The Fragaria vesca homolog of suppressor of overexpression of constans1 represses flowering and promotes vegetative growth

FvbHLH78 interacts with FvCRY2 to promote flowering in woodland strawberry

Flowering is a crucial agricultural trait of strawberries. While the bHLH family comprises numerous members in plants, its function in controlling strawberry flowering remains largely unexplored. In this study, FvbHLH78 was found to be highly expressed in the shoot apices and ripening fruits of woodland strawberry (Fragaria vesca). FvbHLH78 is localized to the nucleus and exhibits self-activating transcriptional properties. Overexpression of FvbHLH78 in woodland strawberry resulted in an early flowering phenotype compared to the control plants. This phenomenon was attributed to FvbHLH78 directly binding to the promoters of the genes associated with flowering, namely FvFT, FvSEP3, FvLFY, and FvAGL42. Moreover, FvbHLH78 interacted with a blue light receptor FvCRY2, which enhances FvbHLH78 promoter-binding affinity to FvFT, FvSEP3, FvLFY, and FvAGL42, thereby accelerating flowering. Collectively, these findings demonstrate that the FvbHLH78-FvCRY2 complex in strawberries acts as an enhancer of genes associated with flowering, thereby accelerating the flowering process. These data offer an understanding for enriching the roles of bHLH78 and accelerating flowering in strawberry.

Constitutive expression of CEN-like protein 2, a TFL1 ortholog of pigeon pea (Cajanus cajan [L.] Millspaugh) delays flowering in transgenic tobacco plants

CEN-like protein 2 of pigeon pea, a candidate anti-florigen gene and a close homolog of AtTFL1 (Arabidopsis Terminal Flower1) of the PEBP family has been characterized through constitutive expression in tobacco. In-silico analysis helped to demonstrate the absence of a nuclear binding domain and the conserveness of substrate binding sites of this protein across angiosperms. Transgenic tobacco lines with 2-eightfold higher expressions of CEN-like protein 2 showed delayed flowering (26-32 days) along with significant morphological changes, including vegetative vigour, number and size of flowers, fruit setting, etc. Together, these findings showed that CEN-like protein 2 not only delays floral transition through repression but also regulates a variety of developmental traits. Expression profiling of upstream and downstream interacting pathway genes explained that their expression modulation led to a prolonged vegetative phase of over-expressed lines. Floral inducer genes like APETALA1 and LEAFY were drastically down-regulated in transgenic lines, reconfirming the role of the CEN-like 2 gene in floral regulation. In conclusion, precisely controlling CcCEN-like 2 gene expression may prove useful for refining pigeon pea breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01572-8.

Transcription factor FveMYB117a inhibits axillary bud outgrowth by regulating cytokinin homeostasis in woodland strawberry

Shoot branching affects plant architecture. In strawberry (Fragaria L.), short branches (crowns) develop from dormant axillary buds to form inflorescences and flowers. While this developmental transition contributes greatly to perenniality and yield in strawberry, its regulatory mechanism remains unclear and understudied. In the woodland strawberry (Fragaria vesca), we identified and characterized 2 independent mutants showing more crowns. Both mutant alleles reside in FveMYB117a, a R2R3-MYB transcription factor gene highly expressed in shoot apical meristems, axillary buds, and young leaves. Transcriptome analysis revealed that the expression of several cytokinin pathway genes was altered in the fvemyb117a mutant. Consistently, active cytokinins were significantly increased in the axillary buds of the fvemyb117a mutant. Exogenous application of cytokinin enhanced crown outgrowth in the wild type, whereas the cytokinin inhibitors suppressed crown outgrowth in the fvemyb117a mutant. FveMYB117a binds directly to the promoters of the cytokinin homeostasis genes FveIPT2 encoding an isopentenyltransferase and FveCKX1 encoding a cytokinin oxidase to regulate their expression. Conversely, the type-B Arabidopsis response regulators FveARR1 and FveARR2b can directly inhibit the expression of FveMYB117a, indicative of a negative feedback regulation. In conclusion, we identified FveMYB117a as a key repressor of crown outgrowth by inhibiting cytokinin accumulation and provide a mechanistic basis for bud fate transition in an herbaceous perennial plant.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

Flowering and Runnering of Seasonal Strawberry under Different Photoperiods Are Affected by Intensity of Supplemental or Night-Interrupting Blue Light

The strawberry (Fragaria × ananassa Duch.) "Sulhyang" is a typical seasonal flowering (SF) strawberry that produces flower buds in day lengths shorter than a critical limit (variable, but often defined as <12 h). There is a trade-off between photoperiod-controlled flowering and gibberellin (GA) signaling pathway-mediated runnering. Some related genes (such as CO, FT1, SOC1, and TFL1) participating in light signaling and circadian rhythm in plants are altered under blue light (BL). Sugars for flowering and runnering are mainly produced by photosynthetic carbon assimilation. The intensity of light could affect photosynthesis, thereby regulating flowering and runnering. Here, we investigated the effect of the intensity of supplemental blue light (S-BL) or night-interrupting blue light (NI-BL) in photoperiodic flowering and runnering regulation by applying 4 h of S-BL or NI-BL with either 0, 10, 20, 30, or 40 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) in a 10 h short-day (SD10) (SD10 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)) or 14 h long-day (LD14) conditions (LD14 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)). Approximately 45 days after the photoperiodic light treatment, generally, whether S-BL or NI-BL, BL (20) was the most promotive in runnering, leading to more runners in both the LD and SD conditions. For flowering, except the treatment LD14 + S-BL, BL (20) was still the key light, either from BL (20) or BL (40), promoting flowering, especially when BL acted as the night-interrupting light, regardless of the photoperiod. At the harvest stage, larger numbers of inflorescences and runners were observed in the LD14 + NI-BL4 treatment, and the most were observed in the LD14 + NI-BL (20). Moreover, the SD10 + NI-BL4 was slightly inferior to the LD14 + NI-BL4 in increasing the numbers of inflorescences and runners, but it caused earlier flowering. Additionally, the circadian rhythm expression of flowering-related genes was affected differently by the S-BL and NI-BL. After the application of BL in LD conditions, the expression of an LD-specific floral activator FaFT1 was stimulated, while that of a flowering suppressor FaTFL1 was inhibited, resetting the balance of expression between these two opposite flowering regulators. The SD runnering was caused by BL in non-runnering SD conditions associated with the stimulation of two key genes that regulate runner formation in the GA pathway, FaGRAS32 and FaGA20ox4. In addition, the positive effects of BL on enhancing photosynthesis and carbohydrate production also provided an abundant energy supply for the flowering and runnering processes.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

Plants must adapt with increasing speed to global warming to maintain their fitness. One rapid adaptation mechanism is epigenetic memory, which may provide organisms sufficient time to adapt to climate change. We studied how the perennial Fragaria vesca adapted to warmer temperatures (28°C vs. 18°C) over three asexual generations. Differences in flowering time, stolon number, and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment. Induced methylome changes differed between the four ecotypes from Norway, Iceland, Italy, and Spain, but shared methylome responses were also identified. Most differentially methylated regions (DMRs) occurred in the CHG context, and most CHG and CHH DMRs were hypermethylated at the warmer temperature. In eight CHG DMR peaks, a highly similar methylation pattern could be observed between ecotypes. On average, 13% of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression. We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. Furthermore, we observed a negative correlation with gene expression when repetitive elements were found near (±2 kb) or inside genes. In conclusion, lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns. Both shared methylation patterns and transcriptome differences between F. vesca accessions were observed, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.

