Rubus corchorifolius (Shanmei or mountain berry, 2n = 14) is widely distributed in China, and its fruits possess high nutritional and medicinal values. Here, we reported a high-quality chromosome-scale genome assembly of Shanmei, with contig size of 215.69 Mb and 26,696 genes. Genome comparison among Rosaceae species showed that Shanmei and Fupenzi (Rubus chingii Hu) were most closely related, followed by blackberry (Rubus occidentalis), and that environmental adaptation-related genes were expanded in the Shanmei genome. Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan, Hunan, Jiangxi, and Sichuan in China revealed that among these samples, the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population. Moreover, the Yunnan population underwent strong selection based on the nucleotide diversity, linkage disequilibrium, and historical effective population size analyses. Furthermore, genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways, indicating the genetic basis of adaptation of Shanmei to the local environment. The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

Rosa beggeriana ‘Aurea’ is a yellow-green leaf (yl) mutant and originated from Rosa beggeriana Schrenk by ⁶⁰Co-γ irradiation, which is an important ornamental woody species. However, the molecular mechanism of the yl mutant remains unknown. Herein, comparative transcriptome profiling was performed between the yl type and normal green color type (WT) by RNA sequencing. A total of 3,372 significantly differentially expressed genes (DEGs) were identified, consisting of 1,585 upregulated genes and 1,787 downregulated genes. Genes that took part in metabolic of biological process (1,090), membrane of cellular component (728), catalytic (1,114), and binding of molecular function (840) were significantly different in transcription level. DEGs involved in chlorophyll biosynthesis, carotenoids biosynthesis, cutin, suberine, wax biosynthesis, photosynthesis, chloroplast development, photosynthesis-antenna proteins, photosystem I (PSI) and photosystem II (PSII) components, CO₂ fixation, ribosomal structure, and biogenesis related genes were downregulated. Meanwhile, linoleic acid metabolism, siroheme biosynthesis, and carbon source of pigments biosynthesis through methylerythritol 4-phosphate (MEP) pathways were upregulated. Moreover, a total of 147 putative transcription factors were signification different expression, involving NAC, WRKY, bHLH, MYB and AP2/ERF, C2H2, GRAS, and bZIP family gene. Our results showed that the disturbed pigments biosynthesis result in yl color by altering the ratio of chlorophylls and carotenoids in yl mutants. The yl mutants may evoke other metabolic pathways to compensate for the photodamage caused by the insufficient structure and function of chloroplasts, such as enhanced MEP pathways and linoleic acid metabolism against oxidative stress. This research can provide a reference for the application of leaf color mutants in the future.

Sugars Will Eventually be Exported Transporter (SWEET) gene family plays indispensable roles in plant physiological activities, development processes, and responses to biotic and abiotic stresses, but no information is known for roses. In this study, a total of 25 RcSWEET genes were identified in Rosa chinensis ‘Old Blush’ by genome-wide analysis and clustered into four subgroups based on their phylogenetic relationships. The genomic features, including gene structures, conserved motifs, and gene duplication among the chromosomes of RcSWEET genes, were characterized. Seventeen types of cis-acting elements among the RcSWEET genes were predicted to exhibit their potential regulatory roles during biotic and abiotic stress and hormone responses. Tissue-specific and cold-response expression profiles based on transcriptome data showed that SWEETs play widely varying roles in development and stress tolerance in two rose species. Moreover, the different expression patterns of cold-response SWEET genes were verified by qRT-PCR between the moderately cold-resistant species R. chinensis ‘Old Blush’ and the extremely cold-resistant species R. beggeriana. Especially, SWEET2a and SWEET10c exhibited species differences after cold treatment and were sharply upregulated in the leaves of R. beggeriana but not R. chinensis ‘Old Blush’, indicating that these two genes may be the crucial candidates that participate in cold tolerance in R. beggeriana. Our results provide the foundation for function analysis of the SWEET gene family in roses, and will contribute to the breeding of cold-tolerant varieties of roses.

