Leaf morphology plays a crucial role in photosynthetic efficiency, environmental adaptation, and stress tolerance. Most Rosa species produce odd-pinnate compound leaves, whereas Rosa persica is the only species with simple leaves. In the wild, a naturally occurring deep-lobed leaf variant resembling a near-compound leaf was identified, providing a unique model for studying leaf development in woody plants. In this study, we aimed to characterize the NAC transcription factor family in R. persica and to investigate their roles in leaf margin morphogenesis. The NAC gene family was comprehensively analyzed using various bioinformatic approaches, including physicochemical property characterization, collinearity analysis and phylogenetic analyses, etc. Furthermore, WGCNA and expression profiling allowed the identification of five RpNAC genes, whose functions were subsequently investigated through subcellular localization, transcriptional activation assays, and heterologous overexpression in Arabidopsis thaliana. Candidate RpNAC proteins were nuclear-localized and exhibited transcriptional activation. Overexpression of RpNAP1 and RpNAC090.2 in Arabidopsis led to wavy leaf margins, increased leaf width, and enhanced chlorophyll content, indicating their important roles in leaf morphology and potential involvement in plant photosynthesis. These findings provide novel insights into the mechanism controlling leaf margin development in Rosa species and may facilitate targeted breeding of ornamental and stress-resilient traits.

Anthocyanin accumulation is a vital agronomic and ornamental trait, as it not only contributes to adaptation to environmental stress but also enhances ornamental value. In this study, a genome-wide association study (GWAS) was conducted using 328 accessions of mei (Prunus mume) to identify single nucleotide polymorphisms (SNPs) associated with red pigmentation in petals, filaments, and xylem. Based on these significant SNPs, we defined two haplotypes (bHLH162hap1 and bHLH162hap2) and identified PmbHLH162, a bHLH transcription factor gene responsible for anthocyanin biosynthesis regulation. Transient silencing of PmbHLH162 in mei petals via Agrobacterium-mediated transformation resulted in significant color fading, whereas its overexpression dramatically elevated anthocyanin levels. Haplotype analysis showed that two promoter variants in bHLH162hap2 (Chr03_2669885 A/C and Chr03_2670272 A/G) alter the binding affinity of transcription factors PmWRKY18 and PmWRKY70. Stronger binding to the G/C alleles gave rise to higher PmbHLH162 expression in bHLH162hap2, thereby promoted red pigmentation in multiple tissues. By contrast, accessions carrying bHLH162hap1 displayed light/colorless phenotype without accumulation of red pigment. Furthermore, PmbHLH162 interacted respectively with PmMYC2, PmTT8, and PmEGL1 to form heterodimers, and markedly enhanced PmMYC2-mediated transcriptional activation of the anthocyanin biosynthetic structural genes PmCHS and PmANS. Geographic haplotype analysis revealed that bHLH162hap2 was predominantly enriched in high-latitude northern populations but was declining markedly at lower latitudes. Collectively, our study reveals the genetic and molecular basis underlying anthocyanin accumulation in mei and identifies a PmbHLH162-PmMYC2 regulatory module in which PmbHLH162 enhances PmMYC2-mediated activation of key anthocyanin biosynthetic genes. The additional interactions of PmbHLH162 with the MBW-associated bHLH factors PmTT8 and PmEGL1 further suggest potential crosstalk between this module and the canonical anthocyanin regulatory network.

Double-flowered cultivars are generally considered more attractive than single-flowered varieties in ornamental plants. The AP2/ERF transcription factors superfamily plays pivotal roles in plant development, including floral organ formation. Here, a total of 248 AP2/ERF genes were identified in the genome of L. speciosa, and these genes were unevenly distributed on the 24 chromosomes. Phylogenetic analysis classified LsAP2/ERF genes into five distinct groups; the ERF subfamily was the largest, whereas the AP2 subfamily was associated with floral development. Gene duplication events contributed to the expansion of LsAP2/ERF family members, with segmental duplication identified as the primary contributor. Promoter cis-element analysis revealed an abundance of light-responsive and hormone-responsive elements. Spatiotemporal expression profiling showed that core AP2 subfamily members (LsAP2/ERF4/9/10/13/219) exhibited distinct expression patterns during flower bud development. Moreover, heterologous overexpression of LsAP2/ERF10 in tobacco resulted in transgenic lines with altered petal morphology, supporting its potential functional involvement in floral development. This study provides comprehensive characterization of the AP2/ERF family in L. speciosa, laying the foundation for elucidating its molecular mechanisms in floral morphogenesis.