Major transcriptomic differences are induced by warmer temperature conditions experienced during asexual and sexual reproduction in Fragaria vesca ecotypes

A major challenge for plants in a rapidly changing climate is to adapt to rising temperatures. Some plants adapt to temperature conditions by generating an epigenetic memory that can be transmitted both meiotically and mitotically. Such epigenetic memories may increase phenotypic variation to global warming and provide time for adaptation to occur through classical genetic selection. The goal of this study was to understand how warmer temperature conditions experienced during sexual and asexual reproduction affect the transcriptomes of different strawberry (Fragaria vesca) ecotypes. We let four European F. vesca ecotypes reproduce at two contrasting temperatures (18 and 28°C), either asexually through stolon formation for several generations, or sexually by seeds (achenes). We then analyzed the transcriptome of unfolding leaves, with emphasis on differential expression of genes belonging to the epigenetic machinery. For asexually reproduced plants we found a general transcriptomic response to temperature conditions but for sexually reproduced plants we found less significant responses. We predicted several splicing isoforms for important genes (e.g. a SOC1, LHY, and SVP homolog), and found significantly more differentially presented splicing event variants following asexual vs. sexual reproduction. This difference could be due to the stochastic character of recombination during meiosis or to differential creation or erasure of epigenetic marks during embryogenesis and seed development. Strikingly, very few differentially expressed genes were shared between ecotypes, perhaps because ecotypes differ greatly both genetically and epigenetically. Genes related to the epigenetic machinery were predominantly upregulated at 28°C during asexual reproduction but downregulated after sexual reproduction, indicating that temperature-induced change affects the epigenetic machinery differently during the two types of reproduction.

Molecular mechanisms of flowering phenology in trees

Flower initiation is a phenological developmental process strictly regulated in all flowering plants. Studies in Arabidopsis thaliana, a model plant organism in plant biology and genetics, and major cereal crops have provided fundamental knowledge and understanding of the underlying molecular mechanisms and regulation in annuals. However, this flowering process and underly molecular mechanisms in perennials are much more complicated than those in annuals and remain poorly understood and documented. In recent years, the increasing availability of perennial plant genomes and advances in biotechnology have allowed the identification and characterization of flowering-associated gene orthologs in perennials. In this review, we compared and summarized the recent progress in regulation of flowering time in perennial trees, with an emphasis on the perennial-specific regulatory mechanisms. Pleiotropic effects on tree growth habits such as juvenility, seasonal activity-dormancy growth, and the applications of tree flowering phenology are discussed.

Effects of gibberellins on important agronomic traits of horticultural plants

Horticultural plants such as vegetables, fruits, and ornamental plants are crucial to human life and socioeconomic development. Gibberellins (GAs), a class of diterpenoid compounds, control numerous developmental processes of plants. The roles of GAs in regulating growth and development of horticultural plants, and in regulating significant progress have been clarified. These findings have significant implications for promoting the quality and quantity of the products of horticultural plants. Here we review recent progress in determining the roles of GAs (including biosynthesis and signaling) in regulating plant stature, axillary meristem outgrowth, compound leaf development, flowering time, and parthenocarpy. These findings will provide a solid foundation for further improving the quality and quantity of horticultural plants products.

Role of FaSOC1 and FaCO in the seasonal control of reproductive and vegetative development in the perennial crop Fragaria × ananassa

The diploid woodland strawberry (F. vesca) represents an important model for the genus Fragaria. Significant advances in the understanding of the molecular mechanisms regulating seasonal alternance of flower induction and vegetative reproduction has been made in this species. However, this research area has received little attention on the cultivated octoploid strawberry (F. × ananassa) despite its enormous agronomical and economic importance. To advance in the characterization of this intricated molecular network, expression analysis of key flowering time genes was performed both in short and long days and in cultivars with seasonal and perpetual flowering. Analysis of overexpression of FaCO and FaSOC1 in the seasonal flowering 'Camarosa' allowed functional validation of a number of responses already observed in F. vesca while uncovered differences related to the regulation of FaFTs expression and gibberellins (GAs) biosynthesis. While FvCO has been shown to promote flowering and inhibit runner development in the perpetual flowering H4 accession of F. vesca, our study showed that FaCO responds to LD photoperiods as in F. vesca but delayed flowering to some extent, possibly by induction of the strong FaTFL1 repressor in crowns. A contrasting effect on runnering was observed in FaCO transgenic plants, some lines showing reduced runner number whereas in others runnering was slightly accelerated. We demonstrate that the role of the MADS-box transcription factor FaSOC1 as a strong repressor of flowering and promoter of vegetative growth is conserved in woodland and cultivated strawberry. Our study further indicates an important role of FaSOC1 in the photoperiodic repression of FLOWERING LOCUS T (FT) genes FaFT2 and FaFT3 while FaTFL1 upregulation was less prominent than that observed in F. vesca. In our experimental conditions, FaSOC1 promotion of vegetative growth do not require induction of GA biosynthesis, despite GA biosynthesis genes showed a marked photoperiodic upregulation in response to long days, supporting GA requirement for the promotion of vegetative growth. Our results also provided insights into additional factors, such as FaTEM, associated with the vegetative developmental phase that deserve further characterization in the future.

Functional diversification and molecular mechanisms of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in horticultural plants

Flowering is an important process in higher plants and is regulated by a variety of factors, including light, temperature, and phytohormones. Flowering restriction has a considerable impact on the commodity value and production cost of many horticultural crops. In Arabidopsis, the FT/TFL1 gene family has been shown to integrate signals from various flowering pathways and to play a key role in the transition from flower production to seed development. Studies in several plant species of the FT/TFL1 gene family have revealed it harbors functional diversity in the regulation of flowering. Here, we review the functional evolution of the FT/TFL1 gene family in horticulture plants and its unique regulatory mechanisms; in addition, the FT/TFL1 family of genes as an important potential breeding target is explored.

Overexpression of HANABA TARANU in cultivated strawberry delays flowering and leads to defective flower and fruit development

Cultivated strawberry is one of the most important horticultural crops in the world, and the fruit yields and economic benefits are largely dependent on the quality of floral initiation and floral organ development. However, the underlying regulatory mechanisms controlling these processes in strawberry are largely unknown. In this study, the function of a GATA transcription factor gene, HANABA TARANU (HAN), in floral initiation and floral organ development was characterized in strawberry. FaHAN is expressed in four whorls of the floral organs. Overexpression (OE) of FaHAN in the strawberry cultivar 'Benihoppe' delayed flowering by at least one week by affecting key genes, such as TERMINAL FLOWER 1, APETALA 1…and increased the number of runners. FaHAN-OE plants also showed malformed floral organs, especially the deformed stigmas with disordered arrangement. Several key genes for pistil apical development such as STYLISH, YUCCA 1, and auxin-related genes such as GH3.5, PIN-FORMED 1, which play important roles in pistil primordium development in many plant species, were all down-regulated in FaHAN-OE plants. Further observations showed that the fruit deformity rate was nearly 4-fold higher than in control plants. Together, this study provides a new approach for exploring floral initiation and floral organ development in strawberry.

