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Article|03 Aug 2022|OPEN
A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome
Katsuhiko Sumitomo1 , , Kenta Shirasawa2 , Sachiko Isobe2 , Hideki Hirakawa2 , Akiho Harata3,4 , Michiharu Nakano5,6 , Yoshihiro Nakano1 , Masafumi Yagi1 and Tamotsu Hisamatsu1 , Hiroyasu Yamaguchi1 , Fumiya Taniguchi,7
1Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
2Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
3Kagoshima Prefectural Institute for Agricultural Development, Minamisatsuma, Kagoshima 899-3401, Japan
4CCS Inc., Kyoto, Kyoto 602-8019, Japan
5Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
6Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi 783-8502, Japan
7Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
*Corresponding author. E-mail:

Horticulture Research 9,
Article number: uhac170 (2022)
Views: 326

Received: 10 Mar 2022
Accepted: 25 Jul 2022
Published online: 03 Aug 2022


White rust caused by Puccinia horiana is one of the most serious diseases of chrysanthemum (Chrysanthemum × morifolium). In this study, we report the DNA markers associated with resistance against P. horiana via a simple approach using the genome of a wild diploid relative, Chrysanthemum seticuspe. 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 C. seticuspe genome was used as a reference. For the fine mapping of P. horiana resistance locus 2 (Phr2), 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 C. seticuspe 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 Phr2 compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F1 progenies originating from resistant “Ariesu” and showed robust transferability for detecting Phr2-conferring resistance among chrysanthemum genetic resources. The wild C. seticuspe pseudomolecule, a de facto 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.