Rosa xanthina, an important species for landscaping and ecological restoration in northern China, possesses strong drought tolerance. However, the molecular mechanisms underlying its drought stress response remain unclear. In this study, we systematically analyzed the physiological changes and transcriptomic responses of two-year-old R. xanthina plants to drought stress (including control, light drought, moderate drought, and severe drought treatments) and subsequent rewatering. Additionally, we conducted a specific examination of the NAC (NAM, ATAF, and CUC) transcription factor (TF) family. Physiological analyses revealed that with increasing drought severity, leaf relative water content (LRWC) decreased significantly, whereas the levels of osmotic regulators (proline - Pro and soluble sugars - SS) and the antioxidant glutathione (GSH) increased. The activity of superoxide dismutase (SOD) increased continuously. The content of chlorophyll a increased, whereas that of chlorophyll b decreased following moderate stress, indicating a significant suppression of the photosynthetic system. Transcriptome sequencing identified 32,857 expressed genes, among which 6,217 were differentially expressed under the experimental conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that these differentially expressed genes (DEGs) were significantly enriched in pathways related to plant hormone signal transduction, glutathione metabolism, photosynthesis, and antioxidant activity. Among these DEGs, members of the NAC TF family constituted the largest group. Genome-wide analysis identified 174 NAC TFs in the R. xanthina genome. Among these, RxNAC105 exhibited significant up-regulation under drought stress. Preliminary functional validation via transient overexpression demonstrated that RxNAC105 significantly increased the activity of key antioxidant enzymes, suggesting its positive role in drought resistance. This study systematically elucidates the molecular mechanisms underlying the drought stress response of R. xanthina at both physiological and transcriptomic levels. The identification of RxNAC105 as a candidate gene for drought tolerance provides crucial genetic resources and a theoretical foundation for drought-resistant breeding in Rosa species.

Plant genomics underpins a foundation for understanding evolution, gene regulation, and fundamental biological processes, subsequently supporting both the conservation and innovative utilization of plant germplasm resources. The Lythraceae family encompasses numerous species of economic and ecological significance, and are valued for their edible, medicinal, and ornamental properties. The family-wide distribution, spanning extreme intertidal zones, semi-deserts and tropical forests, positions Lythraceae as an exemplary model for investigating the genomic mechanisms underlying ecological adaptation. Recent advances in chromosome-level genomes, pan-genomics, genetic mapping, multi-omics integration, and large-scale phenotyping have greatly accelerated research in plant evolution and breeding. Nevertheless, despite the growing genomic and trait-focused studies in Lythraceae, a comprehensive conceptual synthesis linking evolutionary events, structural variation (SV), regulatory networks, and future research directions remain absent. In this review, we present an overview of genomic resources and introduce a unified framework linking whole-genome duplications, lineage-specific SVs, and their functional impacts on species diversification. We also synthesize recent advances in genome evolution, phylogenetic relationships, biotechnology, and molecular mechanisms controlling growth, development, and stress responses. In addition, we address challenges associated with genetic transformation of woody Lythraceae species and discuss strategies to enhance molecular breeding. This review provides a forward-looking perspective on Lythraceae genomics and identifies key scientific questions that will steer future research in evolutionary biology, functional genomics, and crop improvement.