Altered Developmental and Metabolic Gene Expression in Basil Interspecific Hybrids

To understand the altered developmental changes and associated gene expression in inter-genomic combinations, a study was planned in two diverse yet closely related species of Ocimum, targeting their hybrid F1 and amphidiploids. The existing developmental variations between F1 and amphidiploids was analyzed through phenotypical and anatomical assessments. The absence of 8330 transcripts of F1 in amphidiploids and the exclusive presence of two transcripts related to WNK lysine-deficient protein kinase and geranylgeranyl transferase type-2 subunit beta 1-like proteins in amphidiploids provided a set of genes to compare the suppressed and activated functions between F1 and amphidiploids. The estimation of eugenol and methyleugenol, flavonoid, lignin and chlorophyll content was correlated with the average FPKM and differential gene expression values and further validated through qRT-PCR. Differentially expressed genes of stomatal patterning and development explained the higher density of stomata in F1 and the larger size of stomata in amphidiploids. Gene expression study of several transcription factors putatively involved in the growth and developmental processes of plants clearly amalgamates the transcriptome data linking the phenotypic differences in F1 and amphidiploids. This investigation describes the influence of interspecific hybridization on genes and transcription factors leading to developmental changes and alleviation of intergenomic instability in amphidiploids.

Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis

Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.

The high concentrations of abscisic, jasmonic, and salicylic acids produced under long days do not accelerate flowering in Chenopodium ficifolium 459

The survival and adaptation of angiosperms depends on the proper timing of flowering. The weedy species Chenopodium ficifolium serves as a useful diploid model for comparing the transition to flowering with the important tetraploid crop Chenopodium quinoa due to the close phylogenetic relationship. The detailed transcriptomic and hormonomic study of the floral induction was performed in the short-day accession C. ficifolium 459. The plants grew more rapidly under long days but flowered later than under short days. The high levels of abscisic, jasmonic, and salicylic acids at long days were accompanied by the elevated expression of the genes responding to oxidative stress. The increased concentrations of stress-related phytohormones neither inhibited the plant growth nor accelerated flowering in C. ficifolium 459 at long photoperiods. Enhanced content of cytokinins and the stimulation of cytokinin and gibberellic acid signaling pathways under short days may indicate the possible participation of these phytohormones in floral initiation. The accumulation of auxin metabolites suggests the presence of a dynamic regulatory network in C. ficifolium 459.

Time-Course Transcriptomic Profiling of Floral Induction in Cultivated Strawberry

The initiation and quality of flowering directly affect the time to market and economic benefit of cultivated strawberries, but the underlying mechanisms of these processes are largely unknown. To investigate the gene activity during the key period of floral induction in strawberries, time-course transcriptome analysis was performed on the shoot apex of the strawberry cultivar ‘Benihoppe.’ A total of 7177 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into four clusters with dynamic expression patterns. By analyzing the key genes in the potential flowering pathways and the development of the leaf and flower, at least 73 DEGs that may be involved in the regulatory network of floral induction in strawberries were identified, some of which belong to the NAC, MYB, MADS, and SEB families. A variety of eight hormone signaling pathway genes that might play important roles in floral induction were analyzed. In particular, the gene encoding DELLA, a key inhibitor of the gibberellin signaling pathway, was found to be significantly differentially expressed during the floral induction. Furthermore, the differential expression of some important candidate genes, such as TFL1, SOC1, and GAI-like, was further verified by qRT-PCR. Therefore, we used this time-course transcriptome data for a preliminary exploration of the regulatory network of floral induction and to provide potential candidate genes for future studies of flowering in strawberries.

GhSOC1s Evolve to Respond Differently to the Environmental Cues and Promote Flowering in Partially Independent Ways

Gossypium hirsutum is most broadly cultivated in the world due to its broader adaptation to the environment and successful breeding of early maturity varieties. However, how cotton responds to environmental cues to adjust flowering time to achieve reproductive success is largely unknown. SOC1 functions as an essential integrator for the endogenous and exogenous signals to maximize reproduction. Thus we identified six SOC1-like genes in Gossypium that clustered into two groups. GhSOC1-1 contained a large intron and clustered with monocot SOC1s, while GhSOC1-2/3 were close to dicot SOC1s. GhSOC1s expression gradually increased during seedling development suggesting their conserved function in promoting flowering, which was supported by the early flowering phenotype of 35S:GhSOC1-1 Arabidopsis lines and the delayed flowering of cotton silencing lines. Furthermore, GhSOC1-1 responded to short-day and high temperature conditions, while GhSOC1-2 responded to long-day conditions. GhSOC1-3 might function to promote flowering in response to low temperature and cold. Taken together, our results demonstrate that GhSOC1s respond differently to light and temperature and act cooperatively to activate GhLFY expression to promote floral transition and enlighten us in cotton adaptation to environment that is helpful in improvement of cotton maturity.

BcSOC1 Promotes Bolting and Stem Elongation in Flowering Chinese Cabbage

Flowering Chinese cabbage is one of the most economically important stalk vegetables. However, the molecular mechanisms underlying bolting, which is directly related to stalk quality and yield, in this species remain unknown. Previously, we examined five key stem development stages in flowering Chinese cabbage. Here, we identified a gene, BcSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1), in flowering Chinese cabbage using transcriptome analysis, whose expression was positively correlated with bolting. Exogenous gibberellin (GA3) and low-temperature treatments significantly upregulated BcSOC1 and promoted early bolting and flowering. Additionally, BcSOC1 overexpression accelerated early flowering and stem elongation in both Arabidopsis and flowering Chinese cabbage, whereas its knockdown dramatically delayed bolting and flowering and inhibited stem elongation in the latter; the inhibition of stem elongation was more notable than delayed flowering. BcSOC1 overexpression also induced cell expansion by upregulating genes encoding cell wall structural proteins, such as BcEXPA11 (cell wall structural proteins and enzymes) and BcXTH3 (xyloglucan endotransglycosidase/hydrolase), upon exogenous GA3 and low-temperature treatments. Moreover, the length of pith cells was correlated with stem height, and BcSOC1 interacted with BcAGL6 (AGAMOUS-LIKE 6) and BcAGL24 (AGAMOUS-LIKE 24). Thus, BcSOC1 plays a vital role in bolting and stem elongation of flowering Chinese cabbage and may play a novel role in regulating stalk development, apart from the conserved function of Arabidopsis SOC1 in flowering alone.

