Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy “flowers” through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia “Chiang Mai Pink” and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifolia cultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3′5'H, DFR, ANS and several transcription factors for anthocyanin synthesis, as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifolia and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family.

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3′H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.

Curcuma is extensively cultivated as a medicinal and ornamental plant in tropical and subtropical regions. Due to the bright bract color, distinctive inflorescence and long blooming period, it has become a new favorite in terms of the urban landscape, potted flowers and cut flowers. However, little research on breeding new cultivars using traditional plant breeding methods is available on the genus Curcuma. In the present study, pollen viability and stigma receptivity evaluation were performed, and the genetic relationship of 38 Curcuma accessions was evaluated, then 5 C. alismatifolia Gagnep. (Ca), 2 C. hybrid (Ch), 2 C. sparganiifolia Gagnep. cultivars and 4 Curcuma native species were selected as parents for subsequent interspecific cross-breeding. A total of 132 reciprocal crosses were carried out for interspecific hybridization, including 70 obverse and 62 inverse crosses. Obvious discrepancies among fruit-setting rates were manifested in different combinations and in reciprocal crosses. Results showed that the highest fruit-setting rate (87.5%) was observed in the Ca combinations. There were 87 combinations with a fruit-setting rate of 0%, which meant nearly 65.9% was incompatible. We concluded that C. alismatifolia ‘Siam Shadow’ (Ch34) was suitable as a male parent and C. petiolata Roxb. (Cpet) was suitable as a female parent to improve the fruit-setting rates. The maximum number of seeds per fruit (45.4) was obtained when C. alismatifolia ‘Chiang Mai Pink’ (Ca01) was used as a female parent followed by C. attenuata Wall. ex Baker (Catt) (42.8) and C. alismatifolia ‘Splash’ (Ca63) (39.6) as male parents. The highest germination rate was observed for the Ca group followed by Catt and C. sparganiifolia ‘Maetang Sunrise’ (Csms). The germination rates of Ca accessions ranged from 58.2% (C. alismatifolia ‘Siam Scarlet’ (Ca06) as a male parent) to 89.3% (C. alismatifolia ‘Sitone’ (Ca10) as a male parent) with an average value of 74.0%. Based on the results of hybrid identification, all the individuals from the four combinations exhibited paternal-specific bands, indicating that the true hybrid rates of crossings were 100%. Our results would facilitate the interspecific hybridization and introduction of genetic variation from wild species into the cultivars in Curcuma in the future, which could be helpful in realizing the sustainable application in urban green areas.

Caladiums are promising colorful foliage plants due to their dazzling colors of the leaves, veins, stripes, and patches, which are often cultivated in pots or gardens as decorations. Four wild species, including C. bicolor, C. humboldtii, C. praetermissum, and C. lindenii, were employed in this study, where their chloroplast (cp) genomes were sequenced, assembled, and annotated via high-throughput sequencing. The whole cp genome size ranged from 162,776 bp to 168,888 bp, and the GC contents ranged from 35.09% to 35.91%. Compared with the single large copy (LSC) and single small copy (SSC) regions, more conserved sequences were identified in the inverted repeat regions (IR). We further analyzed the different region borders of nine species of Araceae and found the expansion or contraction of IR/SSC regions might account for the cp genome size variation. Totally, 131 genes were annotated in the cp genomes, including 86 protein-coding genes (PCGs), 37 tRNAs, and eight rRNAs. The effective number of codons (ENC) values and neutrality plot analyses provided the foundation that the natural selection pressure could greatly affect the codon preference. The GC₃ content was significantly lower than that of GC₁ and GC₂, and codons ending with A/U had higher usage preferences. Finally, we conducted phylogenetic relationship analysis based on the chloroplast genomes of twelve species of Araceae, in which C. bicolor and C. humboldtii were grouped together, and C. lindenii was furthest from the other three Caladium species occupying a separate branch. These results will provide a basis for the identification, development, and utilization of Caladium germplasm.

Caladiums are promising colorful foliage plants due to their unique leaf shapes and dazzling colors. Until now, over 2000 varieties of Caladium have been cultivated worldwide. The long-term natural variation and artificial selection have enriched the germplasm resources of Caladium in the market, yet have blurred its genetic background. In this study, 16 informative EST-SSR markers were used to screen 144 Caladium accessions, indicating that 16 EST-SSRs could distinguish all genotypes with a minimum cumulative identity probability (PI) of 2.0 2 × 10⁻¹⁵. Using the simulated annealing method, the richest genetic information was acquired at the same compression ratio. A final core of 44 accessions was selected, comprising 30.6% of the individuals and retraining more than 95% of the total genetic information. No significant differences were observed in allele frequency distributions or genetic diversity parameters between the core collection and the entire population. Cluster analysis roughly divided the core collections into four populations, where 66.7% of the private alleles were detected in Pop2. Finally, DNA molecular fingerprints of 44 core accessions were established, including barcodes and quick response (QR) code molecular identities (ID). The results will lay a theoretical foundation for identifying, preserving, and utilizing Caladium germplasm resources.