Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

SUMMARYFlowering is a key event in plant life, and is finely tuned by environmental and endogenous signals to adapt to different environments. In horticulture, continuous flowering (CF) is a popular trait introduced in a wide range of cultivated varieties. It played an essential role in the tremendous success of modern roses and woodland strawberries in gardens. CF genotypes flower during all favourable seasons, whereas once-flowering (OF) genotypes only flower in spring. Here we show that in rose and strawberry continuous flowering is controlled by orthologous genes of the TERMINAL FLOWER 1 (TFL1) family. In rose, six independent pairs of CF/OF mutants differ in the presence of a retrotransposon in the second intron of the TFL1 homologue. Because of an insertion of the retrotransposon, transcription of the gene is blocked in CF roses and the absence of the floral repressor provokes continuous blooming. In OF-climbing mutants, the retrotransposon has recombined to give an allele bearing only the long terminal repeat element, thus restoring a functional allele. In OF roses, seasonal regulation of the TFL1 homologue may explain the seasonal flowering, with low expression in spring to allow the first bloom. In woodland strawberry, Fragaria vesca, a 2-bp deletion in the coding region of the TFL1 homologue introduces a frame shift and is responsible for CF behaviour. A diversity analysis has revealed that this deletion is always associated with the CF phenotype. Our results demonstrate a new role of TFL1 in perennial plants in maintaining vegetative growth and modifying flowering seasonality.

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F(1) diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.

Light environment and crown architecture were investigated in two closely related species (deciduous Vaccinium hirtum and evergreen Vaccinium bracteatum) in a young and an old secondary forest. Light environment was determined by photographic estimation of light above ramets (30–500 cm tall). Crown architecture was examined to determine the effects of ramet age and light level on several architectural traits. In the young secondary forest, both species were mainly found in large gaps. In the old secondary forest, V. bracteatum persisted in deep shade, whereas V. hirtum was concentrated in small gaps. Vaccinium hirtum had narrower crowns and thinner stems than V. bracteatum, indicating lower structural costs in V. hirtum. Older ramets had greater total shoot extension (only V. bracteatum) and shorter length of the current-year shoots (markedly so in V. hirtum) than younger ramets. In higher light levels, V. bracteatum had greater aboveground growth and higher leaf area indices, whereas V. hirtum had only greater flowering intensity. Architectural traits were highly correlated with ramet age in V. hirtum, whereas these were mainly affected by light in V. bracteatum, indicating higher architectural plasticity in the latter species. The differences in architecture and its plasticity can be relevant for the segregation of light habitats between the species.Key words: light environment, crown architecture, leaf display, morphological plasticity, current-year shoot.

We investigated the role of hepatic macrophages in the inflammatory response following reperfusion injury by blocking Kupffer cell phagocytosis with gadolinium chloride (GdCl3). Liver ischemia was induced in rats by occluding the portal vein for 30 minutes. A bolus of GdCl3 (7 mg/kg) was injected intravenously 1 and 2 days before surgery. The serum levels of cytokine-induced neutrophil chemoattractant (CINC) in untreated rats increased following reperfusion, peaked after 6 hours, and then gradually decreased. GdCl3 or heparin alone significantly decreased the serum levels of CINC (P < .05). In addition, pretreatment with GdCl3/heparin further inhibited the rise in the serum levels of CINC following reperfusion compared with those in untreated animals (P < .01). The in vitro production of CINC by Kupffer cells, obtained from animals pretreated with heparin or GdCl3, was significantly lower than that of cells isolated from untreated animals. Pretreatment with GdCl3/heparin further decreased CINC production by Kupffer cells compared with that of cells from animals that were pretreated with heparin or GdCl3 alone. The expression of CINC transcripts in Kupffer cells or in liver tissue peaked 3 hours after reperfusion in untreated animals. Pretreatment with heparin, GdCl3, or both significantly decreased the levels of CINC messenger RNA (mRNA) transcripts. Pretreatment with heparin, GdCl3, or GdCl3/heparin significantly decreased the number of neutrophils that accumulated in the liver 24 hours following reperfusion, compared with those in untreated animals. These results suggest that Kupffer cells release CINC and may play an important role in early neutrophil infiltration into the liver following ischemia/reperfusion.

We investigated the flowering phenology, pollinator visitation, and fruit set of 25 animal-pollinated woody species in a warm temperate secondary forest in Japan. Various species flowered sequentially from February to October. The principal pollinators were bumblebees, honey-bees, flies and/or beetles and birds; bumblebees and flies/beetles pollinated most trees. The duration of flowering was shorter for species that bloomed in the middle of the season than it was for species that bloomed earlier or later in the season. The timing of flowering was more synchronous within species that had a shorter flowering duration; this was also detected when phylogenetically independent contrasts were calculated. This could be important for the effective pollination of species with a short flowering duration because such species bloom sequentially over a short period of less than 1 month around May. Fruit set was related not to pollinator type, sex expression, flowering sequence (in order of the date of peak flowering) or flowering duration, but to the relative abundance of the species in the forest. This correlation was detected for fly-and beetle-pollinated species but not for bumblebeepollinated species. Thus, relatively rare plant species with opportunistic pollinators might experience limited fruit set because of insufficient pollinator services. Bagging experiments conducted on eight hermaphrodite species revealed that the fruit set of bagged flowers was nearly zero, lower than that of control flowers. These results indicate the importance of pollinators for successful reproduction and thus for the coexistence of plants in this secondary forest.

Plants respond to local heterogeneity in abiotic and biotic conditions by changing module-level morphology, growth, and reproductive patterns. This paper presents a conceptual framework for the study of modular responses in plant crowns, clarifies the points that should be considered for scaling up from modular responses to the consequences at the whole-plant level, characterizes the interspecific differences in modular response patterns, and discusses their ecological significance. The modular response was defined as either autonomous or interactive, depending on whether the response of a module to its local condition is independent from the conditions of other modules. For evaluation of the autonomy of the modular response, the importance of considering positional relationships and organizational levels of modules was then proposed as these internally affect the modular response pattern, and their interspecific differences were characterized using several concepts. The identification of an autonomous modular unit is essential for scaling up module-level studies to the whole plant. For understanding the ecological significance of the modular response, further interspecific comparisons and assessments of the scale and the predictability of environmental heterogeneity are required. The conceptual framework will be useful for such purposes.

Light and temperature are two environmental factors that deeply affect bud outgrowth. However, little is known about their impact on the bud burst gradient along a stem and their interactions with the molecular mechanisms of bud burst control. We investigated this question in two acrotonic rose cultivars. We demonstrated that the darkening of distal buds or exposure to cold (5°C) prior to transfer to mild temperatures (20°C) both repress acrotony, allowing the burst of quiescent medial and proximal buds. We sequenced the strigolactone pathway MAX-homologous genes in rose and studied their expression in buds and internodes along the stem. Only expressions of RwMAX1, RwMAX2 and RwMAX4 were detected. Darkening of the distal part of the shoot triggered a strong increase of RwMAX2 expression in darkened buds and bark-phloem samples, whereas it suppressed the acropetal gradient of the expression of RwMAX1 observed in stems fully exposed to light. Cold treatment induced an acropetal gradient of expression of RwMAX1 in internodes and of RwMAX2 in buds along the stem. Our results suggest that the bud burst gradient along the stem cannot be explained by a gradient of expression of RwMAX genes but rather by their local level of expression at each individual position.