MADS-box transcription factors determine the duration of temporary winter dormancy in closely related evergreen and deciduous Iris spp

Winter dormancy (WD) is a crucial strategy for plants coping with potentially deadly environments. In recent decades, this process has been extensively studied in economically important perennial eudicots due to changing climate. However, in evergreen monocots with no chilling requirements, dormancy processes are so far a mystery. In this study, we compared the WD process in closely related evergreen (Iris japonica) and deciduous (I. tectorum) iris species across crucial developmental time points. Both iris species exhibit a 'temporary' WD process with distinct durations, and could easily resume growth under warm conditions. To decipher transcriptional changes, full-length sequencing for evergreen iris and short read RNA sequencing for deciduous iris were applied to generate respective reference transcriptomes. Combining results from a multipronged approach, SHORT VEGETATIVE PHASE and FRUITFULL (FUL) from MADS-box was associated with a dormancy- and a growth-related module, respectively. They were co-expressed with genes involved in phytohormone signaling, carbohydrate metabolism, and environmental adaptation. Also, gene expression patterns and physiological changes in the above pathways highlighted potential abscisic acid and jasmonic acid antagonism in coordinating growth and stress responses, whereas differences in carbohydrate metabolism and reactive oxygen species scavenging might lead to species-specific WD durations. Moreover, a detailed analysis of MIKCCMADS-box in irises revealed common features described in eudicots as well as possible new roles for monocots during temporary WD, such as FLOWERING LOCUS C and FUL. In essence, our results not only provide a portrait of temporary WD in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants.

Natural Variation in the Control of Flowering and Shoot Architecture in Diploid Fragaria Species

In perennial fruit and berry crops of the Rosaceae family, flower initiation occurs in late summer or autumn after downregulation of a strong repressor TERMINAL FLOWER1 (TFL1), and flowering and fruiting takes place the following growing season. Rosaceous fruit trees typically form two types of axillary shoots, short flower-bearing shoots called spurs and long shoots that are, respectively, analogous to branch crowns and stolons in strawberry. However, regulation of flowering and shoot architecture differs between species, and environmental and endogenous controlling mechanisms have just started to emerge. In woodland strawberry (Fragaria vesca L.), long days maintain vegetative meristems and promote stolon formation by activating TFL1 and GIBBERELLIN 20-OXIDASE4 (GA20ox4), respectively, while silencing of these factors by short days and cool temperatures induces flowering and branch crown formation. We characterized flowering responses of 14 accessions of seven diploid Fragaria species native to diverse habitats in the northern hemisphere and selected two species with contrasting environmental responses, Fragaria bucharica Losinsk. and Fragaria nilgerrensis Schlecht. ex J. Gay for detailed studies together with Fragaria vesca. Similar to F. vesca, short days at 18°C promoted flowering in F. bucharica, and the species was induced to flower regardless of photoperiod at 11°C after silencing of TFL1. F. nilgerrensis maintained higher TFL1 expression level and likely required cooler temperatures or longer exposure to inductive treatments to flower. We also found that high expression of GA20ox4 was associated with stolon formation in all three species, and its downregulation by short days and cool temperature coincided with branch crown formation in F. vesca and F. nilgerrensis, although the latter did not flower. F. bucharica, in contrast, rarely formed branch crowns, regardless of flowering or GA20ox4 expression level. Our findings highlighted diploid Fragaria species as rich sources of genetic variation controlling flowering and plant architecture, with potential applications in breeding of Rosaceous crops.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.

Axillary Bud Fate Shapes Plant Architecture in Horticultural Crops

Above-ground plant architecture is dictated to a large extent by the fates and growth rates of aerial plant meristems. Shoot apical meristem gives rise to the fundamental plant form by generating new leaves. However, the fates of axillary meristems located in leaf axils have a great influence on plant architecture and affect the harvest index, yield potential and cultural practices. Improving plant architecture by breeding facilitates denser plantations, better resource use efficiency and even mechanical harvesting. Knowledge of the genetic mechanisms regulating plant architecture is needed for precision breeding, especially for determining feasible breeding targets. Fortunately, research in many crop species has demonstrated that a relatively small number of genes has a large effect on axillary meristem fates. In this review, we select a number of important horticultural and agricultural plant species as examples of how changes in plant architecture affect the cultivation practices of the species. We focus specifically on the determination of the axillary meristem fate and review how plant architecture may change even drastically because of altered axillary meristem fate. We also explain what is known about the genetic and environmental control of plant architecture in these species, and how further changes in plant architectural traits could benefit the horticultural sector.

Woodland strawberry axillary bud fate is dictated by a crosstalk of environmental and endogenous factors

Plant architecture is defined by fates and positions of meristematic tissues and has direct consequences on yield potential and environmental adaptation of the plant. In strawberries (Fragaria vesca L. and F. × ananassa Duch.), shoot apical meristems can remain vegetative or differentiate into a terminal inflorescence meristem. Strawberry axillary buds (AXBs) are located in leaf axils and can either remain dormant or follow one of the two possible developmental fates. AXBs can either develop into stolons needed for clonal reproduction or into branch crowns (BCs) that can bear their own terminal inflorescences under favorable conditions. Although AXB fate has direct consequences on yield potential and vegetative propagation of strawberries, the regulation of AXB fate has so far remained obscure. We subjected a number of woodland strawberry (F. vesca L.) natural accessions and transgenic genotypes to different environmental conditions and growth regulator treatments to demonstrate that strawberry AXB fate is regulated either by environmental or endogenous factors, depending on the AXB position on the plant. We confirm that the F. vesca GIBBERELLIN20-oxidase4 (FvGA20ox4) gene is indispensable for stolon development and under tight environmental regulation. Moreover, our data show that apical dominance inhibits the outgrowth of the youngest AXB as BCs, although the effect of apical dominance can be overrun by the activity of FvGA20ox4. Finally, we demonstrate that the FvGA20ox4 is photoperiodically regulated via FvSOC1 (F. vesca SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1) at 18°C, but at higher temperature of 22°C an unidentified FvSOC1-independent pathway promotes stolon development.

An Evolutionary Analysis of B-Box Transcription Factors in Strawberry Reveals the Role of FaBBx28c1 in the Regulation of Flowering Time

Flowering connects vegetative and generative developmental phases and plays a significant role in strawberry production. The mechanisms that regulate strawberry flowering time are unclear. B-box transcription factors (BBXs) play important roles in the flowering time regulation of plants. Nevertheless, BBXs in octoploid cultivated strawberry (Fragaria ananassa) and their functions in flowering time regulation have not been identified. Here, we identified 51 FaBBXs from cultivated strawberry and 16 FvBBXs from diploid wild strawberry (Fragaria vesca), which were classified into five groups according to phylogenetic analysis. Further evolutionary analysis showed that whole-genome duplication or segmental duplication is a crucial factor that leads to the expansion of the BBX gene family in two strawberry species. Moreover, some loss and acquisition events of FaBBX genes were identified in the genome of cultivated strawberry that could have affected traits of agronomic interest, such as fruit quality. The promoters of FaBBX genes showed an enrichment in light-responsive, cis-regulatory elements, with 16 of these genes showing changes in their transcriptional activity in response to blue light treatment. On the other hand, FaBBX28c1, whose transcriptional activity is reduced in response to blue light, showed a delay in flowering time in Arabidopsis transgenic lines, suggesting its role in the regulation of flowering time in cultivated strawberry. Our results provide new evolutionary insight into the BBX gene family in cultivated strawberry and clues regarding their function in flowering time regulation in plants.