Rosa is considered one of the most challenging and difficult groups in taxonomy and phylogenetics due to its wide distribution, extensive variability, and high hybridization potential, which leads to unclear interspecific boundaries. This paper summarizes and analyzes the progress in the distribution, survey, and classification of Rosa resources in China, based on years of research on the genus and a review of relevant literature. The latest distribution data for Rosa in China was updated, highlighting two key diversity centers where species richness is highest—regions with favorable hydrothermal conditions, minimal seasonal climatic variation, and high habitat heterogeneity. Additionally, 22 previously unpublished Rosa taxa (19 varieties and three forms) and 17 significant cultivars have been introduced. A new identification key for the genus Rosa in China has also been given. We also address issues in the classification of Rosa, offering fresh perspectives on interspecific boundaries, classification methods, and key taxonomic groups. This provides theoretical support for the identification, classification, and evolutionary research of Rosa species, and offers valuable references for the conservation and utilization of Rosa resources.

The chromosomal karyotype characteristics and phylogenetic relationships within 42 germ-plasm accessions from the genus Rosa L. sect. Chinenses were investigated through an integrative cytogenetic approach. Chromosome structural variation and evolutionary patterns were further assessed by combining karyotype clustering, a phylogenetic tree constructed based on SNPs, and fluorescence in situ hybridization (FISH) targeting ribosomal DNA (rDNA) loci. The analysis revealed that the chromosomes of sect. Chinenses are predominantly characterized by median and submedian centromeres, with low karyotype asymmetry indices, reflecting an overall conserved chromosomal architecture. Karyotype-based clustering offered partial resolution of ploidy levels and phylogenetic affinities among accessions, yet discrepancies were observed when compared with the SNP-derived phylogenetic tree, particularly in the delimitation between the `Ser. Chinenses' and the `Ser. Odoratae.' FISH results demonstrated that the number of 45S rDNA loci corresponded well with ploidy levels, while 5S rDNA loci were mainly localized in the centromeric regions. All accessions exhibited a collinear arrangement of 5S and 45S rDNA signals. In triploid accessions, the chromosomal locus composition mirrored that of R. chinensis var. spontanea, suggesting its potential role as a genomic donor. The combined application of karyotype analysis and rDNA-FISH proved effective in elucidating chromosomal evolutionary features within sect. Chinenses, providing valuable cytogenetic evidence for taxonomic classification and phylogenetic studies in Rosa.

The regulatory mechanism underlying plant height determination in woody plants remains a long-standing key scientific issue, and the coordinated manner by which positive and negative regulators maintain endogenous hormone homeostasis and modulate final plant architecture is still poorly understood. Here, we identified LfiRAV7 as a pivotal negative regulator of internode elongation in Lagerstroemia indica, providing novel insights into the functional role of APETALA2/Ethylene-Responsive Factor (AP2/ERF) family Related to ABI3/VP1 (RAV) members in governing woody plant architecture. Silencing of LfiRAV7 alleviated its transcriptional repression on plant height-related pathways, resulting in a 43.3% increase in gibberellin (GA) content and a 30.2% reduction in auxin (IAA) abundance, which further facilitated cell division and consequently promoted internode elongation. Protein-protein interaction assays confirmed that LfiRAV7 physically interacts with the positive regulator LfiGI (GIGANTEA). Silencing of LfiGI suppressed GA biosynthesis and inhibited both cell division and expansion. Integrated multi-omics analysis combining DAP-seq and RNA-seq demonstrated that LfiRAV7 did not exert widespread effects on metabolic pathways; instead, it directly bound to the E-box motif of LfiGA3ox, encoding the terminal rate-limiting enzyme of the GA biosynthesis pathway, and repressed its transcription. Collectively, we uncovered an antagonistic regulatory module consisting of LfiRAV7 and LfiGI, which not only revealed a previously uncharacterized genetic mechanism underlying the regulation of endogenous hormone homeostasis and morphogenesis in woody plants, but also offered key candidate targets for directed creation of ideal plant architecture in woody ornamental species.

The modern cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a globally important ornamental plant, ranking as the second-largest cut flower after roses. Here, to unravel its complex origin and domestication history, we achieved 6 haplotypes of the elite hexaploidy cut chrysanthemum cultivar 'Jinba' (2n = 6x = 54). By constructing a genome-wide variant map across 147 core accessions, we classified current Chrysanthemum varieties into 4 wild and 4 cultivated groups. We observed extensive, intricate gene flow among these groups, demonstrating that wild germplasms from both China and Japan contribute substantially to the formation of modern cultivars. We constructed a global dispersal map for cultivated chrysanthemum and confirmed Chrysanthemum indicum as one of the key ancestral taxa. In addition, we identified candidate loci and genes associated with the development of important agronomic traits, including plant architecture, flower type and flower colour. This study provides crucial insights into the evolutionary history of cultivated chrysanthemums and establishes a robust genomic resource for advancing molecular breeding.

