Expanding the disease-resistance gene repertoire for sunflower breeding through pan-genomic insights

Sunflower presents substantial variability across genotypes in their resistance response to pathogen attacks. A significant part of the reported resistance was inherited from wild relatives through years of conventional breeding. Nevertheless, most of the underlying causative resistance genes remain unknown, thus limiting their application in targeted breeding. Here, we present the identification and characterization of a comprehensive repertoire of disease-resistance genes for the species. First, we complemented the collection of disease-resistance genes previously reported by performing a de novo annotation of the reference genome. Then, given that a single genome does not provide the entire gene repertoire of a species, we analysed sequencing data from 100 cultivated Helianthus accessions and 49 wild relatives, and performed a de novo assembly of reads that did not map to the reference genome to identify disease-resistance pan-genes. A total of 1,365 disease-resistance genes were identified, 198 of which were absent from the reference genome. Genes were not evenly distributed either between or within chromosomes, and a large proportion were arranged in clusters located closer than expected to transposable elements. Polymorphisms (i.e. SNPs, short indels and large deletions) in these genes were also identified. In addition, differential expression analyses under fungal inoculation showed that 481 disease-resistance genes were differentially expressed in at least one genotype. A panel of 33 disease-resistance genes linked to previously reported QTL, including ten that were also differentially expressed after inoculation, together with their associated polymorphisms and five accessions carrying the highest number of disease-resistance genes, emerge as promising resources for assisted breeding. Overall, this study expands the catalogue of resistance genes, variants, and breeding-relevant resources in sunflower.