The FveFT2 florigen/FveTFL1 antiflorigen balance is critical for the control of seasonal flowering in strawberry while FveFT3 modulates axillary meristem fate and yield

Plant architecture is central in determining crop yield. In the short-day species strawberry, a crop vegetatively propagated by daughter-plants produced by stolons, fruit yield is further dependent on the trade-off between sexual reproduction (fruits) and asexual reproduction (daughter-plants). Both are largely dependent on meristem identity, which establishes the development of branches, stolons and inflorescences. Floral initiation and plant architecture are modulated by the balance between two related proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). We explored in woodland strawberry the role of the uncharacterised FveFT2 and FveFT3 genes and of the floral repressor FveTFL1 through gene expression analyses, grafting and genetic transformation (overexpression and gene editing). We demonstrate the unusual properties of these genes. FveFT2 is a nonphotoperiodic florigen permitting short-day (SD) flowering and FveTFL1 is the long-hypothesised long-day systemic antiflorigen that contributes, together with FveFT2, to the photoperiodic regulation of flowering. We additionally show that FveFT3 is not a florigen but promotes plant branching when overexpressed, that is likely to be through changing axillary meristem fate, therefore resulting in a 3.5-fold increase in fruit yield at the expense of stolons. We show that our findings can be translated into improvement of cultivated strawberry in which FveFT2 overexpression significantly accelerates flowering.

Chilling Requirement Validation and Physiological and Molecular Responses of the Bud Endodormancy Release in Paeonia lactiflora 'Meiju'

The introduction of herbaceous peony (Paeonia lactiflora Pall.) in low-latitude areas is of great significance to expand the landscape application of this world-famous ornamental. With the hazards of climate warming, warm winters occurs frequently, which makes many excellent northern herbaceous peony cultivars unable to meet their chilling requirements (CR) and leads to their poor growth and flowering in southern China. Exploring the endodormancy release mechanism of underground buds is crucial for improving low-CR cultivar screening and breeding. A systematic study was conducted on P. lactiflora 'Meiju', a screened cultivar with a typical low-CR trait introduced from northern China, at the morphological, physiological and molecular levels. The CR value of 'Meiju' was further verified as 677.5 CUs based on the UT model and morphological observation. As a kind of signal transducer, reactive oxygen species (ROS) released a signal to enter dormancy, which led to corresponding changes in carbohydrate and hormone metabolism in buds, thus promoting underground buds to acquire strong cold resistance and enter endodormancy. The expression of important genes related to ABA metabolism, such as NCED3, PP2C, CBF4 and ABF2, reached peaks at the critical stage of endodormancy release (9 January) and then decreased rapidly; the expression of the GA2ox8 gene related to GA synthesis increased significantly in the early stage of endodormancy release and decreased rapidly after the release of ecodormancy (23 January). Cytological observation showed that the period when the sugar and starch contents decreased and the ABA/GA ratio decreased was when 'Meiju' bud endodormancy was released. This study reveals the endodormancy regulation mechanism of 'Meiju' buds with the low-CR trait, which lays a theoretical foundation for breeding new herbaceous peony cultivars with the low-CR trait.

GRAS transcription factor LOSS OF AXILLARY MERISTEMS is essential for stamen and runner formation in wild strawberry

Axillary bud development is a major factor that impacts plant architecture. A runner is an elongated shoot that develops from axillary bud and is frequently used for clonal propagation of strawberry. However, the genetic control underlying runner production is largely unknown. Here, we identified and characterized loss of axillary meristems (lam), an ethyl methanesulfonate-induced mutant of the diploid woodland strawberry (Fragaria vesca) that lacked stamens in flowers and had reduced numbers of branch crowns and runners. The reduced branch crown and runner phenotypes were caused by a failure of axillary meristem initiation. The causative mutation of lam was located in FvH4_3g41310, which encodes a GRAS transcription factor, and was validated by a complementation test. lamCR mutants generated by CRISPR/Cas9 produced flowers without stamens and had fewer runners than the wild-type. LAM was broadly expressed in meristematic tissues. Gibberellic acid (GA) application induced runner outgrowth from the remaining buds in lam, but failed to do so at the empty axils of lam. In contrast, treatment with the GA biosynthesis inhibitor paclobutrazol converted the runners into branch crowns. Moreover, genetic studies indicated that lam is epistatic to suppressor of runnerless (srl), a mutant of FveRGA1 in the GA pathway, during runner formation. Our results demonstrate that LAM is required for stamen and runner formation and acts sequentially with GA from bud initiation to runner outgrowth, providing insights into the molecular regulation of these economically important organs in strawberry.

Developmental regulation of stolon and rhizome

Stolons and rhizomes are modified stems for vegetative reproduction. While stolons grow above the ground, rhizomes grow beneath the ground. Stolons and rhizomes maintain the genotypes of hybrids and hence are invaluable for agricultural propagation. Diploid strawberry is a model for studying stolon development. At the axillary meristems, gibberellins and MADS box gene SOC1 promote stolon formation, while the DELLA repressor inhibits stolon development. Photoperiod regulates stolon formation through regulating GA biosynthesis or balancing asexual with sexual mode of reproduction in the axillary meristems. In rhizomatous wild rice, the BLADE-ON-PETIOLE gene promotes sheath-to-blade ratio to confer rhizome tip stiffness and support underground growth. Together, this review aims to encourage further investigations into stolon and rhizome to benefit agriculture and environment.

Molecular cloning and potential role of DiSOC1s in flowering regulation in Davidia involucrata Baill

Davidia involucrata Baill. (dove tree) is unique Tertiary relic plant in China, also known as 'living fossil' and 'giant panda'. The MADS-box family gene SOC1 is involved in the regulatory pathway that integrates flowering signals to promote flowering at the optimal time. In this study, we isolated and identified two dove tree SOC1 homologues, named DiSOC1-a and DiSOC1-b. These two sequences possess highly conserved domains MADS-box and SOC1-motif, as well as the semi-conserved region K-box. DiSOC1-a and DiSOC1-b were expressed at varying levels in all tested tissues of dove tree and shared high levels of expression in the flower buds. The expression tendencies of both genes in bract were initially upward and then downward and were highest in young bracts. Neither DiSOC1-a nor DiSOC1-b was expressed in immature leaves. Proteins encoded by DiSOC1-a and DiSOC1-b were located in the nucleus. In addition, ectopic overexpression of both genes in WT Arabidopsis promoted early flowering and the growth of the main bolt. Taken together, these results suggest that DiSOC1-a and DiSOC1-b are involved in the flowering initiation and the main bolt growth process of dove tree. Our results provide a foundation for horticultural breeding to control flowering time of dove tree.

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.

Woodland strawberry WRKY71 acts as a promoter of flowering via a transcriptional regulatory cascade

The WRKY proteins are a large family of transcription factors that play important roles in stress responses and plant development. However, the roles of most WRKYs in strawberry are not well known. In this study, FvWRKY71 was isolated from the woodland strawberry 'Ruegen'. FvWRKY71 was highly expressed in the shoot apex and red fruit. Subcellular localization analysis showed that FvWRKY71 was located in the nucleus. Transactivation analysis showed that FvWRKY71 presented transcriptional activation activity in yeast. Overexpression of FvWRKY71 in Arabidopsis and woodland strawberry revealed early flowering in the transgenic plants compared with the wild-type control. Gene expression analysis indicated that the transcript levels of the flowering time and development integrator genes AP1, LFY, FT, AGL42, FUL, FPF1, SEP1, SEP2, and SEP3 were increased in FvWRKY71-overexpressing Arabidopsis and strawberry plants compared with the wild-type controls, which may result in accelerated flowering in transgenic plants. Furthermore, FvWRKY71 was proven to directly bind to the W-boxes (TTGACT/C) of the FvFUL, FvSEP1, FvAGL42, FvLFY, and FvFPF1 promoters in vitro and in vivo. Taken together, our results reveal a transcriptional regulatory cascade of FvWRKY71 involved in promoting flowering in woodland strawberry.

