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Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing. Nakano et al. sequenced the genome of a model species for hexaploid cultivated chrysanthemum, an important cut flower. While they investigated evolution, duplication events, and a novel retrotransposon in this study, they also demonstrated the translational implication of the genome sequence in breeding the economically important plant. [ABSTRACT FROM AUTHOR]

It has long been proposed that white-flowered chrysanthemums ( Chrysanthemum morifolium Ramat.) have a single dominant gene that inhibits carotenoid formation or accumulation in ray petals. However, the precise function of the proposed gene was unknown. We previously isolated a gene encoding carotenoid cleavage dioxygenase 4, designated CmCCD4a, which is specifically expressed in the ray petals of white-flowered chrysanthemums. Because CmCCD4a was a strong candidate for the single dominant gene, we analyzed the relationship between CmCCD4a expression and carotenoid content in two sets of petal color mutants. Here, we show that CmCCD4a represents a small gene family containing at least four members. Two of them, CmCCD4a- 1 and CmCCD4a- 2, were highly expressed in ray petals of two taxa with low carotenoid levels. In petal color mutants derived from these taxa, increases in carotenoid levels accompanied decreases in CmCCD4a expression levels in ray petals. Two different circumstances reduced the levels of CmCCD4a expression in the mutants: either a CmCCD4a gene was lost from the genome or the expression of a CmCCD4a gene was suppressed. In the latter case, suppression may be caused by the loss of a function that normally enhances CmCCD4a transcription. A stepwise decrease in the amount of CmCCD4a expression in either L1 or L2 resulted in a corresponding stepwise increase in the carotenoid content in ray petals. From these results, we propose that CmCCD4a expression is the key factor that controls the carotenoid content in ray petals of chrysanthemum. [ABSTRACT FROM AUTHOR]

Most chrysanthemum ( Chrysanthemum morifolium Ramat.) flowers have a central capitulum, composed of many disc florets that is surrounded by ray petals. CmCCD4a, a gene that encodes a carotenoid cleavage dioxygenase (CCD), is expressed specifically in the ray petals of chrysanthemum cultivars, and its expression leads to white ray petals as a result of carotenoid degradation. Here, we show that wild chrysanthemums with white ray petals have CmCCD4a orthologs, whereas those with yellow ray petals lack these orthologs, as is the case in chrysanthemum cultivars. CmCCD4a orthologs also exist in some lines of Chrysanthemum pacificum and Chrysanthemum shiwogiku, even though these species lack ray petals. Interspecific hybridization between C. shiwogiku and a yellow-flowered chrysanthemum cultivar showed that the CmCCD4a orthologs from C. shiwogiku lead to the development of white ray petals. This indicates that the translation products of the CmCCD4a orthologs maintain enzymatic activity that can degrade carotenoids in chrysanthemums, irrespective of whether or not the ray petals that CmCCD4a expression actually occurred. [ABSTRACT FROM AUTHOR]

Bacterial wilt caused by Burkholderia caryophylli is one of the most important and damaging diseases of carnations (Dianthus caryophyllus) in Japan. We aimed to identify random amplified polymorphic DNA (RAPD) markers associated with the genes controlling bacterial wilt resistance in a resistance-segregating population of 134 progeny plants derived from a cross between ‘Carnation Nou No. 1’ (a carnation breeding line resistant to bacterial wilt) and ‘Pretty Favvare’ (a susceptible cultivar). We screened a total of 505 primers to obtain RAPD markers useful for selecting resistant carnation lines: 8 RAPD markers identified by bulked segregant analysis were linked to a major resistance gene; of these, WG44-1050 had the greatest effect on resistance to bacterial wilt. A locus with large effect on bacterial resistance was mapped around WG44-1050 through QTL analysis. The RAPD marker WG44-1050 was successfully converted to a sequence-tagged site (STS) marker suitable for marker-assisted selection (MAS). Five combinations of primers were designed for specific amplification of WG44-1050. In addition, the STS marker we developed was useful and reliable as a selection marker for breeding for resistance to bacterial wilt, using a highly resistant wild species, D. capitatus ssp. andrzejowskianus and a resistant line, ‘Carnation Nou No. 1’, as breeding materials. [ABSTRACT FROM AUTHOR]

In vegetatively propagated plants, branches of periclinal chimera give rise to bud mutants, or `sports', which have been used to breed new cultivars. Here, we have examined DNA methylation profiles in the cells of the L1 and L2+3 layers from single plants of vegetatively propagated carnations. The band patterns of methylation-sensitive amplified fragment polymorphism (M-AFLP) of the genomic DNAs in the L1 and L2+3 layers of the carnation cultivar, `White Sim', vegetatively propagated over the past 50 years, were completely different. The bud mutant, `White Mind', obtained from `White Sim' about 25 years ago, also had very different M-AFLP patterns to the parental `White Sim' line. The cultivar, `Red', which was separated from `Satisfaction' as a bud mutant two years ago, showed similar patterns to `Satisfaction' in each corresponding layer. However, we were able to detect minor, but significantly different M-AFLP patterns between the cultivars, `Red' and `Satisfaction'. The number of bands that differed between these cultivars was larger in the L2+3 layers than in the L1 layers. The results indicate that the DNA methylation profiles differ between each cell layer derived from distinct cell lineages of vegetatively propagated plants, and that changes in these profiles occur frequently and accumulate in the cells of the L2+3 layers, rather than in the L1 layer. [ABSTRACT FROM AUTHOR]