A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome.

White rust caused by is one of the most serious diseases of chrysanthemum ( × ). In this study, we report the DNA markers associated with resistance against via a simple approach using the genome of a wild diploid relative, . First, we identified the important region of the genome in the resistant cultivar "Ariesu" via a genome-wide association study. Simplex single nucleotide polymorphism (SNP) markers mined from ddRAD-Seq were used in a biparental population originating from crosses between resistant "Ariesu" and susceptible "Yellow Queen". The genome was used as a reference. For the fine mapping of resistance locus 2 (), a comparative whole genome sequencing study was conducted. Although the genome sequences of chrysanthemum cultivars assembled via the short-read approach were fragmented, reliable genome alignments were reconstructed by mapping onto the chromosome level of the pseudomolecule. Base variants were then identified by comparing the assembled genome sequences of resistant "Ariesu" and susceptible "Yellow Queen". Consequently, SNP markers that were closer to compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F progenies originating from resistant "Ariesu" and showed robust transferability for detecting -conferring resistance among chrysanthemum genetic resources. The wild pseudomolecule, a monoploid genome used for ddRAD-Seq analysis and assembled genome sequence comparison, demonstrated this method's utility as a model for developing DNA markers in hexaploid chrysanthemum cultivars.