A Long-Day Photoperiod and 6-Benzyladenine Promote Runner Formation through Upregulation of Soluble Sugar Content in Strawberry

Commercial strawberries are mainly propagated using daughter plants produced on aerial runners because asexual propagation is faster than seed propagation, and daughter plants retain the characteristics of the mother plant. This study was conducted to investigate the effective factors for runner induction, as well as the molecular mechanisms behind the runner induction. An orthogonal test with 4 factors (photoperiod, temperature, gibberellin, and 6-benzyladenine), each with 3 levels was performed. Proteins were also extracted from the crowns with or without runners and separated by two-dimensional electrophoresis. The results of the orthogonal test showed that a long-day (LD) environment was the most influential factor for the runner formation, and 50 mg·L⁻¹ of 6-BA significantly increased the number of runners. A proteomic analysis revealed that 32 proteins were differentially expressed (2-fold, p < 0.05) in the strawberry crowns with and without runners. A total of 16 spots were up-regulated in the crowns with runners induced by LD treatment. Identified proteins were classified into seven groups according to their biological roles. The most prominent groups were carbohydrate metabolism and photosynthesis, which indicated that the carbohydrate content may increase during runner formation. A further analysis demonstrated that the soluble sugar content was positively correlated with the number of runners. Thus, it is suggested that the photoperiod and 6-BA break the dormancy of the axillary buds and produce runners by increasing the soluble sugar content in strawberry.

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.

Dormancy-Associated MADS-Box (DAM) Genes Influence Chilling Requirement of Sweet Cherries and Co-Regulate Flower Development with SOC1 Gene

Floral bud dormancy release of fruit tree species is greatly influenced by climate change. The lack of chilling accumulation often results in the occurrence of abnormal flower and low yields of sweet cherries (Prunus avium L.) in warm regions. To investigate the regulation of dormancy in sweet cherries, six DAM genes with homology to peach DAM, designated PavDAM1-6, have been identified and characterized. Phylogenetic analysis indicate that these genes are similar to DAMs in peach, apple and pear. The expression patterns of the PavDAMs in the low-chill cultivar ‘Royal Lee’ were different from that in the high-chill cultivar ‘Hongdeng’. ‘Royal Lee’ exhibits lower transcriptional level of PavDAM1 compared to ‘Hongdeng’, especially at the stage of chilling accumulation, and transcriptional levels of PavDAM4/5 were high in both cultivars during the endodormancy. Ectopic expression of PavDAM1 and PavDAM5 in Arabidopsis resulted in plants with abnormal flower and seed development, especially the PavDAM5. Higher transcriptional levels of SOC1 were observed in transgenic PavDAM1/5 lines, and ectopic expression of PavSOC1 had the similar floral phenotype. Further, protein interaction analysis demonstrated that PavDAM1/5 could interact with PavSOC1 in vivo and in vitro, which will help clarify the molecular mechanism of the flower development in sweet cherry or other fruit trees.

Identifying phenological phases in strawberry using multiple change-point models

Plant development studies often generate data in the form of multivariate time series, each variable corresponding to a count of newly emerged organs for a given development process. These phenological data often exhibit highly structured patterns, and the aim of this study was to identify such patterns in cultivated strawberry. Six strawberry genotypes were observed weekly for their course of emergence of flowers, leaves, and stolons during 7 months. We assumed that these phenological series take the form of successive phases, synchronous between individuals. We applied univariate multiple change-point models for the identification of flowering, vegetative development, and runnering phases, and multivariate multiple change-point models for the identification of consensus phases for these three development processes. We showed that the flowering and the runnering processes are the main determinants of the phenological pattern. On this basis, we propose a typology of the six genotypes in the form of a hierarchical classification. This study introduces a new longitudinal data modeling approach for the identification of phenological phases in plant development. The focus was on development variables but the approach can be directly extended to growth variables and to multivariate series combining growth and development variables.

Evaluating the Comprehensive Performance of Herbaceous Peonies at low latitudes by the Integration of Long-running Quantitative Observation and Multi-Criteria Decision Making Approach

Enlarging the planting area of economic plants, such as the "Southward Planting of Herbaceous Peony" (Paeonia lactiflora. Pall), is significant for improving people's lives. Peony is globally known as an ornamental because of gorgeous flowers and is mainly cultivated in the temperate regions with relatively cool and dry climates in the Northern Hemisphere. Promoting the landscape application of peony to the lower latitude regions is difficult because of the hot-humid climate. In this study, 29 northern peony cultivars and a unique Chinese southern peony, 'Hang Baishao', were introduced to Hangzhou, located in the central subtropics. Annual growth cycles, resistances and dormancy durations were measured, and crossbreeding between the southern and northern peonies was performed for six years, from 2012 to 2017. Based on data collected from the long-running quantitative observation (LQO), a multi-criteria decision making (MCDM) system was established to evaluate the comprehensive planting performance of these 30 cultivars in the central subtropics. 'Qihua Lushuang', 'Hang Baishao' and 'Meiju' were highly recommended, while 'Zhuguang' and 'Qiaoling' were scarcely recommended for the Hangzhou landscape. This study highlights the dependability and comprehensiveness of integrating the LQO and MCDM approaches for evaluating the introduction performance of ornamental plants.

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA₃ treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA₃ treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.

Identification and functional characterization of SOC1-like genes in Pyrus bretschneideri

Flowering is a prerequisite for pear fruit production. Therefore, the development of flower buds and the control of flowering time are important for pear trees. However, the molecular mechanism of pear flowering is unclear. SOC1, a member of MADS-box family, is known as a flowering signal integrator in Arabidopsis. We identified eight SOC1-like genes in Pyrus bretschneideri and analyzed their basic information and expression patterns. Some pear SOC1-like genes were regulated by photoperiod in leaves. Moreover, the expression patterns were diverse during the development of pear flower buds. Two members of the pear SOC1-like genes, PbSOC1d and PbSOC1g, could lead to early flowering phenotype when overexpressed in Arabidopsis. PbSOC1d and PbSOC1g were identified as activators of the floral meristem identity genes AtAP1 and AtLFY and promote flowering time. These results suggest that PbSOC1d and PbSOC1g are promoters of flowering time and may be involved in flower bud development in pear.

Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

BACKGROUND

Consumers purchase fresh strawberries all year long. Extending the fruiting season for new strawberry cultivars is a common breeding goal. Understanding the inheritance of repeat fruiting is key to improving breeding efficiency. Several independent research groups using multiple genotypes and analytic approaches have all identified a single genomic region in strawberry associated with repeat fruiting. Markers mapped to this region were used to evaluate breeding parents from the United States Department of Agriculture - Agricultural Research Service (USDA-ARS) strawberry breeding program at Beltsville, Maryland.

