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.

中文翻译：

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具有野生二倍体参考基因组的六倍体菊花品种抗白锈病的全基因组关联和精细定位研究。

由Puccinia horiana引起的白锈病是菊花（Chrysanthemum × morifolium）最严重的病害之一。在这项研究中，我们通过使用野生二倍体亲缘菊花的基因组的简单方法报告了与对 P. horiana 抗性相关的 DNA 标记。首先，我们通过全基因组关联研究确定了抗性品种“Ariesu”基因组的重要区域。从 ddRAD-Seq 挖掘的单纯性单核苷酸多态性 (SNP) 标记用于源自抗性“Ariesu”和易感“黄皇后”之间杂交的双亲群体。C. seticuspe 基因组用作参考。对于 P. horiana 抗性基因座 2 (Phr2) 的精细定位，进行了比较全基因组测序研究。尽管通过短读长方法组装的菊花品种的基因组序列是片段化的，但通过映射到 C. seticuspe 假分子的染色体水平上重建了可靠的基因组比对。然后通过比较抗性“Ariesu”和易感“Yellow Queen”的组装基因组序列来鉴定碱基变体。因此，获得了与 ddRAD-Seq 标记相比更接近 Phr2 的 SNP 标记。这些 SNP 标记与源自抗性“Ariesu”的 F1 后代中的抗性共分离，并显示出强大的可转移性，用于检测菊花遗传资源中赋予 Phr2 的抗性。野生的 C. seticuspe 假分子，一种事实上的单倍体基因组，用于 ddRAD-Seq 分析和组装的基因组序列比较，