Rosa persica is known for its purple-red basal spots and is considered the primary genetic source of spotted cultivars within the Rosa genus. The formation of these red spots is primarily attributed to the specific accumulation of anthocyanins. However, the regulatory mechanisms underlying this pigmentation remain poorly characterized. To investigate this process, we first combined microscopic and metabolomic analyses, revealing that three cyanidin derivatives (Cy3G5G, Cy3G, and Cy3R) accumulate exclusively in the upper epidermis of the spot region. Subsequently, we identified an R2R3-MYB transcription factor, RpMYB113, as a key regulator. Functional validation showed that transient overexpression of RpMYB113 in R. chinensis 'Old Blush' induced intense anthocyanin production, a result corroborated in stably transformed Nicotiana tabacum. Simultaneously, Y1H assays confirmed that RpMYB113 directly binds to the RpDFR promoter, identifying RpDFR as a direct target. Importantly, population genetic analysis established that RpMYB113 and its associated Hap4 haplotype were defined as a core genetic unit that has undergone repeated selection during evolution and can achieve the same complex phenotype across genetic backgrounds. Thus, through a multi-tiered approach spanning cellular, metabolic, molecular, and population-level evidence, this study elucidates the mechanistic basis of anthocyanin patterning in R. persica petal spots. Keymessage We revealed a critical role of RpMYB113 in regulating anthocyanin accumulation within the petal spot zones of Rosa persica, providing a potential target for molecular breeding of spotted cultivars in Rosa species.

To efficiently produce polyploid Lagerstroemia, the development process of the female and male gametes of Lagerstroemia cultivar ‘Whit III’ was observed. It was found that when the diameter of the flower bud was from 5.1 to 5.6 mm, the length of the anther was from 0.8 to 1.2 mm, the color of the anther was light yellow-green, and the diameter of the ovary was from 1.5 to 2.0 mm, both the microspores and megaspores were in the meiosis period. Subsequently, the female gametes were in the embryo sac development stage, with embryo sacs reaching maturity when the flower bud diameter was 7.0 mm. The inflorescences with the most flower buds in this stage were treated by high temperature to induce 2n gametes, and the optimal treatment for producing 2n pollen was 44 °C for 6 h, with 2n pollen rate of 66.03

Lagerstroemia comes in a variety of bright petal colors, but it lacks yellow flowers. To breed yellow-flowered cultivars, eight Lagerstroemia and two Heimia species were used for intergeneric hybridization. Mentor pollen was applied to enhance pollination efficiency, and GA3 and 2,4-D were sprayed onto stigmas after pollination to extend hybrid fruit development. Progenies were obtained by embryo rescue and identified as hybrids between Lagerstroemia and Heimia by SSR markers. The results showed that there was strong reproductive isolation between Lagerstroemia and Heimia. When Lagerstroemia was the female parent, the fruits dropped within 5 d after pollination, and when Heimia was the female parent, the fruits did not drop, but dried up within 15 d. After pollination, pollen tubes of Heimia in the styles of Lagerstroemia halted at one-fourth of the style length, with few entering the ovary. While pollen tubes of Lagerstroemia in the style of Heimia reached the stigma base but rarely entered the ovary. Mentor pollen reduced callose production and promoted the growth of pollen tubes. Most hybrid embryos aborted on plants naturally, and applying 200 mgL-1 GA3 to Lagerstroemia pistils and 20 mgL-1 2,4-D to Heimia pistils promoted some of the hybrid fruits to the heart-shaped embryo stage. In our experiment, a total of 12,350 flowers were pollinated, and only four hybrid progenies were obtained by embryo rescue, with one hybrid confirmed as a true hybrid. The results provided a foundation for breeding yellow-flowered Lagerstroemia cultivars.