RESULTS

Markers mapped to repeat fruiting identified once-fruiting genotypes but not repeat-fruiting genotypes. Eleven of twenty-three breeding parents with repeat-fruiting marker profiles were actually once fruiting, indicating at least one additional locus acting epistatically to suppress repeat fruiting. Family segregation ratios could not be predicted reliably by the combined use of parental phenotypes and marker profiles, when using a single-gene model. Expected segregation ratios were calculated for all phenotypic and marker-profile combinations possible from the mapped locus combined with a hypothetical dominant or recessive suppressor locus. Segregation ratios specific to an epistatic suppressor acting on the mapped locus were observed in four families. The segregation ratios for two families were best explained by a dominant suppressor acting on the mapped locus, and, for the other two, by a recessive suppressor. Not all of the observed ratios could be explained by one model or the other, and when multiple families with a common parent were compared, there was no predicted genotype for the common parent that would lead to all of the observed segregation ratios.

CONCLUSIONS

Considering all lines of evidence in this study and others, repeat-fruiting in commercial strawberry is controlled primarily by a dominant allele at a single locus, previously mapped by multiple groups. At least two additional genes, one dominant and one recessive, exist that act epistatically to suppress repeat fruiting. Environmental effects and/or incomplete penetrance likely affect phenotype through the suppressor loci, rather than the primary mapped locus. One of the dominant suppressors acts only in the first year, the year the plant is germinated from seed, and not after the plant has experienced a winter.

Expression Pattern of FT/TFL1 and miR156-Targeted SPL Genes Associated with Developmental Stages in Dendrobium catenatum

Time to flower, a process either referring to juvenile-adult phase change or vegetative-reproductive transition, is strictly controlled by an intricate regulatory network involving at least both FT/TFL1 and the micro RNA (miR)156-regulated SPL family members. Despite substantial progresses recently achieved in Arabidopsis and other plant species, information regarding the involvement of these genes during orchid development and flowering competence is still limited. Dendrobium catenatum, a popular orchid species, exhibits a juvenile phase of at least three years. Here, through whole-genome mining and whole-family expression profiling, we analyzed the homologous genes of FT/TFL1, miR156, and SPL with special reference to the developmental stages. The FT/TFL1 family contains nine members; among them, DcHd3b transcribes abundantly in young and juvenile tissues but not in adult, contrasting with the low levels of others. We also found that mature miR156, encoded by a single locus, accumulated in large quantity in protocorms and declined by seedling development, coincident with an increase in transcripts of three of its targeted SPL members, namely DcSPL14, DcSPL7, and DcSPL18. Moreover, among the seven predicted miR156-targeted SPLs, only DcSPL3 was significantly expressed in adult plants and was associated with plant maturation. Our results might suggest that the juvenile phase change or maturation in this orchid plant likely involves both the repressive action of a TFL1-like pathway and the promotive effect from an SPL3-mediated mechanism.

Histone modification and activation by SOC1-like and drought stress-related transcription factors may regulate AcSVP2 expression during kiwifruit winter dormancy

The SHORT VEGETATIVE PHASE (SVP)-like and DORMANCY ASSOCIATED MADS-BOX (DAM) genes have been shown to regulate winter dormancy in woody perennials. In kiwifruit, AcSVP2 affects the duration of dormancy in cultivars that require high chill for dormancy release. In this study, we used a low-chill kiwifruit Actinidia chinensis 'Hort16A' to further study the function and regulation of AcSVP2. Overexpression of AcSVP2 in transgenic A. chinensis delayed budbreak in spring. A reduction in the active trimethylation histone marks of the histone H3K4 and acetylation of histone H3 contributed to the reduction of AcSVP2 expression towards dormancy release, while the inactive histone marks of trimethylation of the histone H3K27 and H3K9 in AcSVP2 locus did not show significant enrichment at the end of winter dormancy. Analysis of expression in shoot buds showed that AcSVP2 transcript was elevated in dormant buds during winter months and declined prior to budbreak, which was coordinated with expression of some of kiwifruit SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like genes. Screening of 101 transcription factors in an assay with a 2.3 kb promoter region of AcSVP2 found that kiwifruit SOC1-like genes are able to activate the AcSVP2 promoter. We further identified additional transcription factors associated with drought/osmotic stress and dormancy which may regulate AcSVP2 expression.

Identification and expression analysis of strigolactone biosynthetic and signaling genes reveal strigolactones are involved in fruit development of the woodland strawberry (Fragaria vesca)

BACKGROUND

The development and ripening of fresh fruits is an important trait for agricultural production and fundamental research. Almost all plant hormones participate in this process. Strigolactones (SLs) are a new class of plant hormones that regulate plant organ development and stress tolerance, but little is known about their roles in fruit development.

RESULTS

In this study, we identified SL biosynthetic and signaling genes in woodland strawberry, a typical non-climacteric fruit, and analyzed the expression patterns of these genes in different plant tissues and developing fruits. One D27, two MAX1, and one LBO gene were identified as involved in SL biosynthesis, and one D14, one D3, and two D53 genes as related to SL signaling. The proteins encoded by these genes had similar motifs as SL biosynthetic and signaling proteins in rice and Arabidopsis. The genes had different expression levels in the root, stem, leaf, and petiole of woodland strawberry. In addition, the expression of most SL biosynthetic genes was high in developing carpel, anther, and style, while that of SL signaling genes was high in carpel and style, but low in anther, suggesting active SL biosynthesis and signaling in the developing carpel and style. Notably, the expression of SL biosynthetic and signaling genes was significantly increased in the receptacle after pollination and decreased during receptacle development. Moreover, low or no expression of these genes was detected in ripening fruits.

CONCLUSIONS

Our results suggest that SLs play a role in the early stages of woodland strawberry fruit development. Our findings provide insight into the function of SLs and will facilitate further study of the regulation by SLs of fresh fruit development.

The Role of EjSOC1s in Flower Initiation in Eriobotrya japonica

The MADS-box transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates environmental and endogenous signals to promote flowering in Arabidopsis. However, the role of SOC1 homologs in regulating flowering time in fruit trees remains unclear. To better understand the molecular mechanism of flowering regulation in loquat (Eriobotrya japonica Lindl.), two SOC1 homologs (EjSOC1-1 and EjSOC1-2) were identified and characterized in this work. Sequence analysis showed that EjSOC1-1 and EjSOC1-2 have conserved MADS-box and K-box domains. EjSOC1-1 and EjSOC1-2 were clearly expressed in vegetative organs, and high expression was detected in flower buds. As observed in paraffin-embedded sections, expression of the downstream flowering genes EjAP1s and EjLFYs started to increase at the end of June, a time when flower bud differentiation occurs. Additionally, high expression of EjSOC1-1 and EjSOC1-2 began 10 days earlier than that of EjAP1s and EjLFYs in shoot apical meristem (SAM). EjSOC1-1 and EjSOC1-2 were inhibited by short-day (SD) conditions and exogenous GA₃, and flower bud differentiation did not occur after these treatments. EjSOC1-1 and EjSOC1-2 were found to be localized to the nucleus. Moreover, ectopic overexpression of EjSOC1-1 and EjSOC1-2 in wild-type Arabidopsis promoted early flowering, and overexpression of both was able to rescue the late flowering phenotype of the soc1-2 mutant. In conclusion, the results suggest that cultivated loquat flower bud differentiation in southern China begins in late June to early July and that EjSOC1-1 and EjSOC1-2 participate in the induction of flower initiation. These findings provide new insight into the artificial regulation of flowering time in fruit trees.

