid sterility outright. respect the structural architecture of the Take Helianthus debilis, a close sunflower cousin oftengenome. That means sequencing more tapped for introgression. It differs from cultivated sunflower bypangenomes, mapping SVs across popula-eight large translocations. Try crossing the two, and youll findtions, and using gene editing to decouple yourself fighting suppressed recombination and plummetingtrait trade-offs, and designing breed-seed viability. ing programs that recognize when the It raises a big evolutionary question: If structural vari- roadblock isnt the geneits the context ants reduce fitness, how do they become established? We usedit lives in.to think this was due to chance (i.e., genetic drift). Now, weThe genomic revolution gave us suspect something else female meiotic drive, in which selfishsharper questions. The answers will genetic elements compete for inclusion in the egg, with thedecide the future of breedingand structural variants along for the ride. Either way, theyre notwhether were ready to work with natures going anywhere. blueprints, instead of against them. 40 SEEDWORLD.COM/CANADAJULY 2025'