Crape myrtle is an important summer flowering shrub with abundant flowers and long flowering period, and widely used in gardens around the world. Though the MADS-box genes have profound impacts on floral organogenesis in other plants, their function and expression patterns in Lagerstroemia remain unclear. In the study, we conducted the comprehensive analysis of the MADS-box family from three Lagerstroemia species, including 94 genes in L. suprareticulata, 83 genes in L. speciosa and 79 genes in L. indica. The MADS-box genes were classified into Type I (104 genes) and Type II (152 genes). The difference in gene numbers observed among the three species was closely related to tandem and segmental duplication. Homologous gene pairs were prevalent among Lagerstroemia species, offering a profound understanding of the evolutionary dynamics of MADS-box gene family. The promoter regions of type II genes are mostly composed of light-responsive and hormone-inducible elements. Expression profiles of ABCDE-class genes showed differences in the four-whorl flower organ. Yeast two-hybrid assay and luciferase complementation assay indicated that LiMADS53 and LiMADS60 synergistically regulated sepal initiation while LiMADS49 and LiMADS42 exhibited expression in petals and stamens. LiMADS42 and LiMADS53 contributed to stamen development. These results provide a basis for mining the genes that determine flower organs of crape myrtle, and lay a solid foundation for improving flower type and breeding of new cultivars.

Primula forbesii, which blooms profusely in early spring with fragrant flowers and a long flowering period, is a distylous species with heteromorphic self-incompatibility. However, its floral characteristics and the mechanism of heteromorphic self-incompatibility remain poorly understood. In this study, floral morphological variations, pollen transcriptomic profiles, and reproductive biology traits between the two floral morphs were investigated. Morphometric analysis revealed the ancillary dimorphisms in style, stigma, stigmatic papillae and pollen in P. forbesii. The pollen transcriptome showed that there were 3495 differentially expressed genes between pin and thrum pollen. Weighted gene co-expression network analysis (WGCNA) revealed pollen-associated high correlation modules, with pin pollen showing enrichment in carbohydrate metabolic processes and thrum pollen demonstrating cell wall biosynthesis involvement. There was severe fertilization failure in self-crossing and intra-morph crossing. Pollination performed 3 days before flowering, 5 days after flowering, or using of mentor pollens slightly increased the fruit setting rate and seed quantity of self- and intra-morph pollinations of the pin morph, but had no effects on the thrum morph. The corresponding behavior of pollen tubes confirmed this result. In general, different pollination methods could not break heteromorphic self-incompatibility of P. forbesii. Compared with pin morph, thrum morph showed a stronger self-incompatibility.

Double flower, which is one of the most important characteristics of ornamental plants, is closely related to their ornamental and commercial value. The double-flower trait in rose was mainly due to the increase in petal number caused by stamen petalization. However, the mechanism regulating petal number is not clear. In this study, the Rosa chinensis "Zhaiye Tengben Yuejihua" × R. chinensis "Old Blush" population was used for QTL detection and NGS-based BSA analysis to identify candidate genes related to petal number. It was found that RcAP2L and RcAS1 were highly expressed in double-flower rose, while RcAGL80 was highly expressed in single-flower rose. Silencing RcAP2L and RcAS1 reduced the petal number by inhibiting homeotic conversion of stamens to petals, separately. However, silencing RcAGL80 increased the petal number by promoting homeotic conversion of stamens to petals. The results of Y2H and BiFC assays showed that RcAP2L interacted with RcAS1. The dual-luciferase assay showed that RcAP2L was bound to the promoter of RcAGL80 and suppressed RcAGL80 transcription. In total, we found a new function of AS1 in specifying flower organ identity, and a new pathway for regulating the number of petals by RcAS1, RcAGL80, and RcAP2L, which provides new information for elucidating the mechanism of the formation of double flower in rose.

