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Plant height (PH) is a crucial trait determining plant architecture in chrysanthemum. To better understand the genetic basis of PH, we investigated the variations of PH, internode number (IN), internode length (IL), and stem diameter (SD) in a panel of 200 cut chrysanthemum accessions. Based on 330 710 high-quality SNPs generated by genotyping by sequencing, a total of 42 associations were identified via a genome-wide association study (GWAS), and 16 genomic regions covering 2.57 Mb of the whole genome were detected through selective sweep analysis. In addition, two SNPs, Chr1_339370594 and Chr18_230810045, respectively associated with PH and SD, overlapped with the selective sweep regions from FSTand π ratios. Moreover, candidate genes involved in hormones, growth, transcriptional regulation, and metabolic processes were highlighted based on the annotation of homologous genes in Arabidopsisand transcriptomes in chrysanthemum. Finally, genomic selection for four PH-related traits was performed using a ridge regression best linear unbiased predictor model (rrBLUP) and six marker sets. The marker set constituting the top 1000 most significant SNPs identified via GWAS showed higher predictabilities for the four PH-related traits, ranging from 0.94 to 0.97. These findings improve our knowledge of the genetic basis of PH and provide valuable markers that could be applied in chrysanthemum genomic selection breeding programs.

MYB transcription factors are widely involved in the development of and physiological processes in plants. Here, we isolated the chrysanthemum R2R3-MYB family transcription factor CmMYB15, a homologous gene of AtMYB15. It was demonstrated that CmMYB15expression was induced by aphids and that CmMYB15 could bind to AC elements, which usually exist in the promoter of lignin biosynthesis genes. Overexpression of CmMYB15in chrysanthemum enhanced the resistance of aphids. Additionally, the content of lignin and the expression of several lignin biosynthesis genes increased. In summary, the results indicate that CmMYB15regulates lignin biosynthesis genes that enhance the resistance of chrysanthemum to aphids.

Chrysanthemum Fusarium wilt is a soil-borne disease that causes serious economic losses to the chrysanthemum industry. However, the molecular mechanism underlying the response of chrysanthemum WRKY to Fusarium oxysporuminfection remains largely unknown. In this study, we isolated CmWRKY6–1from chrysanthemum ‘Jinba’ and identified it as a transcriptional repressor localized in the nucleus via subcellular localization and transcriptional activation assays. We found that CmWRKY6–1negatively regulated resistance to F. oxysporumand affected reactive oxygen species (ROS) and salicylic acid (SA) pathways using transgenic experiments and transcriptomic analysis. Moreover, CmWRKY6–1bound to the W-box element on the CmWRKY15-likepromoter and inhibited its expression. Additionally, we observed that CmWRKY15-likesilencing in chrysanthemum reduced its resistance to F. oxysporumvia transgenic experiments. In conclusion, we revealed the mechanism underlying the CmWRKY6–1–CmWRKY15-like cascade response to F. oxysporuminfection in chrysanthemum and demonstrated that CmWRKY6–1and CmWRKY15-likeregulates the immune system.

The Mildew Resistance Locus O(MLO) gene family has been investigated in many species. However, there are few studies on chrysanthemum MLOgenes. We report in this study that CmMLO17in Chrysanthemum morifoliumwas upregulated after Alternaria alternatainfection. Silencing of CmMLO17by artificial microRNA resulted in reduced susceptibility of chrysanthemum to A. alternatainfection. Genes in the abscisic acid (ABA) and Ca2+signaling pathways were upregulated in the CmMLO17-silenced line R20 compared to the wild-type plants. We speculated that CmMLO17-silenced plants had a faster and stronger defense response that was mediated by the ABA and Ca2+signaling pathways, resulting in reduced susceptibility of chrysanthemum to A. alternatainfection. In addition, a candidate gene, CmKIC, that may interact with CmMLO17 was discovered by the yeast two-hybrid assay. The interaction between CmMLO17 and CmKIC was confirmed using the yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC) analysis. CmMLO17 and CmKIC were both located on the plasma membrane, and CmKIC was also located on the nucleus. CmKICoverexpression increased the susceptibility of chrysanthemum to A. alternata, whereas CmKICsilencing resulted in reduced susceptibility. Therefore, CmMLO17 and CmKIC may work together in C. morifoliumto support the growth of A. alternata. The results of this study will provide insight into the potential function of MLO and improve the understanding of plant defense responses to necrotrophic pathogens.

Chrysanthemum (Chrysanthemum morifolium) black spot disease (CBS) poses a major threat to Chrysanthemum cultivation owing to suitable climate conditions and current lack of resistant cultivars for greenhouse cultivation. In this study, we identified a number of genes that respond to Alternaria alternatainfection in resistant and susceptible Chrysanthemum cultivars. Based on RNA sequencing technology and a weighted gene coexpression network analysis (WGCNA), we constructed a model to elucidate the response of Chrysanthemum leaves to A. alternatainfection at different stages and compared the mapped response of the resistant cultivar ‘Jinba’ to that of the susceptible cultivar ‘Zaoyihong’. In the early stage of infection, when lesions had not yet formed, abscisic acid (ABA), salicylic acid (SA) and EDS1-mediated resistance played important roles in the Chrysanthemum defense system. With the formation of necrotic lesions, ethylene (ET) metabolism and the Ca2+signal transduction pathway strongly responded to A. alternatainfection. During the late stage, when necrotic lesions continued to expand, members of the multidrug and toxic compound extrusion (MATE) gene family were highly expressed, and their products may be involved in defense against A. alternatainvasion by exporting toxins produced by the pathogen, which plays important roles in the pathogenicity of A. alternata. Furthermore, the function of hub genes was verified by qPCR and transgenic assays. The identification of hub genes at different stages, the comparison of hub genes between the two cultivars and the highly expressed genes in the resistant cultivar ‘Jinba’ provide a theoretical basis for breeding cultivars resistant to CBS.