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

Abstract

The co-evolutionary arms race between crops and their parasites requires continuous identification of new resistance mechanisms. Broomrape (Orobanche cumana), a root parasitic plant, poses a severe threat to sunflower (Helianthus annuus) production, yet the genetic architecture underlying host resistance remains poorly understood. To address this, we established a high-throughput phenotyping platform to quantify root infestation across a diverse sunflower association mapping (SAM) population. Combining this phenotypic resource with a dual genome-wide association study (GWAS) strategy based on both single nucleotide polymorphisms (SNPs) and k-mers, we highlight the genetic basis of broomrape resistance at unprecedented resolution. Our analyses revealed quantitative trait loci (QTLs) and identified novel candidate genes, including putative leucine-rich repeat receptor kinases potentially involved in parasite recognition and defense activation. Importantly, the k-mer approach circumvented reference genome bias and uncovered key genomic introgressions from wild Helianthus relatives that contribute substantially to resistance. These findings demonstrate the utility of integrating high-resolution phenotyping with advanced association mapping to dissect complex host-parasite interactions. Moreover, they emphasize the enduring value of wild germplasm as a reservoir of adaptive variation, providing crop breeders with crucial tools to counter the rapid evolutionary dynamics of parasitic plants.

Code and data availability

The paper's Data availability statement explicitly deposits the paper-specific raw phenotyping images on Zenodo, the k-mer genotype data on the sunflower genome database, and the authors' analysis code on the Hübner lab GitHub repository, all with public URLs.