Roses are one of the most important flowers applied to landscape, cut flowers, fragrance and food industries widely. As an effective method for plant reproduction, the regeneration via somatic embryos is the most promising method for breed improvement and genetic transformation of woody plants. However, lower somatic embryogenesis (SE) induction rates and genotypic constraints impede progress in genetic transformation in rose. This study describes a plant regeneration system for the famous red cut flower cultivar Rosa hybrida ‘Carola’. The stems without petioles cultured on Murashige and Skoog (MS) medium supplemented with 1.0 mg·L⁻¹ 6-benzylaminopurine (6-BA), 0.05 mg·L⁻¹ a-naphthalene acetic acid (NAA) and 30 g·L⁻¹ sucrose showed the maximum proliferation coefficient of shoots with 3.41 for the micropropagation system. We evaluated the effects of different plant growth regulators (PGRs) on the induction, proliferation and conversion of somatic embryos. The induction rate of calli reached 100% on MS medium supplemented with 2.0 g·L⁻¹ NAA and 30 g·L⁻¹ glucose. The highest induction rate of somatic embryos achieved a frequency of 13.33% on MS medium supplemented with 2.0 mg·L⁻¹ zeatin (ZT), 0.1 mg·L⁻¹ NAA and 30 g·L⁻¹ glucose. The most suitable carbohydrate with 60 g·L⁻¹ glucose resulted in a proliferation rate of somatic embryos (4.02) on MS medium containing 1.5 mg·L⁻¹ ZT, 0.2 mg·L⁻¹ NAA and 0.1 mg·L⁻¹ gibberellic acid (GA₃). The highest somatic embryos germination rate (43.33%) was obtained from the MS medium supplemented with 1.0 mg·L⁻¹ 6-BA, 0.01 mg·L⁻¹ IBA and 30 g·L⁻¹ glucose. Finally, the germinated somatic embryos successfully rooted on 1/2 MS medium containing 1.0 mg·L⁻¹ NAA, 30 g·L⁻¹ sucrose, and the vigorous plantlets were obtained after hardening-off culture. This study provided a stable and efficient protocol for plant regeneration via somatic embryos in R. hybrida ‘Carola’, which will be beneficial to the further theoretical study and genetic improvement in roses.

Aerides rosea (Orchidaceae) boasts high ornamental value due to its pleasant aroma, foxtail spike, and elegant floral morphology. Inducing A. rosea to become tetraploid enhances horticultural traits and facilitates fertile intergeneric hybrids through crosses with other market-available tetraploid species. The experimental design involved the application of colchicine at varying concentrations—0.05%, 0.1%, and 0.2%—to a solid medium. Exposure durations were 5, 10, and 15 days, with treatments conducted under sterile conditions on 6-week-old protocorms post-germination. Results indicated that the protocorms were sensitive to colchicine concentrations exceeding 0.05%, with high concentrations leading to a mortality rate exceeding 50%. Flow cytometry (FCM) with 4′,6-diamidino-2-phenylindole (DAPI) staining confirmed a doubling of chromosome numbers in tetraploid plants (2n = 4x = 76) compared to diploid controls (2n = 2x = 38). Induction efficiency was significantly influenced by colchicine concentration and treatment duration. A 10-day treatment with 0.2% colchicine yielded a 70.00% tetraploid induction rate; however, considering protocorm survival, a 5-day treatment with 0.05% colchicine was preferable, achieving a 63.55% survival rate and a 56.67% tetraploid induction rate. Tetraploid plants exhibited distinct morphological traits, such as a more compact growth habit, thicker leaves, and increased stem and root thickness. Leaf morphology changes included larger stomata with reduced density, denser spongy mesophyll, and more pronounced venation. Tetraploids also demonstrated a 1.94-fold increase in genome size compared to diploids. The tetraploid genotypes developed in this study hold significant potential for future Aerides breeding programs.