The Role of EjSOC1s in Flower Initiation in Eriobotrya japonica

The MADS-box transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates environmental and endogenous signals to promote flowering in Arabidopsis. However, the role of SOC1 homologs in regulating flowering time in fruit trees remains unclear. To better understand the molecular mechanism of flowering regulation in loquat (Eriobotrya japonica Lindl.), two SOC1 homologs (EjSOC1-1 and EjSOC1-2) were identified and characterized in this work. Sequence analysis showed that EjSOC1-1 and EjSOC1-2 have conserved MADS-box and K-box domains. EjSOC1-1 and EjSOC1-2 were clearly expressed in vegetative organs, and high expression was detected in flower buds. As observed in paraffin-embedded sections, expression of the downstream flowering genes EjAP1s and EjLFYs started to increase at the end of June, a time when flower bud differentiation occurs. Additionally, high expression of EjSOC1-1 and EjSOC1-2 began 10 days earlier than that of EjAP1s and EjLFYs in shoot apical meristem (SAM). EjSOC1-1 and EjSOC1-2 were inhibited by short-day (SD) conditions and exogenous GA₃, and flower bud differentiation did not occur after these treatments. EjSOC1-1 and EjSOC1-2 were found to be localized to the nucleus. Moreover, ectopic overexpression of EjSOC1-1 and EjSOC1-2 in wild-type Arabidopsis promoted early flowering, and overexpression of both was able to rescue the late flowering phenotype of the soc1-2 mutant. In conclusion, the results suggest that cultivated loquat flower bud differentiation in southern China begins in late June to early July and that EjSOC1-1 and EjSOC1-2 participate in the induction of flower initiation. These findings provide new insight into the artificial regulation of flowering time in fruit trees.

Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca

Fragaria vesca, a wild diploid strawberry, has recently emerged as a model for the cultivated strawberry and other members of the Rosaceae. Differentiation and maintenance of meristems largely determines plant architecture, flower development and ultimately fruit yield. However, in strawberry, our knowledge of molecular regulation of meristems in different developmental context is limited. In this study, we hand dissected three types of tissues than contain meristematic tissues corresponding to shoot apical meristem (SAM), flower meristem (FM), and receptacle meristem (REM), in F. vesca for RNA-seq analyses. A total of 3,009 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into nine clusters with dynamic and distinct expression patterns. In these nine clusters, 336 transcription factor genes belong to 46 families were identified; some of which were significantly enriched in FM and REM such as the MADS-box family or in REM such as the B3 family. We found conserved and distinctive expression patterns of totally 149 genes whose homologs regulate flowering time or SAM, leaf, and flower development in other plant species. In addition to the ABCE genes in flower development, new MADS box genes were identified to exhibit differential expression in these different tissues. Additionally, the cytokinin and auxin pathway genes also exhibited distinct expression patterns. The Arabidopsis homeobox gene WUSCHEL (WUS), essential for stem cell maintenance, is expressed in organizing center of meristems. The F. vesca homolog FvWUS1 exhibited a broader expression domain in young strawberry flowers than its Arabidopsis counterpart. Altogether, this work provides a valuable data resource for dissecting gene regulatory networks operating in different meristematic tissues in strawberry.

The cotton HD-Zip transcription factor GhHB12 regulates flowering time and plant architecture via the GhmiR157-GhSPL pathway

Domestication converts perennial and photoperiodic ancestral cotton to day-neutral cotton varieties, and the selection of short-season cotton varieties is one of the major objectives of cotton breeding. However, little is known about the mechanism of flowering time in cotton. Here, we report a cotton HD-ZIP I-class transcription factor (GhHB12) specifically expressed in axillary buds, which antagonisticlly interacts with GhSPL10/13 to repress the expression of GhFT, GhFUL, and GhSOC1, resulting in bushy architecture and delayed flowering under long-day conditions. We found that GhHB12-mediated ancestral upland cotton phenotypes (bushy architecture and delayed flowering) could be rescued under short-day conditions. We showed that overexpressing of GhrSPL10 partially rescues the bushy architecture and delayed flowering phenotypes, while overexpression of GhmiR157 reinforced these phenotypes in GhHB12-overexpressing plants. This study defines a regulatory module which regulates cotton architecture, phase transition and could be applied in the breeding of early maturing cotton varieties.

Xin He et al. present a characterization of GhHB12, a HD-ZIP family transcription factor expressed in upland cotton axillary buds. They show that GhHB12 regulates flowering time, plant architecture and phase transition via a regulatory module that could be harnessed to improve cotton for mechanical harvesting.

A SOC1-like gene MtSOC1a promotes flowering and primary stem elongation in Medicago

Medicago flowering, like that of Arabidopsis, is promoted by vernalization and long days, but alternative mechanisms are predicted because Medicago lacks the key regulators CO and FLC. Three Medicago SOC1-like genes, including MtSOC1a, were previously implicated in flowering control, but no legume soc1 mutants with altered flowering were reported. Here, reverse transciption-quantitative PCR (RT-qPCR) indicated that the timing and magnitude of MtSOC1a expression was regulated by the flowering promoter FTa1, while in situ hybridization indicated that MtSOC1a expression increased in the shoot apical meristem during the floral transition. A Mtsoc1a mutant showed delayed flowering and short primary stems. Overexpression of MtSOC1a partially rescued the flowering of Mtsoc1a, but caused a dramatic increase in primary stem height, well before the transition to flowering. Internode cell length correlated with stem height, indicating that MtSOC1a promotes cell elongation in the primary stem. However, application of gibberellin (GA3) caused stem elongation in both the wild type and Mtsoc1a, indicating that the mutant was not defective in gibberellin responsiveness. These results indicate that MtSOC1a may function as a floral integrator gene and promotes primary stem elongation. Overall, this study suggests that apart from some conservation with the Arabidopsis flowering network, MtSOC1a has a novel role in regulating aspects of shoot architecture.

LCM-seq reveals the crucial role of LsSOC1 in heat-promoted bolting of lettuce (Lactuca sativa L.)

Lettuce (Lactuca sativa L.) is one of the most economically important vegetables. The floral transition in lettuce is accelerated under high temperatures, which can significantly decrease yields. However, the molecular mechanism underlying the floral transition in lettuce is poorly known. Using laser capture microdissection coupled with RNA sequencing, we isolated shoot apical meristem cells from the bolting-sensitive lettuce line S39 at four critical stages of development. Subsequently, we screened specifically for the flowering-related gene LsSOC1 during the floral transition through comparative transcriptomic analysis. Molecular biology, developmental biology, and biochemical tools were combined to investigate the biological function of LsSOC1 in lettuce. LsSOC1 knockdown by RNA interference resulted in a significant delay in the timing of bolting and insensitivity to high temperature, which indicated that LsSOC1 functions as an activator during heat-promoted bolting in lettuce. We determined that two heat shock transcription factors, HsfA1e and HsfA4c, bound to the promoter of LsSOC1 to confirm that LsSOC1 played an important role in heat-promoted bolting. This study indicates that LsSOC1 plays a crucial role in the heat-promoted bolting process in lettuce. Further investigation of LsSOC1 may be useful for clarification of the bolting mechanism in lettuce.