Rose flowers are abundant in bioactive compounds and increasingly recognized for their use in functional foods. Among these, anthocyanins in rose petals serve as both natural colorants and bioactive agents. However, the genetic basis and regulatory mechanisms underlying anthocyanin biosynthesis in roses are not yet fully elucidated, posing challenges for targeted breeding of high-anthocyanin varieties. In this study, genome-wide association studies (GWAS) were employed to identify major QTLs linked to key anthocyanin components in rose petals. Candidate transcription factors were screened using qRT-PCR, leading to the identification of two key regulatory genes, RcHY5 and RcMYB44, with opposing roles in anthocyanin biosynthesis. Overexpression of RcHY5 markedly enhanced anthocyanin accumulation in rose petals, whereas RcMYB44 overexpression inhibited the accumulation of cyanidin- and pelargonidin-based anthocyanins. These findings provide valuable insights into the genetic basis and regulatory mechanisms of the anthocyanin biosynthesis, offering potential strategies for breeding rose varieties with high anthocyanin content.

Primula forbesii, a dimorphic species with a short growth cycle and high ornamental value, is an important model for studying distyly. However, the absence of a reliable genetic transformation system has limited molecular research in this species. In this study, we monitored pollen germination and pollen tube growth within the pistil to determine the optimal timing for transformation. We further examined the effects of transformation buffer composition, Agrobacterium cell density, and infection method on transformation efficiency. Based on these analyses, we established a stable pollen tube–mediated genetic transformation protocol for P. forbesii. The transformation efficiency reached 5.33

Plant height and branching are critical architectural traits in woody plants, influencing plant appearance and ornamental value. To elucidate the regulatory mechanisms, we investigated the genetic basis of plant architecture in Lagerstroemia indica by comparing a low-compact cultivar 'Fenjingling' with its tall mutants. Phenotypic and cytological traits were measured, single nucleotide polymorphisms (SNPs), insertions/deletions (InDels) and structural variations (SVs) were identified by whole-genome resequencing (WGRS), and the key variants were validated by Sanger sequencing and transcriptomic data. The results showed that compared with 'Fenjingling', the plant height, xylem cell number, xylem cell length, pith cell number, and pith cell length of the mutant increased by 3.4, 4.2, 1.9, 3.4, and 1.6 times, respectively; while the number of branches and internodes decreased by 68.49 % and 47.36 %, respectively. The coding sequences (CDS) variations of WRKY40 between 'Fenjingling' and its mutants were related to plant height. Virus-induced gene silencing (VIGS) results confirmed that a 343 bp region sequence in WRKY40 caused functional alteration, and regulated plant height by regulating cell proliferation and growth. The results provided new insights into the genetic mechanisms of plant architecture in crape myrtle.

The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today's most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.

Black spot disease, caused by Marssonina rosae (syn. Diplocarpon rosae), poses a significant threat to rose growth and quality, yet the molecular mechanisms underlying its suppression of host immunity remain largely unknown. In this study, we identified MrSEP20, a virulence effector secreted by M. rosae. Its expression increased during M. rosae infecting rose. Overexpression of MrSEP20 enhanced rose susceptibility to M. rosae by suppressing H2O2 accumulation, callose deposition, and salicylic acid (SA)-mediated defense gene expression. Conversely, host-induced gene silencing of MrSEP20 attenuated disease symptoms on rose. MrSEP20 directly interacted with RcPsaL and RcPsbX in rose, which are key subunits of photosystem I (PSI) and photosystem II (PSII), respectively. Both RcPsaL and RcPsbX positively regulated rose immunity. Overexpression of RcPsaL and RcPsbX enhanced H2O2 accumulation, callose deposition, and SA signaling, thereby reducing the black spot area by 21.01 % and 15.49 % in R12-26, respectively. In contrast, silencing RcPsaL increased the black spot area by 378.43 % in R13-54 and 16.47 % in R12-26, while silencing RcPsbX led to increase of 425.32 % and 17.26 %, respectively. Notably, MrSEP20-mediated disruption of photosystem integrity impaired reactive oxygen species (ROS) generation and SA biosynthesis, thus compromising defense activation in rose. The results highlighted a novel virulence strategy whereby M. rosae effectors targeted photosystem components to modulate rose immunity, underscoring the pivotal role of photosystem function in plant-pathogen interactions, which providing new clue for elucidating the mechanism of black spot disease-resistance in roses.