Wild genes to the rescue: High-throughput genomics uncovers the wild source of broomrape resistance in sunflower

Abstract

Summary The ongoing evolutionary arms race between crop plants and their parasites necessitates a constant exploration of new genetic resistance. Broomrape ( Orobanche cumana ), a devastating parasitic plant, presents a formidable challenge to sunflower production, yet the genetic mechanisms underlying host resistance are still largely unknown. To address this gap, we developed a high-throughput phenotyping platform to quantify root infestation in a highly diverse sunflower association mapping (SAM) population. Using a dual GWAS approach with both SNPs and k-mers, we were able to pinpoint the genetic basis of resistance. Our findings validate previously identified QTLs with greater resolution and reveal several novel candidate genes conferring resistance, including putative leucine-rich repeat receptor kinases. Critically, the k-mer mapping approach circumvented reference genome bias, highlighting key introgressions from wild Helianthus species that have contributed to broomrape resistance. This research provides a powerful methodology for gene discovery and demonstrates that wild relatives remain a vital source of genetic material, offering breeders a significant advantage in the ongoing battle against rapidly evolving parasites.

Code and data availability

The paper describes a rhizotron phenotyping platform, image analysis, and SNP/k-mer GWAS for broomrape resistance in the SAM population, but no block contains author-deposited phenotype datasets, root images, analysis code, or trained models with a public URL. The genotype data were obtained from the pre-existing sunfl

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