Whole-genome sequencing enables molecular dissection and candidate gene identification of the rust resistance gene R in sunflower (Helianthus annuus L.).

We finely mapped the rust resistance gene R to a 0.1248-cM region, identified a potential R candidate gene in the XRQ reference genome, and developed three diagnostic SNP markers for R. Rust is a devastating disease in sunflower that is damaging to the sunflower production globally. Identification and utilization of host-plant resistance are proven to be preferable means for disease control. The rust resistance gene R with broad-spectrum specificity to rust was previously localized to a 2.4 Mb region on sunflower chromosome 11. To understand the molecular mechanism of resistance, we conducted whole-genome sequencing of RHA 464 (R donor line) and reference genome-based fine mapping of the gene R. Overall, the 213 markers including 186 SNPs and 27 SSRs' were identified from RHA 464 sequences and used to survey polymorphisms between the parents HA 89 and RHA 464. Saturation mapping identified 26 new markers positioned in the R region, and fine mapping with a large population of 2004 individuals positioned R at a genetic distance of 0.1248 cM flanked by SNP markers C11_150451336 and S11_189205190. One gene, HanXRQChr11g0348661, with a defense-related NB-ARC-LRR domain, was identified in the XRQr1.0 genome assembly in the R region; it is predicted to be a potential R candidate gene. Comparative analysis clearly distinguished R from the rust R gene located in the vicinity of the R gene on chromosome 11. Three diagnostic SNP markers, C11_147181749, C11_147312085, and C11_149085167, specific for R were developed in the current study, facilitating more accurate and efficient selection in sunflower rust resistance breeding. The current study provides a new genetic resource and starting point for cloning R in the future.